SOE.bib

@article{mills_fisheries_2013,
	title = {Fisheries Management in a Changing Climate: Lessons From the 2012 Ocean Heat Wave in the Northwest Atlantic},
	volume = {26},
	issn = {10428275},
	url = {https://tos.org/oceanography/article/fisheries-management-in-a-changing-climate-lessonsfrom-the-2012-ocean-heat-},
	doi = {10.5670/oceanog.2013.27},
	shorttitle = {Fisheries Management in a Changing Climate},
	number = {2},
	journaltitle = {Oceanography},
	shortjournal = {oceanog},
	author = {Mills, Katherine and Pershing, Andrew and Brown, Curtis and Chen, Yong and Chiang, Fu-Sung and Holland, Daniel and Lehuta, Sigrid and Nye, Janet and Sun, Jenny and Thomas, Andrew and Wahle, Richard},
	urldate = {2020-02-10},
	date = {2013},
	file = {Full Text:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\DY4W3JYE\\Mills et al. - 2013 - Fisheries Management in a Changing Climate Lesson.pdf:application/pdf},
}

@article{lawson_important_1998,
	title = {Important prey species of marine vertebrate predators in the northwest Atlantic: proximate composition and energy density},
	volume = {164},
	issn = {0171-8630},
	url = {https://www.jstor.org/stable/24825521},
	shorttitle = {Important prey species of marine vertebrate predators in the northwest Atlantic},
	abstract = {Prey energy density values are crucial inputs to bioenergetic consumption models. Vertebrate predators in the northwest Atlantic consume a variety of prey species, but the proximate composition ({PC}; proportions of lipid, protein, ash and water) and energy density ({ED}; {kJ} g–1) of prey, and their variability, are known poorly. In this study, key prey species from Newfoundland and Labrador were studied: Atlantic cod Gadus morhua, American plaice Hippoglossoides platessoides, sand lance Ammodytes dubius, Arctic cod Boreogadus saida, northern shrimp Pandalus borealis, redfish Sebastes spp., Greenland halibut Reinhardtius hippoglossoides, squid Illex illecebrosus and Gonatus fabricii, capelin Mallotus villosus, Atlantic herring Clupea harengus and daubed shanny Lumpenus maculatus. {PC} and {ED} varied greatly among species and were influenced by size, season, geography and year. Herring, capelin and G. fabricii had the highest {ED}, whereas Atlantic cod, plaice, sand lance and shrimp had the lowest. Halibut and I. illecebrosus increased in {ED} with size. {EDs} of capelin and redfish varied seasonally; that of plaice and sand lance did not. Herring and halibut had higher {ED} in the early 1990s than in recent years. Such variation in prey {ED} has important implications for digestive efficiency, foraging energetics, and dietary preferences of vertebrate predators.},
	pages = {13--20},
	journaltitle = {Marine Ecology Progress Series},
	author = {Lawson, John W. and Magalhães, Alexandra M. and Miller, Edward H.},
	urldate = {2020-02-13},
	date = {1998},
}

@article{hobday_hierarchical_2016,
	title = {A hierarchical approach to defining marine heatwaves},
	volume = {141},
	issn = {0079-6611},
	url = {http://www.sciencedirect.com/science/article/pii/S0079661116000057},
	doi = {10.1016/j.pocean.2015.12.014},
	abstract = {Marine heatwaves ({MHWs}) have been observed around the world and are expected to increase in intensity and frequency under anthropogenic climate change. A variety of impacts have been associated with these anomalous events, including shifts in species ranges, local extinctions and economic impacts on seafood industries through declines in important fishery species and impacts on aquaculture. Extreme temperatures are increasingly seen as important influences on biological systems, yet a consistent definition of {MHWs} does not exist. A clear definition will facilitate retrospective comparisons between {MHWs}, enabling the synthesis and a mechanistic understanding of the role of {MHWs} in marine ecosystems. Building on research into atmospheric heatwaves, we propose both a general and specific definition for {MHWs}, based on a hierarchy of metrics that allow for different data sets to be used in identifying {MHWs}. We generally define a {MHW} as a prolonged discrete anomalously warm water event that can be described by its duration, intensity, rate of evolution, and spatial extent. Specifically, we consider an anomalously warm event to be a {MHW} if it lasts for five or more days, with temperatures warmer than the 90th percentile based on a 30-year historical baseline period. This structure provides flexibility with regard to the description of {MHWs} and transparency in communicating {MHWs} to a general audience. The use of these metrics is illustrated for three 21st century {MHWs}; the northern Mediterranean event in 2003, the Western Australia ‘Ningaloo Niño’ in 2011, and the northwest Atlantic event in 2012. We recommend a specific quantitative definition for {MHWs} to facilitate global comparisons and to advance our understanding of these phenomena.},
	pages = {227--238},
	journaltitle = {Progress in Oceanography},
	shortjournal = {Progress in Oceanography},
	author = {Hobday, Alistair J. and Alexander, Lisa V. and Perkins, Sarah E. and Smale, Dan A. and Straub, Sandra C. and Oliver, Eric C. J. and Benthuysen, Jessica A. and Burrows, Michael T. and Donat, Markus G. and Feng, Ming and Holbrook, Neil J. and Moore, Pippa J. and Scannell, Hillary A. and Sen Gupta, Alex and Wernberg, Thomas},
	urldate = {2020-02-10},
	date = {2016-02-01},
	langid = {english},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\EAJ6P3XR\\Hobday et al. - 2016 - A hierarchical approach to defining marine heatwav.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\B4WY7WYM\\S0079661116000057.html:text/html},
}

@article{steimle_energy_1985,
	title = {Energy Equivalents of Marine Organisms from the Continental Shelf of the Temperate Northwest Atlantic},
	volume = {6},
	doi = {10.2960/J.v6.a11},
	abstract = {The availability of appropriate energy equivalents is one of the needs in species or community bioenergetic models. Energy­ equivalent data for 151 common invertebrate and vertebrate species on the continental shelf of the temperate Northwest Atlantic from Nova Scotia to North Carolina are presented and compared with the more limited results of other studies. Energy equivalents were found to be variable among major taxonomic ortrophic groups and general trends were not evident. A review of equivalents from some recent ecosystem models for the Northwest Atlnatic indicates that the models can be substantially improved.},
	journaltitle = {Journal of Northwest Atlantic Fishery Science},
	shortjournal = {Journal of Northwest Atlantic Fishery Science},
	author = {Steimle, Frank and Terranova, Russell},
	date = {1985-12-01},
	file = {Full Text:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\C3HQBRTS\\Jr and Terranova - 1985 - Energy Equivalents of Marine Organisms from the Co.pdf:application/pdf},
}

@article{tam_comparing_2017,
	title = {Comparing Apples to Oranges: Common Trends and Thresholds in Anthropogenic and Environmental Pressures across Multiple Marine Ecosystems},
	volume = {4},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2017.00282/full},
	doi = {10.3389/fmars.2017.00282},
	shorttitle = {Comparing Apples to Oranges},
	abstract = {Ecosystem-based management ({EBM}) in marine ecosystems considers impacts caused by complex interactions between environmental and anthropogenic pressures (i.e. oceanographic, climatic, socio-economic) and marine communities. {EBM} depends, in part, on ecological indicators that facilitate understanding of inherent properties and the dynamics of pressures within marine communities. Thresholds of ecological indicators delineate ecosystem status because they represent points at which a small increase in one or many pressure variables results in an abrupt change of ecosystem responses. The difficulty in developing appropriate thresholds and reference points for {EBM} lies in the multidimensionality of both the ecosystem responses and the pressures impacting the ecosystem. Here, we develop thresholds using gradient forest for a suite of ecological indicators in response to multiple pressures that convey ecosystem status for large marine ecosystems from the {US} Pacific, Atlantic, sub-Arctic, and Gulf of Mexico. We detected these thresholds of ecological indicators based on multiple pressures. Commercial fisheries landings above approximately 2-4.5 t km-2 and fisheries exploitation above 20-40\% of the total estimated biomass (of invertebrates and fish) of the ecosystem resulted in a change in the direction of ecosystem structure and functioning in the ecosystems examined. Our comparative findings reveal common trends in ecosystem thresholds along pressure gradients and also indicate that thresholds of ecological indicators are useful tools for comparing the impacts of environmental and anthropogenic pressures across multiple ecosystems. These critical points can be used to inform the development of {EBM} decision criteria.},
	journaltitle = {Frontiers in Marine Science},
	shortjournal = {Front. Mar. Sci.},
	author = {Tam, Jamie C. and Link, Jason S. and Large, Scott I. and Andrews, Kelly and Friedland, Kevin D. and Gove, Jamison and Hazen, Elliott and Holsman, Kirstin and Karnauskas, Mandy and Samhouri, Jameal F. and Shuford, Rebecca and Tomilieri, Nick and Zador, Stephani},
	urldate = {2020-03-09},
	date = {2017},
	note = {Publisher: Frontiers},
	keywords = {anthropogenic and environmental pressures, comparative analysis, Ecological Indicators, ecosystem-based management, Gradient forest, thresholds-based reference points},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\RTFYBX68\\Tam et al. - 2017 - Comparing Apples to Oranges Common Trends and Thr.pdf:application/pdf},
}

@article{thorson_guidance_2019,
	title = {Guidance for decisions using the Vector Autoregressive Spatio-Temporal ({VAST}) package in stock, ecosystem, habitat and climate assessments},
	volume = {210},
	issn = {0165-7836},
	url = {http://www.sciencedirect.com/science/article/pii/S0165783618302820},
	doi = {10.1016/j.fishres.2018.10.013},
	abstract = {Fisheries scientists provide stock, ecosystem, habitat, and climate assessments to support interdisplinary fisheries management in the {US} and worldwide. These assessment activities have evolved different models, using different review standards, and are communicated using different vocabulary. Recent research shows that spatio-temporal models can estimate population density for multiple locations, times, and species, and that this is a “common currency” for addressing core goals in stock, ecosystem, habitat, and climate assessments. I therefore review the history and “design principles” for one spatio-temporal modelling package, the Vector Autoregressive Spatio-Temporal ({VAST}) package. I then provide guidance on fifteen major decisions that must be made by users of {VAST}, including: whether to use a univariate or multivariate model; when to include spatial and/or spatio-temporal variation; how many factors to use within a multivariate model; whether to include density or catchability covariates; and when to include a temporal correlation on model components. I finally demonstrate these decisions using three case studies. The first develops indices of abundance, distribution shift, and range expansion for arrowtooth flounder (Atheresthes stomias) in the Eastern Bering Sea, showing the range expansion for this species. The second involves “species ordination” of eight groundfishes in the Gulf of Alaska bottom trawl survey, which highlights the different spatial distribution of flathead sole (Hippoglossoides elassodon) relative to sablefish (Anoplopoma fimbria) and dover sole (Microstomus pacificus). The third involves a short-term forecast of the proportion of coastwide abundance for five groundfishes within three spatial strata in the {US} West Coast groundfish bottom trawl survey, and predicts large interannual variability (and high uncertainty) in the distribution of lingcod (Ophiodon elongatus). I conclude by recommending further research exploring the benefits and limitations of a “common currency” approach to stock, ecosystem, habitat, and climate assessments, and discuss extending this approach to optimal survey design and economic assessments.},
	pages = {143--161},
	journaltitle = {Fisheries Research},
	shortjournal = {Fisheries Research},
	author = {Thorson, James T.},
	urldate = {2020-02-24},
	date = {2019-02-01},
	langid = {english},
	keywords = {Climate vulnerability analysis, Distribution shift, Habitat assessment, Index standardization, Integrated ecosystem assessment, Spatio-temporal model, Stock assessment, {VAST}},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\W7IBXWVK\\Thorson - 2019 - Guidance for decisions using the Vector Autoregres.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\V3KPTUYK\\S0165783618302820.html:text/html},
}

@article{hardison_simulation_2019,
	title = {A simulation study of trend detection methods for integrated ecosystem assessment},
	volume = {76},
	issn = {1054-3139},
	url = {https://academic.oup.com/icesjms/article/76/7/2060/5512306},
	doi = {10.1093/icesjms/fsz097},
	abstract = {Abstract.  The identification of trends in ecosystem indicators has become a core component of ecosystem approaches to resource management, although oftentimes},
	pages = {2060--2069},
	number = {7},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} J Mar Sci},
	author = {Hardison, Sean and Perretti, Charles T. and {DePiper}, Geret S. and Beet, Andrew},
	urldate = {2020-02-26},
	date = {2019-12-01},
	langid = {english},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\TCF5T9KA\\Hardison et al. - 2019 - A simulation study of trend detection methods for .pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\77FEQEX7\\5512306.html:text/html},
}

@article{ekstrom_vulnerability_2015,
	title = {Vulnerability and adaptation of {US} shellfisheries to ocean acidification},
	volume = {5},
	rights = {2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1758-6798},
	url = {https://www.nature.com/articles/nclimate2508},
	doi = {10.1038/nclimate2508},
	abstract = {Understanding the vulnerability of different {US} coastal communities to the likely harmful effects of ocean acidification on shellfisheries should inform the development of effective adaptation measures.},
	pages = {207--214},
	number = {3},
	journaltitle = {Nature Climate Change},
	author = {Ekstrom, Julia A. and Suatoni, Lisa and Cooley, Sarah R. and Pendleton, Linwood H. and Waldbusser, George G. and Cinner, Josh E. and Ritter, Jessica and Langdon, Chris and van Hooidonk, Ruben and Gledhill, Dwight and Wellman, Katharine and Beck, Michael W. and Brander, Luke M. and Rittschof, Dan and Doherty, Carolyn and Edwards, Peter E. T. and Portela, Rosimeiry},
	urldate = {2020-03-06},
	date = {2015-03},
	langid = {english},
	note = {Number: 3
Publisher: Nature Publishing Group},
	file = {Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XJCI7DCX\\nclimate2508.html:text/html},
}

@article{large_defining_2013,
	title = {Defining trends and thresholds in responses of ecological indicators to fishing and environmental pressures},
	volume = {70},
	issn = {1054-3139, 1095-9289},
	url = {http://icesjms.oxfordjournals.org/content/70/4/755},
	doi = {10.1093/icesjms/fst067},
	abstract = {Large, S. I., Fay, G., Friedland, K. D., and Link, J. S. 2013. Defining trends and thresholds in responses of ecological indicators to fishing and environmental pressures. – {ICES} Journal of Marine Science, 70: 755–767. Both fishing and environmental forces can influence the structure of marine ecosystems. To further understand marine ecosystems and to implement ecosystem-based fisheries management ({EBFM}), an evaluation of ecosystem indicators is warranted. In this context, it is particularly important to identify thresholds where fishing and environmental pressures significantly influence ecological indicators. We empirically determined numerical values of environmental forces and fishing pressure that significantly altered the response of ecological indicators for the Northeast Shelf Large Marine Ecosystem. Generalized additive models predicted a non-linear relationship for each pressure–response pairing. With this smoother, 95\% confidence intervals ({CI}) for estimated first and second derivatives for each relationship were determined via parametric bootstrap. A significant trend or threshold was noted when the {CI} for the first or second derivative was greater or less than zero, delineating the level at which pressure variables influence the rate and direction of ecosystem indicator responses. We identify reference levels where environmental forces and fishing pressure result in ecosystem change by collectively examining the responses of multiple ecological indicators. Individual indicators showed unique responses to pressures, however, similar values for the pressures were associated with significant changes for multiple indicators. These reference levels establish a foundation for implementation of {EBFM}.},
	pages = {755--767},
	number = {4},
	journaltitle = {{ICES} Journal of Marine Science: Journal du Conseil},
	shortjournal = {{ICES} J. Mar. Sci.},
	author = {Large, Scott I. and Fay, Gavin and Friedland, Kevin D. and Link, Jason S.},
	urldate = {2016-10-14},
	date = {2013-07-01},
	langid = {english},
	keywords = {decision criteria, Ecosystem-based management, generalized additive model, overfishing, reference points},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\8JFINTNX\\Large et al. - 2013 - Defining trends and thresholds in responses of eco.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\HHWWVVBA\\Large et al. - 2013 - Defining trends and thresholds in responses of eco.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XDCNX8QE\\755.html:text/html;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\IHJNGJTU\\727721.html:text/html},
}

@article{miller_state-space_2016,
	title = {A state-space approach to incorporating environmental effects on recruitment in an age-structured assessment model with an application to southern New England yellowtail flounder},
	volume = {73},
	issn = {0706-652X},
	url = {https://www.nrcresearchpress.com/doi/10.1139/cjfas-2015-0339},
	doi = {10.1139/cjfas-2015-0339},
	abstract = {The state-space model framework provides a natural, probabilistic approach to stock assessment by modeling the stochastic nature of population survival and recruitment separately from sampling uncertainty inherent in observations on the population. We propose a state-space assessment model that is expanded to simultaneously treat environmental covariates as stochastic processes and estimate their effects on recruitment. We apply the model to southern New England yellowtail flounder (Limanda ferruginea) using data from the most recent benchmark assessment to evaluate evidence for effects of the mid-Atlantic cold pool and spawning stock biomass on recruitment. Based on Akaike’s information criterion, both the cold pool and spawning stock biomass were important predictors of recruitment and led to annual variation in estimated biomass reference points and associated yield. We also demonstrate the effect of the stochasticity of the mid-Atlantic cold pool on short-term forecasts of the stock size, biomass reference point, and stock status.},
	pages = {1261--1270},
	number = {8},
	journaltitle = {Canadian Journal of Fisheries and Aquatic Sciences},
	shortjournal = {Can. J. Fish. Aquat. Sci.},
	author = {Miller, Timothy J. and Hare, Jonathan A. and Alade, Larry A.},
	urldate = {2020-02-10},
	date = {2016-02-10},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\22GJMCCS\\Miller et al. - 2016 - A state-space approach to incorporating environmen.pdf:application/pdf;NRC Research Press Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\GXGW3JES\\cjfas-2015-0339.html:text/html;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\LXNLXZIV\\cjfas-2015-0339.html:text/html},
}

@article{chen_seasonal_2018,
	title = {Seasonal Variability of the Cold Pool Over the Mid-Atlantic Bight Continental Shelf},
	volume = {123},
	issn = {21699275},
	url = {http://doi.wiley.com/10.1029/2018JC014148},
	doi = {10.1029/2018JC014148},
	abstract = {The Mid-Atlantic Bight ({MAB}) Cold Pool is a distinctive cold (lower than 10 ∘C) and relatively fresh (lower than 34 practical salinity unit) water mass. It is located over the middle and outer shelf of the {MAB}, below the seasonal thermocline, and is attached to the bottom. Following this definition, we put forward a method that includes three criteria to capture and quantify Cold Pool characteristics, based on a 50-year (1958–2007) high-resolution regional ocean model hindcast. The seasonal climatology of the Cold Pool and its properties are investigated during its onset-peak-decline cycle. Three stages of the Cold Pool event are defined according to its evolution and characteristics. The Cold Pool cores travel along the 60-m isobath starting south of the New England shelf to the Hudson Shelf Valley at a speed of 2–3 cm/s. Furthermore, the northern extent of the Cold Pool retreats about 2.6 times faster than the southern extent during the summer progression. The heat balance of near-bottom waters over the {MAB} and Georges Bank is computed and it is found that the heat advection, rather than vertical diffusion, dominates the resulting spatial patterns of warming. Possible origins of the Cold Pool are investigated by performing a lead-lag correlation analysis. Results suggest that the Cold Pool originates not only from local remnants of winter water near the Nantucket Shoals, but has an upstream source traveling in the spring time from the southwestern flank of the Georges Bank along the 80-m isobath.},
	pages = {8203--8226},
	number = {11},
	journaltitle = {Journal of Geophysical Research: Oceans},
	author = {Chen, Zhuomin and Curchitser, Enrique and Chant, Robert and Kang, Dujuan},
	urldate = {2020-05-18},
	date = {2018-11},
	langid = {english},
	file = {Chen et al. - 2018 - Seasonal Variability of the Cold Pool Over the Mid.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\YT6J2CZS\\Chen et al. - 2018 - Seasonal Variability of the Cold Pool Over the Mid.pdf:application/pdf},
}

@article{pdf,
	title = {Optimization and assessment of phytoplankton size class algorithms for ocean color data on the Northeast U.S. continental shelf},
	volume = {267},
	issn = {0034-4257},
	doi = {https://doi.org/10.1016/j.rse.2021.112729},
	abstract = {The size structure of phytoplankton communities influences important ecological and biogeochemical processes, including the transfer of energy through marine food webs. A variety of algorithms have been developed to estimate phytoplankton size classes ({PSCs}) from satellite ocean color data. However, many of these algorithms were developed for application to the global ocean, and their performance in more productive, optically complex coastal and continental shelf regions warrants evaluation. In this study, several existing {PSC} models were applied in the Northeast U.S. continental shelf ({NES}) region and compared with in situ {PSC} estimates derived from a local {HPLC} pigment data set. The effect of regional re-parameterization and incorporation of sea surface temperature ({SST}) into existing abundance-based model frameworks was investigated and model performance was assessed using an independent data set. Abundance-based model re-parameterization alone did not result in significant improvement in model performance compared with other models. However, the inclusion of {SST} led to a consistent reduction in model error for all size classes. Of two absorption-based algorithms tested, the best performing approach displayed similar performance metrics to the regional {SST}-dependent abundance-based model. The {SST}-dependent model and the absorption-based method were applied to monthly composites of the {NES} region for April and September 2019 and qualitatively compared. The results highlight the benefit of considering {SST} in abundance-based models and the applicability of absorption-based {PSC} methods in optically complex regions.},
	pages = {112729},
	journaltitle = {Remote Sensing of Environment},
	author = {Turner, Kyle J. and Mouw, Colleen B. and Hyde, Kimberly J. W. and Morse, Ryan and Ciochetto, Audrey B.},
	date = {2021-12-15},
	file = {Turner_etal-RSE_2021 Optimization and assessme:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\F6TA9NTB\\Turner_etal-RSE_2021 Optimization and assessme.pdf:application/pdf},
}

@article{pendleton_decadal-scale_2022,
	title = {Decadal-scale phenology and seasonal climate drivers of migratory baleen whales in a rapidly warming marine ecosystem},
	volume = {28},
	rights = {© 2022 The Authors. Global Change Biology published by John Wiley \& Sons Ltd.},
	issn = {1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.16225},
	doi = {10.1111/gcb.16225},
	abstract = {Species' response to rapid climate change can be measured through shifts in timing of recurring biological events, known as phenology. The Gulf of Maine is one of the most rapidly warming regions of the ocean, and thus an ideal system to study phenological and biological responses to climate change. A better understanding of climate-induced changes in phenology is needed to effectively and adaptively manage human-wildlife conflicts. Using data from a 20+ year marine mammal observation program, we tested the hypothesis that the phenology of large whale habitat use in Cape Cod Bay has changed and is related to regional-scale shifts in the thermal onset of spring. We used a multi-season occupancy model to measure phenological shifts and evaluate trends in the date of peak habitat use for North Atlantic right (Eubalaena glacialis), humpback (Megaptera novaeangliae), and fin (Balaenoptera physalus) whales. The date of peak habitat use shifted by +18.1 days (0.90 days/year) for right whales and +19.1 days (0.96 days/year) for humpback whales. We then evaluated interannual variability in peak habitat use relative to thermal spring transition dates ({STD}), and hypothesized that right whales, as planktivorous specialist feeders, would exhibit a stronger response to thermal phenology than fin and humpback whales, which are more generalist piscivorous feeders. There was a significant negative effect of western region {STD} on right whale habitat use, and a significant positive effect of eastern region {STD} on fin whale habitat use indicating differential responses to spatial seasonal conditions. Protections for threatened and endangered whales have been designed to align with expected phenology of habitat use. Our results show that whales are becoming mismatched with static seasonal management measures through shifts in their timing of habitat use, and they suggest that effective management strategies may need to alter protections as species adapt to climate change.},
	pages = {4989--5005},
	number = {16},
	journaltitle = {Global Change Biology},
	author = {Pendleton, Daniel E. and Tingley, Morgan W. and Ganley, Laura C. and Friedland, Kevin D. and Mayo, Charles and Brown, Moira W. and {McKenna}, Brigid E. and Jordaan, Adrian and Staudinger, Michelle D.},
	urldate = {2024-02-02},
	date = {2022},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.16225},
	keywords = {climate change, endangered species, fin whale, Gulf of Maine, humpback whale, North Atlantic right whale, ocean warming, phenology},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\U95ZX4Z7\\Pendleton et al. - 2022 - Decadal-scale phenology and seasonal climate drive.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\LTR2A577\\gcb.html:text/html},
}

@article{northeast_fisheries_science_center_us_state_2022,
	title = {State of the Ecosystem 2022: Mid-Atlantic},
	url = {https://repository.library.noaa.gov/view/noaa/38949},
	doi = {10.25923/5S5Y-0H81},
	shorttitle = {State of the Ecosystem 2022},
	author = {Northeast Fisheries Science Center (U.S.)},
	urldate = {2023-03-02},
	date = {2022},
	note = {Publisher: Northeast Fisheries Science Center (U.S.)},
}

@article{hernandez_seasonal_2019,
	title = {Seasonal variability and individual consistency in gray seal (Halichoerus grypus) isotopic niches},
	volume = {97},
	issn = {0008-4301},
	url = {https://cdnsciencepub.com/doi/10.1139/cjz-2019-0032},
	doi = {10.1139/cjz-2019-0032},
	abstract = {Although it is often assumed that individuals in generalist populations are equivalent, recent research indicates that individual dietary specialization can be common in marine predators. Gray seals (Halichoerus grypus (Fabricius, 1791)) were considered locally extinct in United States waters by 1958 but have since recolonized the region. Although considered generalists, less is known about gray seal foraging ecology in the United States. To address this, we used carbon and nitrogen stable isotope analyses to investigate the foraging niches of adult gray seals in Massachusetts, {USA}. We examined skin, fur, and blood components to investigate seasonal variability and individual consistency in foraging niches, and serially sampled vibrissae to quantify the degree of individual foraging specialization in this population. Our results suggest that seals shift from coastal foraging habitats before molt to offshore habitats after molt, with a coincident shift from higher to lower trophic-level prey. Adult gray seals also exhibited individual consistency in foraging niches independent of population-level shifts and reflect a generalist population composed of individual foraging specialists. These findings serve as a baseline for subsequent research on gray seals in United States waters that could help to determine the mechanisms which promote individual specialization in this population.},
	pages = {1071--1077},
	number = {11},
	journaltitle = {Canadian Journal of Zoology},
	shortjournal = {Can. J. Zool.},
	author = {Hernandez, K.M. and Bogomolni, A.L. and Moxley, J.H. and Waring, G.T. and {DiGiovanni}, R.A. and Hammill, M.O. and Johnston, D.W. and Sette, L. and Polito, M.J.},
	urldate = {2023-02-10},
	date = {2019-11},
	note = {Publisher: {NRC} Research Press},
}

@article{northeast_fisheries_science_center_us_state_2022-1,
	title = {State of the Ecosystem 2022: New England},
	url = {https://repository.library.noaa.gov/view/noaa/38948},
	doi = {10.25923/YPV2-MW79},
	shorttitle = {State of the Ecosystem 2022},
	author = {Northeast Fisheries Science Center (U.S.)},
	urldate = {2023-03-02},
	date = {2022},
	note = {Publisher: Northeast Fisheries Science Center (U.S.)},
}

@article{fabrizio_characterization_2022,
	title = {Characterization of Nursery Habitats used by Black Sea Bass and Summer Flounder in Chesapeake Bay and the Coastal Lagoons},
	url = {https://scholarworks.wm.edu/reports/2837},
	doi = {doi: 10.25773/PJCC-RG41},
	journaltitle = {Reports},
	author = {Fabrizio, Mary and Tuckey, Troy and Smith, Shannon and Ross, Paige and Snyder, Richard and Wang, Harry and Bever, Aaron},
	date = {2022-01-01},
	file = {"Characterization of Nursery Habitats used by Black Sea Bass and Summer" by Mary C. Fabrizio, Troy D. Tuckey et al.:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\Z39AE9UV\\2837.html:text/html},
}

@article{mccosker_metabarcoding_2020,
	title = {Metabarcoding Fecal {DNA} Reveals Extent of Halichoerus grypus (Gray Seal) Foraging on Invertebrates and Incidence of Parasite Exposure},
	volume = {27},
	issn = {1092-6194, 1938-5307},
	url = {https://bioone.org/journals/northeastern-naturalist/volume-27/issue-4/045.027.0409/Metabarcoding-Fecal-DNA-Reveals-Extent-of-Halichoerus-grypus-Gray-Seal/10.1656/045.027.0409.full},
	doi = {10.1656/045.027.0409},
	abstract = {Halichoerus grypus (Gray Seal) is a top predator in New England waters, yet little data exists on seals foraging on invertebrate prey. We combined analysis of hard parts of scat samples (n = 98) from 2 breeding sites in Massachusetts with metabarcoding of fecal {DNA}. Invertebrates were detected in 4 samples via analysis of hard parts (4.1\%) but in 35 samples (35.7\%) using a metabarcoding approach. Metabarcoding also detected parasite {DNA} in 82.7\% of scat samples. Nematode {DNA} (78.6\%) was more prevalent than trematode (28.6\%) or cestode (22.5\%) {DNA}. Prey species, biomass, and diversity within each sample were not affected by seal sex, parasite exposure, or type of parasitic exposure. Previous diet studies may have underestimated the diversity and abundance of invertebrates in the diet of Gray Seals.},
	pages = {681--700},
	number = {4},
	journaltitle = {Northeastern Naturalist},
	shortjournal = {nena},
	author = {{McCosker}, Christina and Flanders, Kelly and Ono, Kathryn and Dufault, Michelle and Mellone, Dominique and Olson, Zachary},
	urldate = {2023-02-10},
	date = {2020-11},
	note = {Publisher: Eagle Hill Institute},
}

@article{ono_detecting_2019,
	title = {Detecting spiny dogfish in grey seal diets},
	volume = {11},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-018-1044-x},
	doi = {10.1007/s12686-018-1044-x},
	abstract = {Grey seal (Halichoerus grypus) populations declined dramatically in U.S. waters during the nineteenth and twentieth centuries, but have rebounded in recent decades as a result of legal protection. In the Gulf of Maine, increasing grey seal populations have the potential to impact commercially important groundfish species such as cod and haddock, but the potential also exists for more complex ecological interactions to occur given the recent increase of spiny dogfish (Squalus acanthias), another potential groundfish predator. Specifically, seal predation on dogfish could free groundfish species from additional predation pressure. Little quantitative data exists on intraguild predation rates by grey seals on spiny dogfish, in part because of the limitations of current methods of food habits analysis for grey seals. We report the development, validation, and field testing of a non-invasive genetic method for the detection of spiny dogfish in grey seal diets using {DNA} collected from seal feces. Our method amplified spiny dogfish {DNA} from 10 of 10 positive control scats from a captive seal with a known diet, and amplified spiny dogfish {DNA} from 0 of 10 negative control scats. We field tested the method on 20 scats from wild seals and detected spiny dogfish in two of the samples. All positive amplifications were sequenced to verify the species identify, and all were spiny dogfish. Our method has the potential to provide valuable information about changing predator prey dynamics in the Gulf of Maine and elsewhere.},
	pages = {481--485},
	number = {4},
	journaltitle = {Conservation Genetics Resources},
	shortjournal = {Conservation Genet Resour},
	author = {Ono, Kathryn A. and Steinbeiser, Cathleen M. and Coco, Austin B. and Sheehan, Matthew J. and Beck, Abigail J. and Dufault, Michelle N. and Gilbert, Katelyn M. and Antonez, Jessica J. and Olson, Zachary H.},
	urldate = {2023-02-10},
	date = {2019-12-01},
	langid = {english},
}

@article{flanders_utilizing_2020,
	title = {Utilizing next-generation sequencing to identify prey {DNA} in western North Atlantic grey seal Halichoerus grypus diet},
	volume = {655},
	issn = {0171-8630, 1616-1599},
	url = {https://www.int-res.com/abstracts/meps/v655/p227-240/},
	doi = {10.3354/meps13520},
	abstract = {Increasing grey seal Halichoerus grypus abundance in coastal New England is leading to social, political, economic, and ecological controversies. Central to these issues is the foraging ecology and diet composition of the seals. We studied grey seal feeding habits through next-generation sequencing of prey {DNA} using 16S amplicons from seal scat (n = 74) collected from a breeding colony on Monomoy Island in Massachusetts, {USA}, and report frequency of occurrence and relative read abundance. We also assigned seal sex to scat samples using a revised {PCR} assay. In contrast to current understanding of grey seal diet from hard parts and fatty acid analysis, we found no significant difference between male and female diet measured by alpha and beta diversity. Overall, we detected 24 prey groups, 18 of which resolved to species. Sand lance Ammodytes spp. were the most frequently consumed prey group, with a frequency of occurrence ({FO}) of 97.3\%, consistent with previous studies, but Atlantic menhaden Brevoortia tyrannus, the second most frequently consumed species ({FO} = 60.8\%), has not previously been documented in {US} grey seal diet. Our results suggest that a metabarcoding approach to seal food habits can yield important new ecological insights, but that traditional hard parts analysis does not underestimate consumption of Atlantic cod Gadus morhua ({FO} = 6.7\%, Gadidae spp.) and salmon Salmo salar ({FO} = 0\%), 2 particularly valuable species of concern.},
	pages = {227--240},
	journaltitle = {Marine Ecology Progress Series},
	author = {Flanders, Kelly R. and Olson, Zachary H. and Ono, Kathryn A.},
	urldate = {2023-02-10},
	date = {2020-11-26},
	langid = {english},
	keywords = {Diet, Foraging ecology, Grey seal, Halichoerus grypus, Molecular scatology, Next-generation sequencing, Prey {DNA}},
}

@article{saba_recommended_2019,
	title = {Recommended priorities for research on ecological impacts of ocean and coastal acidification in the U.S. Mid-Atlantic},
	volume = {225},
	issn = {0272-7714},
	url = {https://www.sciencedirect.com/science/article/pii/S0272771418308710},
	doi = {10.1016/j.ecss.2019.04.022},
	abstract = {The estuaries and continental shelf system of the United States Mid-Atlantic are subject to ocean acidification driven by atmospheric {CO}2, and coastal acidification caused by nearshore and land-sea interactions that include biological, chemical, and physical processes. These processes include freshwater and nutrient input from rivers and groundwater; tidally-driven outwelling of nutrients, inorganic carbon, alkalinity; high productivity and respiration; and hypoxia. Hence, these complex dynamic systems exhibit substantial daily, seasonal, and interannual variability that is not well captured by current acidification research on Mid-Atlantic organisms and ecosystems. We present recommendations for research priorities that target better understanding of the ecological impacts of acidification in the U. S. Mid-Atlantic region. Suggested priorities are: 1) Determining the impact of multiple stressors on our resource species as well as the magnitude of acidification; 2) Filling information gaps on major taxa and regionally important species in different life stages to improve understanding of their response to variable temporal scales and sources of acidification; 3) Improving experimental approaches to incorporate realistic environmental variability and gradients, include interactions with other environmental stressors, increase transferability to other systems or organisms, and evaluate community and ecosystem response; 4) Determining the capacity of important species to acclimate or adapt to changing ocean conditions; 5) Considering multi-disciplinary, ecosystem-level research that examines acidification impacts on biodiversity and biotic interactions; and 6) Connecting potential acidification-induced ecological impacts to ecosystem services and the economy. These recommendations, while developed for the Mid-Atlantic, can be applicable to other regions will help align research towards knowledge of potential larger-scale ecological and economic impacts.},
	pages = {106188},
	journaltitle = {Estuarine, Coastal and Shelf Science},
	shortjournal = {Estuarine, Coastal and Shelf Science},
	author = {Saba, Grace K. and Goldsmith, Kaitlin A. and Cooley, Sarah R. and Grosse, Daniel and Meseck, Shannon L. and Miller, A. Whitman and Phelan, Beth and Poach, Matthew and Rheault, Robert and St.Laurent, Kari and Testa, Jeremy M. and Weis, Judith S. and Zimmerman, Richard},
	urldate = {2023-02-10},
	date = {2019-09-30},
	langid = {english},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\CH36QAJB\\Saba et al. - 2019 - Recommended priorities for research on ecological .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\SAP7FLGR\\S0272771418308710.html:text/html},
}

@article{zakroff_antagonistic_2020,
	title = {Antagonistic Interactions and Clutch-Dependent Sensitivity Induce Variable Responses to Ocean Acidification and Warming in Squid (Doryteuthis pealeii) Embryos and Paralarvae},
	volume = {11},
	issn = {1664-042X},
	url = {https://www.frontiersin.org/articles/10.3389/fphys.2020.00501},
	abstract = {Ocean acidification ({OA}) and warming seas are significant concerns for coastal systems and species. The Atlantic longfin squid, Doryteuthis pealeii, a core component of the Northwest Atlantic trophic web, has demonstrated impacts, such as reduced growth and delayed development, under high chronic exposure to acidification (2200 ppm), but the combined effects of {OA} and warming have not been explored in this species. In this study, D. pealeii egg capsules were reared under a combination of several acidification levels (400, 2200, and 3500 ppm) and temperatures (20 and 27°C). Hatchlings were measured for a range of metrics [dorsal mantle length ({DML}), yolk sac volume ({YV}), malformation, and hatching success] in three trials over the 2016 breeding season (May – October). Although notable resistance to stressors was seen, highlighting variability within and between clutches, reduced {DML} and malformation of the embryos occurred at the highest {OA} exposure. Surprisingly, increased temperatures did not appear to exacerbate {OA} impacts, although responses were variable. Time to hatching, which increased with acidification, decreased much more drastically under warming and, further, decreased or removed delays caused by acidification. Hatching success, while variable by clutch, showed consistent patterns of greater late stage loss of embryos under acidification and greater early stage loss under warming, highlighting the potential difference in timing between these stressors for this system, i.e., that acidification stress builds up and causes impacts over time within the egg capsule as the embryos grow and respire. High {OA}-exposed hatchlings from the warmer conditions often showed reduced impacts compared to those reared in ambient temperatures. This may be due to the increased developmental rate and subsequently reduced {OA} exposure time of embryos in the higher temperature treatment. These results indicate a substantive potential plasticity to multiple stressors during the embryonic development of this species of squid, but do not predict how this species would fare under these future ocean scenarios.},
	journaltitle = {Frontiers in Physiology},
	author = {Zakroff, Casey J. and Mooney, T. Aran},
	urldate = {2023-02-09},
	date = {2020},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\IIG335QG\\Zakroff and Mooney - 2020 - Antagonistic Interactions and Clutch-Dependent Sen.pdf:application/pdf},
}

@article{chavez-rosales_detection_2022,
	title = {Detection of Habitat Shifts of Cetacean Species: A Comparison Between 2010 and 2017 Habitat Suitability Conditions in the Northwest Atlantic Ocean},
	volume = {9},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.877580},
	shorttitle = {Detection of Habitat Shifts of Cetacean Species},
	abstract = {The simultaneous effects of human activities in the ocean and climate change have already produced a series of responses from the marine ecosystems. With the potential increment of future human activities, such as offshore renewable energy developments, proactive management is required. To facilitate effective management and conservation actions, it is imperative to identify species potentially at risk and their critical habitats. Here we examine 16 cetacean species habitat suitability in the western North Atlantic Ocean using generalized additive models developed from data collected by {NOAA}- Northeast and Southeast Fisheries Science Centers from 2010 to 2017. The models were based on observed species distribution as a function of 21 environmental covariates and compare species-specific core habitats between 2010 and 2017. We identified seasonal differences in patterns of habitat change across guilds and an average northward shift of 178 km across the study area. The effects of these shifts are still unknown, but for already stressed species, the contraction or displacement of their historical habitat could worsen their population status. Therefore, the imminent development of offshore regions, in addition to the effects of climate change emphasize the need of adaptively managing ecosystems on the face of multiple challenges.},
	journaltitle = {Frontiers in Marine Science},
	author = {Chavez-Rosales, Samuel and Josephson, Elizabeth and Palka, Debra and Garrison, Lance},
	urldate = {2023-02-09},
	date = {2022},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\CVGTYCW6\\Chavez-Rosales et al. - 2022 - Detection of Habitat Shifts of Cetacean Species A.pdf:application/pdf},
}

@article{zakroff_dose-dependence_2019,
	title = {Dose-dependence and small-scale variability in responses to ocean acidification during squid, Doryteuthis pealeii, development},
	volume = {166},
	issn = {1432-1793},
	url = {https://doi.org/10.1007/s00227-019-3510-8},
	doi = {10.1007/s00227-019-3510-8},
	abstract = {Coastal squids lay their eggs on the benthos, leaving them to develop in a dynamic system that is undergoing rapid acidification due to human influence. Prior studies have broadly investigated the impacts of ocean acidification on embryonic squid, but have not addressed the thresholds at which these responses occur or their potential variability. We raised squid, Doryteuthis pealeii (captured in Vineyard Sound, Massachusetts, {USA}: 41°23.370'N 70°46.418′W), eggs in three trials across the breeding season (May–September, 2013) in a total of six chronic {pCO}2 exposures (400, 550, 850, 1300, 1900, and 2200 ppm). Hatchlings were counted and subsampled for mantle length, yolk volume, hatching time, hatching success, and statolith morphology. New methods for analysis of statolith shape, rugosity, and surface degradation were developed and are presented (with code). Responses to acidification (e.g., reduced mantle lengths, delayed hatching, and smaller, more degraded statoliths) were evident at {\textasciitilde} 1300 ppm {CO}2. However, patterns of physiological response and energy management, based on comparisons of yolk consumption and growth, varied among trials. Interactions between {pCO}2 and hatching day indicated a potential influence of exposure time on responses, while interactions with culture vessel highlighted the substantive natural variability within a clutch of eggs. While this study is consistent with, and expands upon, previous findings of sensitivity of the early life stages to acidification, it also highlights the plasticity and potential for resilience in this population of squid.},
	pages = {62},
	number = {5},
	journaltitle = {Marine Biology},
	shortjournal = {Mar Biol},
	author = {Zakroff, Casey and Mooney, T. Aran and Berumen, Michael L.},
	urldate = {2023-02-09},
	date = {2019-04-19},
	langid = {english},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\GR29VF7U\\Zakroff et al. - 2019 - Dose-dependence and small-scale variability in res.pdf:application/pdf},
}

@article{cameron_effects_2022,
	title = {Effects of elevated {pCO}2 and temperature on the calcification rate, survival, extrapallial fluid chemistry, and respiration of the Atlantic Sea scallop Placopecten magellanicus},
	volume = {67},
	issn = {1939-5590},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/lno.12153},
	doi = {10.1002/lno.12153},
	abstract = {Anthropogenic {CO}2-emission is causing ocean warming and acidification. Understanding how basic physiological processes of marine organisms respond to these stressors is important for predicting their responses to future global change. We examined the effects of elevated {pCO}2 and temperature ({pCO}2 = 344–2199 ppm; temperature = 6°C, 9°C, and 12°C) on the calcification rate, extrapallial fluid ({EPF}) carbonate chemistry, respiration, and survivorship of Atlantic sea scallops (Placopecten magellanicus) in a fully crossed 143-d experiment. Rates of calcification and respiration were inhibited by elevated {pCO}2, and mortality occurred when elevated {pCO}2 was accompanied by high-temperature stress. Declines in growth and survivorship were likely caused by external shell dissolution, thermal stress, and hypercapnic reduction of metabolism under elevated {pCO}2. Concentrations of dissolved inorganic carbon ({DIC}) and total alkalinity in the {EPF} increased above seawater concentrations in response to elevated {pCO}2. {EPF} {pH} declined, but did not decline as much as seawater {pH}, indicating that scallops regulate {EPF} {pH} to support calcification. The combination of {EPF} {pH} regulation and {DIC} elevation yielded an increase in {EPF} [{CO}32−] under elevated {pCO}2 treatments. The combination of low respiration rates, high {EPF} [{CO}32−], and low calcification rates under elevated {pCO}2 suggests that the impaired calcification arises more from hypercapnic inhibition of metabolic activity and external shell dissolution than from chemically unfavorable conditions in the {EPF}. These results demonstrate the importance of {EPF} chemistry for bivalve biomineralization, but show that regulation efforts are insufficient to fully offset the deleterious effects of elevated {pCO}2 on scallop performance.},
	pages = {1670--1686},
	number = {8},
	journaltitle = {Limnology and Oceanography},
	author = {Cameron, Louise P. and Grabowski, Jonathan H. and Ries, Justin B.},
	urldate = {2023-02-09},
	date = {2022},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/lno.12153},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\YYPRLBMB\\Cameron et al. - 2022 - Effects of elevated pCO2 and temperature on the ca.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\R9LYV4DJ\\lno.html:text/html},
}

@article{kroeker_impacts_2013,
	title = {Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming},
	volume = {19},
	issn = {1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.12179},
	doi = {10.1111/gcb.12179},
	shorttitle = {Impacts of ocean acidification on marine organisms},
	abstract = {Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, and policy. As research on the topic expands at an exponential rate, a comprehensive understanding of the variability in organisms' responses and corresponding levels of certainty is necessary to forecast the ecological effects. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining biological responses to ocean acidification. The results reveal decreased survival, calcification, growth, development and abundance in response to acidification when the broad range of marine organisms is pooled together. However, the magnitude of these responses varies among taxonomic groups, suggesting there is some predictable trait-based variation in sensitivity, despite the investigation of approximately 100 new species in recent research. The results also reveal an enhanced sensitivity of mollusk larvae, but suggest that an enhanced sensitivity of early life history stages is not universal across all taxonomic groups. In addition, the variability in species' responses is enhanced when they are exposed to acidification in multi-species assemblages, suggesting that it is important to consider indirect effects and exercise caution when forecasting abundance patterns from single-species laboratory experiments. Furthermore, the results suggest that other factors, such as nutritional status or source population, could cause substantial variation in organisms' responses. Last, the results highlight a trend towards enhanced sensitivity to acidification when taxa are concurrently exposed to elevated seawater temperature.},
	pages = {1884--1896},
	number = {6},
	journaltitle = {Global Change Biology},
	author = {Kroeker, Kristy J. and Kordas, Rebecca L. and Crim, Ryan and Hendriks, Iris E. and Ramajo, Laura and Singh, Gerald S. and Duarte, Carlos M. and Gattuso, Jean-Pierre},
	urldate = {2023-02-09},
	date = {2013},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.12179},
	keywords = {climate change, calcification, carbonate chemistry, cumulative effects, {pH}},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\DYRRBCYG\\Kroeker et al. - 2013 - Impacts of ocean acidification on marine organisms.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\CX69QCAH\\gcb.html:text/html},
}

@incollection{intergovernmental_panel_on_climate_change_ipcc_technical_2022,
	location = {Cambridge},
	title = {Technical Summary},
	isbn = {978-1-00-915796-4},
	url = {https://www.cambridge.org/core/books/ocean-and-cryosphere-in-a-changing-climate/technical-summary/3428BF3C6ADE0C52755DBC3AA5CFE48B},
	pages = {39--70},
	booktitle = {The Ocean and Cryosphere in a Changing Climate: Special Report of the Intergovernmental Panel on Climate Change},
	publisher = {Cambridge University Press},
	editor = {{Intergovernmental Panel on Climate Change (IPCC)}},
	urldate = {2023-02-09},
	date = {2022},
	doi = {10.1017/9781009157964.002},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\HHCSDHSB\\Intergovernmental Panel on Climate Change (IPCC) - 2022 - Technical Summary.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\GRTJWG2H\\3428BF3C6ADE0C52755DBC3AA5CFE48B.html:text/html},
}

@article{cheng_another_2023,
	title = {Another Year of Record Heat for the Oceans},
	issn = {1861-9533},
	url = {https://doi.org/10.1007/s00376-023-2385-2},
	doi = {10.1007/s00376-023-2385-2},
	abstract = {Changes in ocean heat content ({OHC}), salinity, and stratification provide critical indicators for changes in Earth’s energy and water cycles. These cycles have been profoundly altered due to the emission of greenhouse gasses and other anthropogenic substances by human activities, driving pervasive changes in Earth’s climate system. In 2022, the world’s oceans, as given by {OHC}, were again the hottest in the historical record and exceeded the previous 2021 record maximum. According to {IAP}/{CAS} data, the 0–2000 m {OHC} in 2022 exceeded that of 2021 by 10.9 ± 8.3 {ZJ} (1 Zetta Joules = 1021 Joules); and according to {NCEI}/{NOAA} data, by 9.1 ± 8.7 {ZJ}. Among seven regions, four basins (the North Pacific, North Atlantic, the Mediterranean Sea, and southern oceans) recorded their highest {OHC} since the 1950s. The salinity-contrast index, a quantification of the “salty gets saltier—fresh gets fresher” pattern, also reached its highest level on record in 2022, implying continued amplification of the global hydrological cycle. Regional {OHC} and salinity changes in 2022 were dominated by a strong La Niña event. Global upper-ocean stratification continued its increasing trend and was among the top seven in 2022.},
	journaltitle = {Advances in Atmospheric Sciences},
	shortjournal = {Adv. Atmos. Sci.},
	author = {Cheng, Lijing and Abraham, John and Trenberth, Kevin E. and Fasullo, John and Boyer, Tim and Mann, Michael E. and Zhu, Jiang and Wang, Fan and Locarnini, Ricardo and Li, Yuanlong and Zhang, Bin and Yu, Fujiang and Wan, Liying and Chen, Xingrong and Feng, Licheng and Song, Xiangzhou and Liu, Yulong and Reseghetti, Franco and Simoncelli, Simona and Gouretski, Viktor and Chen, Gengxin and Mishonov, Alexey and Reagan, Jim and Li, Guancheng},
	urldate = {2023-02-09},
	date = {2023-01-11},
	langid = {english},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\Q3V76Y9J\\Cheng et al. - 2023 - Another Year of Record Heat for the Oceans.pdf:application/pdf},
}

@article{northeast_fisheries_science_center_us_noaa_2022,
	title = {{NOAA} Fisheries and {BOEM} Federal Survey Mitigation Implementation Strategy - Northeast U.S. Region},
	url = {https://repository.library.noaa.gov/view/noaa/47925},
	doi = {10.25923/jqse-x746},
	series = {{NOAA} technical memorandum {NMFS}-{NE} ; 292},
	abstract = {This Federal Survey Mitigation Strategy (hereafter Strategy) is intended to guide the development and implementation of a program to mitigate impacts of wind energy development on fisheries surveys over the expected full duration (30+ years) of wind energy development in the Northeast U.S. (Mitigation Program). The Mitigation Program will include survey-specific mitigation plans for each impacted survey, including both vessel and aerial surveys (Survey Specific Mitigation Plans). This strategy is specific to the Northeast U.S. Region (Maine to North Carolina) and generally applicable to other regions of the country.},
	author = {Hare, J.A. and Blythe, B.J. and Ford, K.H. and Godfrey-McKee, S. and Hooker, B.R. and Jensen, B.M. and Lipsky, A. and Nachman, C. and Pfeiffer, L. and Rasser, M. and Renshaw, K.},
	editor = {{Northeast Fisheries Science Center (U.S.)}},
	date = {2022},
	keywords = {Effect of wind power plants on, Fish surveys},
}

@article{pousse_dynamic_2022,
	title = {Dynamic energy budget modeling of Atlantic surfclam, Spisula solidissima, under future ocean acidification and warming},
	volume = {177},
	issn = {0141-1136},
	url = {https://www.sciencedirect.com/science/article/pii/S0141113622000472},
	doi = {10.1016/j.marenvres.2022.105602},
	abstract = {A dynamic energy budget ({DEB}) model integrating {pCO}2 was used to describe ocean acidification ({OA}) effects on Atlantic surfclam, Spisula solidissima, bioenergetics. Effects of elevated {pCO}2 on ingestion and somatic maintenance costs were simulated, validated, and adapted in the {DEB} model based upon growth and biological rates acquired during a 12-week laboratory experiment. Temperature and {pCO}2 were projected for the next 100 years following the intergovernmental panel on climate change representative concentration pathways scenarios (2.6, 6.0, and 8.5) and used as forcing variables to project surfclam growth and reproduction. End-of-century water warming and acidification conditions resulted in simulated faster growth for young surfclams and more energy allocated to reproduction until the beginning of the 22nd century when a reduction in maximum shell length and energy allocated to reproduction was observed for the {RCP} 8.5 scenario.},
	pages = {105602},
	journaltitle = {Marine Environmental Research},
	shortjournal = {Marine Environmental Research},
	author = {Pousse, Émilien and Munroe, Daphne and Hart, Deborah and Hennen, Daniel and Cameron, Louise P. and Rheuban, Jennie E. and Wang, Zhaohui Aleck and Wikfors, Gary H. and Meseck, Shannon L.},
	urldate = {2023-02-07},
	date = {2022-05-01},
	langid = {english},
	keywords = {Atlantic surfclam, Climate change, Dynamic energy budget, Ocean acidification},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\82SNY4Q3\\S0141113622000472.html:text/html},
}

@article{jacox_global_2022,
	title = {Global seasonal forecasts of marine heatwaves},
	volume = {604},
	rights = {2022 This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/s41586-022-04573-9},
	doi = {10.1038/s41586-022-04573-9},
	abstract = {Marine heatwaves ({MHWs})—periods of exceptionally warm ocean temperature lasting weeks to years—are now widely recognized for their capacity to disrupt marine ecosystems1–3. The substantial ecological and socioeconomic impacts of these extreme events present significant challenges to marine resource managers4–7, who would benefit from forewarning of {MHWs} to facilitate proactive decision-making8–11. However, despite extensive research into the physical drivers of {MHWs}11,12, there has been no comprehensive global assessment of our ability to predict these events. Here we use a large multimodel ensemble of global climate forecasts13,14 to develop and assess {MHW} forecasts that cover the world’s oceans with lead times of up to a year. Using 30 years of retrospective forecasts, we show that the onset, intensity and duration of {MHWs} are often predictable, with skilful forecasts possible from 1 to 12 months in advance depending on region, season and the state of large-scale climate modes, such as the El Niño/Southern Oscillation. We discuss considerations for setting decision thresholds based on the probability that a {MHW} will occur, empowering stakeholders to take appropriate actions based on their risk profile. These results highlight the potential for operational {MHW} forecasts, analogous to forecasts of extreme weather phenomena, to promote climate resilience in global marine ecosystems.},
	pages = {486--490},
	number = {7906},
	journaltitle = {Nature},
	author = {Jacox, Michael G. and Alexander, Michael A. and Amaya, Dillon and Becker, Emily and Bograd, Steven J. and Brodie, Stephanie and Hazen, Elliott L. and Pozo Buil, Mercedes and Tommasi, Desiree},
	urldate = {2023-02-07},
	date = {2022-04},
	langid = {english},
	note = {Number: 7906
Publisher: Nature Publishing Group},
	keywords = {Natural hazards, Physical oceanography},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\UUUPVNQR\\Jacox et al. - 2022 - Global seasonal forecasts of marine heatwaves.pdf:application/pdf},
}

@article{jacox_thermal_2020,
	title = {Thermal displacement by marine heatwaves},
	volume = {584},
	rights = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/s41586-020-2534-z},
	doi = {10.1038/s41586-020-2534-z},
	abstract = {Marine heatwaves ({MHWs})—discrete but prolonged periods of anomalously warm ocean temperatures—can drastically alter ocean ecosystems, with profound ecological and socioeconomic impacts1–8. Considerable effort has been directed at understanding the patterns, drivers and trends of {MHWs} globally9–11. Typically, {MHWs} are characterized on the basis of their intensity and persistence at a given location—an approach that is particularly relevant for corals and other sessile organisms that must endure increased temperatures. However, many ecologically and commercially important marine species respond to environmental disruptions by relocating to favourable habitats, and dramatic range shifts of mobile marine species are among the conspicuous impacts of {MHWs}1,4,12,13. Whereas spatial temperature shifts have been studied extensively in the context of long-term warming trends14–18, they are unaccounted for in existing global {MHW} analyses. Here we introduce thermal displacement as a metric that characterizes {MHWs} by the spatial shifts of surface temperature contours, instead of by local temperature anomalies, and use an observation-based global sea surface temperature dataset to calculate thermal displacements for all {MHWs} from 1982 to 2019. We show that thermal displacements during {MHWs} vary from tens to thousands of kilometres across the world’s oceans and do not correlate spatially with {MHW} intensity. Furthermore, short-term thermal displacements during {MHWs} are of comparable magnitude to century-scale shifts inferred from warming trends18, although their global spatial patterns are very different. These results expand our understanding of {MHWs} and their potential impacts on marine species, revealing which regions are most susceptible to thermal displacement, and how such shifts may change under projected ocean warming. The findings also highlight the need for marine resource management to account for {MHW}-driven spatial shifts, which are of comparable scale to those associated with long-term climate change and are already happening.},
	pages = {82--86},
	number = {7819},
	journaltitle = {Nature},
	author = {Jacox, Michael G. and Alexander, Michael A. and Bograd, Steven J. and Scott, James D.},
	urldate = {2023-02-07},
	date = {2020-08},
	langid = {english},
	note = {Number: 7819
Publisher: Nature Publishing Group},
	keywords = {Natural hazards, Physical oceanography, Environmental health},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\ZCEBPKE5\\Jacox et al. - 2020 - Thermal displacement by marine heatwaves.pdf:application/pdf},
}

@article{jiang_climatological_2015,
	title = {Climatological distribution of aragonite saturation state in the global oceans},
	volume = {29},
	issn = {1944-9224},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/2015GB005198},
	doi = {10.1002/2015GB005198},
	abstract = {Aragonite saturation state (Ωarag) in surface and subsurface waters of the global oceans was calculated from up-to-date (through the year of 2012) ocean station dissolved inorganic carbon ({DIC}) and total alkalinity ({TA}) data. Surface Ωarag in the open ocean was always supersaturated (Ω {\textgreater} 1), ranging between 1.1 and 4.2. It was above 2.0 (2.0–4.2) between 40°N and 40°S but decreased toward higher latitude to below 1.5 in polar areas. The influences of water temperature on the {TA}/{DIC} ratio, combined with the temperature effects on inorganic carbon equilibrium and apparent solubility product (K′sp), explain the latitudinal differences in surface Ωarag. Vertically, Ωarag was highest in the surface mixed layer. Higher hydrostatic pressure, lower water temperature, and more {CO}2 buildup from biological activity in the absence of air-sea gas exchange helped maintain lower Ωarag in the deep ocean. Below the thermocline, aerobic decomposition of organic matter along the pathway of global thermohaline circulation played an important role in controlling Ωarag distributions. Seasonally, surface Ωarag above 30° latitudes was about 0.06 to 0.55 higher during warmer months than during colder months in the open-ocean waters of both hemispheres. Decadal changes of Ωarag in the Atlantic and Pacific Oceans showed that Ωarag in waters shallower than 100 m depth decreased by 0.10 ± 0.09 (−0.40 ± 0.37\% yr−1) on average from the decade spanning 1989–1998 to the decade spanning 1998–2010.},
	pages = {1656--1673},
	number = {10},
	journaltitle = {Global Biogeochemical Cycles},
	author = {Jiang, Li-Qing and Feely, Richard A. and Carter, Brendan R. and Greeley, Dana J. and Gledhill, Dwight K. and Arzayus, Krisa M.},
	urldate = {2023-02-06},
	date = {2015},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/2015GB005198},
	keywords = {{pH}, aragonite saturation state, climatology, global oceans, ocean acidification, omega},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\4YWKM4FH\\Jiang et al. - 2015 - Climatological distribution of aragonite saturatio.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\ANLLFDHC\\Jiang et al. - 2015 - Climatological distribution of aragonite saturatio.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\UHSW7LKY\\2015GB005198.html:text/html},
}

@article{frick_spatiotemporal_2022,
	title = {Spatiotemporal Variation in Distribution, Size, and Relative Abundance within a Salish Sea Nearshore Forage Fish Community},
	volume = {14},
	issn = {1942-5120},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mcf2.10202},
	doi = {10.1002/mcf2.10202},
	abstract = {Forage fish are schooling species commonly occurring in both offshore pelagic and nearshore coastal habitats. Beyond use by some species for spawning, the dynamics of nearshore habitat use are not well understood. The objective of our study was to evaluate the spring–summer dynamics of forage fish occurrence in nearshore habitats of the Strait of Juan de Fuca, Washington. We suspected that habitat changes resulting from removal of two large dams on the Elwha River (2009–2011) may have altered fish presence and abundance. Monthly beach seine sampling in four regions along 40 km of shoreline was conducted from April to September between 2006 and 2019. We caught nearly 600,000 fish, comprising 82 different species. Nine species of forage fish accounted for 81.7\% of all fishes caught; most were classified as postlarvae and juveniles based on size. There were spatial differences in the forage fish assemblage between two of our sites but no discernable year effects and no obvious impact of dam removal on forage community composition. Three species represented 78.8\% of the catch: Pacific Herring Clupea pallasii, Pacific Sand Lance Ammodytes hexapterus, and Surf Smelt Hypomesus pretiosus. We used a Bayesian generalized linear mixed model to evaluate spatial and temporal variability in the probability of occurrence of these species. Each species exhibited a unique pattern of intra-annual, interannual, and regional fluctuations. Pacific Herring occurrence progressively increased monthly, Pacific Sand Lance occurrence decreased, and Surf Smelt probability of occurrence peaked in June. Temporal variations in distribution and abundance of these species are likely driven by life history differences and biological requirements. We speculate that specific characteristics of each region, including proximity to spawning areas, spawn timing, extant current patterns, and ecosystem processes, drove variations in distribution between species.},
	pages = {e10202},
	number = {2},
	journaltitle = {Marine and Coastal Fisheries},
	author = {Frick, Kinsey E. and Kagley, Anna N. and Fresh, Kurt L. and Samhouri, Jameal F. and Ward, Larry S. and Stapleton, Justin T. and Shelton, Andrew O.},
	urldate = {2023-01-30},
	date = {2022},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/mcf2.10202},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\DVX64IVC\\Frick et al. - 2022 - Spatiotemporal Variation in Distribution, Size, an.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\G39AQAUN\\mcf2.html:text/html},
}

@article{schonfeld_spatial_2022,
	title = {Spatial differences in estuarine utilization by seasonally resident species in Mid-Atlantic Bight, {USA}},
	volume = {31},
	issn = {1365-2419},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12611},
	doi = {10.1111/fog.12611},
	abstract = {Climate-driven distributional shifts have been well-documented for fisheries resources along the East Coast of the United States, yet little attention has been given to adjacent estuarine systems. The Chesapeake Bay is the largest estuary in the continental United States and serves as important habitat for a diversity of fishes and invertebrates, many of which are seasonal residents. Survey data indicate that relative abundance of finfish in Chesapeake Bay has diminished substantially, while coastwide stock status has remained unchanged. In response to warming, seasonal estuarine residents may remain in coastal waters or inhabit a northerly estuary, but the extent to which changing environmental conditions may drive exchange between the coastal ocean and estuarine systems remains unresolved. This study analyzed data collected from 2008 to 2019 by three fisheries-independent trawl surveys to explore temporal patterns and associated environmental drivers of the estuarine–coastal ocean exchange in the Mid-Atlantic for eight economically and ecologically important species. Relative habitat utilization of Chesapeake Bay declined for most species, while utilization patterns for Delaware Bay were largely constant or increasing over time. Broad-scale, multispecies analyses of relative habitat utilization time series revealed that the North Atlantic Oscillation ({NAO}) was an important driver of Chesapeake Bay exchange, but that average Apr/May coastal ocean bottom temperature was significant for Delaware Bay. Collectively, the results demonstrate that several Mid-Atlantic species have altered their estuarine habitat use over time, climate drivers associated with estuarine–coastal ocean exchange operate on different time scales, and that the impacts of warming within the Mid-Atlantic vary spatially.},
	pages = {615--628},
	number = {6},
	journaltitle = {Fisheries Oceanography},
	author = {Schonfeld, Adena J. and Gartland, James and Latour, Robert J.},
	urldate = {2022-11-02},
	date = {2022},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/fog.12611},
	keywords = {climate change, Chesapeake Bay, dynamic factor analysis, ecosystem exchange, quantitative fisheries ecology},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\GSNGARVS\\Schonfeld et al. - 2022 - Spatial differences in estuarine utilization by se.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\8L95MKRE\\Schonfeld et al. - 2022 - Spatial differences in estuarine utilization by se.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\22R23CIQ\\Schonfeld et al. - 2022 - Spatial differences in estuarine utilization by se.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\B7GJJU76\\fog.html:text/html},
}

@article{depiper_learning_2021,
	title = {Learning by doing: collaborative conceptual modelling as a path forward in ecosystem-based management},
	volume = {78},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsab054},
	doi = {10.1093/icesjms/fsab054},
	shorttitle = {Learning by doing},
	abstract = {Managers, stakeholders, and scientists recognize the need for collaborative, transparent, integrated approaches to complex resource management issues, and frameworks to address these complex issues are developing. Through the course of 2019, the Mid-Atlantic Fishery Management Council developed a conceptual model of ecosystem linkages and risks for summer flounder, a species of recreational and commercial fisheries importance. The proximal aim of the model was to develop a list of integrated management questions that could be refined and addressed through a future quantitative management strategy evaluation. As such, this conceptual model served as a scoping tool. However, the true value of the conceptual model lays elsewhere: familiarizing resource managers historically focused on single-species management with the potential utility of an ecosystem approach to management. This paper details the goals and development of the conceptual model and situates this process in the broader context of best practices for collaborative open science and scientific reproducibility. Further, it highlights a successful path by which the shift towards ecosystem-based management can be actuated.},
	pages = {1217--1228},
	number = {4},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} Journal of Marine Science},
	author = {{DePiper}, Geret and Gaichas, Sarah and Muffley, Brandon and Ardini, Greg and Brust, Jeffrey and Coakley, Jessica and Dancy, Kiley and Elliott, G Warren and Leaning, Dustin C and Lipton, Douglas and {McNamee}, Jason and Perretti, Charles and Rootes-Murdy, Kirby and Wilberg, Michael J},
	urldate = {2022-08-08},
	date = {2021-08-04},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\C3RGFFYZ\\DePiper et al. - 2021 - Learning by doing collaborative conceptual modell.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\3MH8VAJU\\6207633.html:text/html},
}

@article{caracappa_northeast_2022,
	title = {A northeast United States Atlantis marine ecosystem model with ocean reanalysis and ocean color forcing},
	volume = {471},
	issn = {0304-3800},
	url = {https://www.sciencedirect.com/science/article/pii/S030438002200148X},
	doi = {10.1016/j.ecolmodel.2022.110038},
	abstract = {The northeast United States Atlantis model ({NEUSv}2) is an end-to-end ecosystem model that can simulate biogeochemical, ecological, fishery, management, and socio-economic processes within marine ecosystems. As a major update to the original model, {NEUSv}2 includes changes to the model's functional group definitions and forcing data. {NEUSv}2 is the first Atlantis model to use a satellite-ocean-color-derived phytoplankton size class model that was tuned specifically for the region to force marine primary production. Additionally, physical ocean variables (currents, temperature, and salinity) were updated using a high-resolution global ocean reanalysis. Despite its coarse resolution, {NEUSv}2 was capable of reproducing the broad spatial patterns seen in the physical and biological forcing sources, with the exception of some circulation features. {NEUSv}2 produced plausible zooplankton and planktivore biomass, a stable lower trophic food web, and recent trends in zooplankton biomass. {NEUSv}2 meets calibration criteria for the persistence and long-term stability of functional group biomass. Given the success of this new Atlantis forcing approach, we detail the observations and challenges regarding spatial scale-related processes, data assimilation, and biological calibration. We also discuss possible tradeoffs with model scope, calibration, and the availability of feedback mechanisms. This {NEUSv}2 hindcast is well suited for exploring ecosystem-level sensitivity to lower trophic processes and for testing alternative biogeochemical forcing. Further developments will improve model performance for higher trophic levels.},
	pages = {110038},
	journaltitle = {Ecological Modelling},
	shortjournal = {Ecological Modelling},
	author = {Caracappa, Joseph C. and Beet, Andrew and Gaichas, Sarah and Gamble, Robert J. and Hyde, Kimberly J. W. and Large, Scott I. and Morse, Ryan E. and Stock, Charles A. and Saba, Vincent S.},
	urldate = {2022-08-08},
	date = {2022-09-01},
	langid = {english},
	keywords = {Atlantis, biogeochemical forcing, end-to-end models, global reanalysis, lower trophic levels, marine ecosystem models, ocean color, primary production},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\DILX5W83\\Caracappa et al. - 2022 - A northeast United States Atlantis marine ecosyste.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\S672JAVG\\S030438002200148X.html:text/html},
}

@article{christiansen_emergence_2022,
	title = {Emergence of Large-Scale Hydrodynamic Structures Due to Atmospheric Offshore Wind Farm Wakes},
	volume = {9},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2022.818501},
	abstract = {The potential impact of offshore wind farms through decreasing sea surface wind speed on the shear forcing and its consequences for the ocean dynamics are investigated. Based on the unstructured-grid model {SCHISM}, we present a new cross-scale hydrodynamic model setup for the southern North Sea, which enables high-resolution analysis of offshore wind farms in the marine environment. We introduce an observational-based empirical approach to parameterize the atmospheric wakes in a hydrodynamic model and simulate the seasonal cycle of the summer stratification in consideration of the recent state of wind farm development in the southern North Sea. The simulations show the emergence of large-scale attenuation in the wind forcing and associated alterations in the local hydro- and thermodynamics. The wake effects lead to unanticipated spatial variability in the mean horizontal currents and to the formation of large-scale dipoles in the sea surface elevation. Induced changes in the vertical and lateral flow are sufficiently strong to influence the residual currents and entail alterations of the temperature and salinity distribution in areas of wind farm operation. Ultimately, the dipole-related processes affect the stratification development in the southern North Sea and indicate potential impact on marine ecosystem processes. In the German Bight, in particular, we observe large-scale structural change in stratification strength, which eventually enhances the stratification during the decline of the summer stratification toward autumn.},
	journaltitle = {Frontiers in Marine Science},
	author = {Christiansen, Nils and Daewel, Ute and Djath, Bughsin and Schrum, Corinna},
	urldate = {2022-03-09},
	date = {2022},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\TEC2AI85\\Christiansen et al. - 2022 - Emergence of Large-Scale Hydrodynamic Structures D.pdf:application/pdf},
}

@article{quintana-rizzo_residency_2021,
	title = {Residency, demographics, and movement patterns of North Atlantic right whales Eubalaena glacialis in an offshore wind energy development area in southern New England, {USA}},
	volume = {45},
	issn = {1863-5407, 1613-4796},
	url = {https://www.int-res.com/abstracts/esr/v45/p251-268/},
	doi = {10.3354/esr01137},
	abstract = {Offshore wind energy development is growing quickly around the world. In southern New England, {USA}, one of the largest commercial offshore wind energy farms in the {USA} will be established in the waters off Massachusetts and Rhode Island, an area used by the Critically Endangered North Atlantic right whale Eubalaena glacialis. Prior to 2011, little was known about the use of this area by right whales. We examined aerial survey data collected between 2011-2015 and 2017-2019 to quantify right whale distribution, residency, demography, and movements in the region. Right whale occurrence increased during the study period. Since 2017, whales have been sighted in the area nearly every month, with peak sighting rates between late winter and spring. Model outputs suggest that 23\% of the species’ population is present from December through May, and the mean residence time has tripled to an average of 13 d during these months. Age and sex ratios of the individuals present in the area are similar to those of the species as a whole, with adult males the most common demographic group. Movement models showed that southern New England is an important destination for right whales, including conceptive and reproductive females, and qualitative observations included animals feeding and socializing. Implementing mitigation procedures in coordination with these findings will be crucial in lessening the potential impacts on right whales from construction noise, increased vessel traffic, and habitat disruption in this region.},
	pages = {251--268},
	journaltitle = {Endangered Species Research},
	author = {Quintana-Rizzo, E. and Leiter, S. and Cole, T. V. N. and Hagbloom, M. N. and Knowlton, A. R. and Nagelkirk, P. and O’Brien, O. and Khan, C. B. and Henry, A. G. and Duley, P. A. and Crowe, L. M. and Mayo, C. A. and Kraus, S. D.},
	urldate = {2022-03-09},
	date = {2021-07-29},
	langid = {english},
	keywords = {Aerial surveys, Alternative energy, Migratory species},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\LJSI7QIZ\\Quintana-Rizzo et al. - 2021 - Residency, demographics, and movement patterns of .pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\E7DCYRH5\\p251-268.html:text/html},
}

@article{du_pontavice_incorporating_nodate,
	title = {Incorporating environmental effects from ocean models improves a marine fish stock assessment},
	journaltitle = {{ICES} Journal of Marine Science},
	author = {du Pontavice, H. and Miller, Timothy J. and Stock, Brian C. and Chen, Zhuomin and Saba, Vincent S.},
}

@article{gawarkiewicz_increasing_nodate,
	title = {Increasing Frequency of Mid-depth Salinity Maximum Intrusions in the Middle Atlantic Bight},
	journaltitle = {Journal of Geophysical Research: Oceans},
	author = {Gawarkiewicz, Glen and Fratantoni, Paula and Bahr, Frank and Ellertson, Aubrey},
}

@article{farr_assessment_2021,
	title = {An assessment of marine, estuarine, and riverine habitat vulnerability to climate change in the Northeast U.S.},
	volume = {16},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0260654},
	doi = {10.1371/journal.pone.0260654},
	abstract = {Climate change is impacting the function and distribution of habitats used by marine, coastal, and diadromous species. These impacts often exacerbate the anthropogenic stressors that habitats face, particularly in the coastal environment. We conducted a climate vulnerability assessment of 52 marine, estuarine, and riverine habitats in the Northeast U.S. to develop an ecosystem-scale understanding of the impact of climate change on these habitats. The trait-based assessment considers the overall vulnerability of a habitat to climate change to be a function of two main components, sensitivity and exposure, and relies on a process of expert elicitation. The climate vulnerability ranks ranged from low to very high, with living habitats identified as the most vulnerable. Over half of the habitats examined in this study are expected to be impacted negatively by climate change, while four habitats are expected to have positive effects. Coastal habitats were also identified as highly vulnerable, in part due to the influence of non-climate anthropogenic stressors. The results of this assessment provide regional managers and scientists with a tool to inform habitat conservation, restoration, and research priorities, fisheries and protected species management, and coastal and ocean planning.},
	pages = {e0260654},
	number = {12},
	journaltitle = {{PLOS} {ONE}},
	shortjournal = {{PLOS} {ONE}},
	author = {Farr, Emily R. and Johnson, Michael R. and Nelson, Mark W. and Hare, Jonathan A. and Morrison, Wendy E. and Lettrich, Matthew D. and Vogt, Bruce and Meaney, Christopher and Howson, Ursula A. and Auster, Peter J. and Borsuk, Frank A. and Brady, Damian C. and Cashman, Matthew J. and Colarusso, Phil and Grabowski, Jonathan H. and Hawkes, James P. and Mercaldo-Allen, Renee and Packer, David B. and Stevenson, David K.},
	urldate = {2022-03-02},
	date = {2021-12-09},
	langid = {english},
	note = {Publisher: Public Library of Science},
	keywords = {Climate change, Anthropogenic climate change, Habitats, Marine fish, Reefs, Surface water, Water columns, Wetlands},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\6RBHCZHP\\Farr et al. - 2021 - An assessment of marine, estuarine, and riverine h.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XIDW7DS9\\article.html:text/html},
}

@article{schick_striking_2009,
	title = {Striking the right balance in right whale conservation},
	volume = {66},
	issn = {0706-652X},
	url = {https://cdnsciencepub.com/doi/10.1139/F09-115},
	doi = {10.1139/F09-115},
	pages = {1399--1403},
	number = {9},
	journaltitle = {Canadian Journal of Fisheries and Aquatic Sciences},
	shortjournal = {Can. J. Fish. Aquat. Sci.},
	author = {Schick, Robert S. and Halpin, Patrick N. and Read, Andrew J. and Slay, Christopher K. and Kraus, Scott D. and Mate, Bruce R. and Baumgartner, Mark F. and Roberts, Jason J. and Best, Benjamin D. and Good, Caroline P. and Loarie, Scott R. and Clark, James S.},
	urldate = {2022-03-09},
	date = {2009-09},
	note = {Publisher: {NRC} Research Press},
	file = {Submitted Version:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\HND4AUNI\\Schick et al. - 2009 - Striking the right balance in right whale conserva.pdf:application/pdf},
}

@book{boem_vineyard_2020,
	title = {Vineyard Wind 1 Offshore Wind Energy Project Supplement to the Draft Environmental Impact Statement. {OCS} {EIS}/{EA}, {BOEM} 2020-025},
	url = {https://www.boem.gov/sites/default/files/documents/renewable-energy/Vineyard-Wind-1-Supplement-to-EIS.pdf},
	pagetotal = {420},
	author = {{BOEM}},
	urldate = {2022-02-11},
	date = {2020},
	file = {Vineyard-Wind-1-Supplement-to-EIS.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\YKRBWL2B\\Vineyard-Wind-1-Supplement-to-EIS.pdf:application/pdf},
}

@article{perretti_regime_2017,
	title = {Regime shifts in fish recruitment on the Northeast {US} Continental Shelf},
	volume = {574},
	issn = {0171-8630, 1616-1599},
	url = {http://www.int-res.com/abstracts/meps/v574/p1-11/},
	doi = {10.3354/meps12183},
	abstract = {There is accumulating evidence for decadal-scale regime shifts at the base of the food web on the Northeast {US} Continental Shelf. However, less evidence exists for regime shifts in fish recruitment success, particularly for synchronized regimes across multiple species. Here, we analyzed stock assessment output and survey data to test for regimes in the recruitment success of 18 commercially important marine species over a 29 yr timespan. We then tested whether recruitment regimes coincide with regimes in the zooplankton community, and whether the abundance of large spawners could explain the patterns in recruitment. We found evidence for 3 decadal-scale recruitment regimes: low recruitment success in the 1980s, high success in the 1990s, and a return to low recruitment success in the 2000s. This general pattern was found in all datasets of recruitment. The abundance of large spawners did not appear to be a broad-scale driver of recruitment success; however, recruitment regimes coincided with regimes in copepod abundance and size structure.},
	pages = {1--11},
	journaltitle = {Marine Ecology Progress Series},
	shortjournal = {Mar. Ecol. Prog. Ser.},
	author = {Perretti, Ct and Fogarty, Mj and Friedland, Kd and Hare, Ja and Lucey, Sm and {McBride}, Rs and Miller, Tj and Morse, Re and O’Brien, L and Pereira, Jj and Smith, La and Wuenschel, Mj},
	urldate = {2022-02-10},
	date = {2017-07-04},
	langid = {english},
	file = {Perretti et al. - 2017 - Regime shifts in fish recruitment on the Northeast.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\NRAGBLGA\\Perretti et al. - 2017 - Regime shifts in fish recruitment on the Northeast.pdf:application/pdf;Perretti et al. - 2017 - Regime shifts in fish recruitment on the Northeast.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\ZXKKMXZZ\\Perretti et al. - 2017 - Regime shifts in fish recruitment on the Northeast.pdf:application/pdf},
}

@article{johnson_savory_2015,
	title = {The Savory Swimmer Swims North: A Northern Range Extension of the Blue Crab Callinectes Sapidus?},
	volume = {35},
	issn = {0278-0372},
	url = {https://doi.org/10.1163/1937240X-00002293},
	doi = {10.1163/1937240X-00002293},
	shorttitle = {The Savory Swimmer Swims North},
	abstract = {Worldwide, climate-change is shifting species distributions poleward. Here I present recent (2012-2014) observations of the blue crab, Callinectes {sapidusRathbun}, 1896, in the Gulf of Maine ({GoM}), north of its historical range of Cape Cod, Massachusetts. To test the hypothesis of a climate-driven range expansion, I examined near-surface ocean temperatures. On average, ocean temperatures in the {GoM} in summer 2012 and 2013 were up to \$1.3{\textasciicircum}{\textbackslash}circ\{{\textbackslash}rm\{C\}\}\$ higher than the average of the previous decade, suggesting that warmer waters may have promoted the recruitment of C. sapidus to the {GoM}. Previous ephemeral populations of C. sapidus in the Gulf of Maine have been reported since the 1860s. Recent observations and continued warming in the northwest Atlantic may signal a permanent poleward expansion of C. sapidus into the {GoM}. If so, then a key goal for ecologists and managers will be to understand the effect of C. sapidus on {GoM} food-webs and fisheries.},
	pages = {105--110},
	number = {1},
	journaltitle = {Journal of Crustacean Biology},
	shortjournal = {Journal of Crustacean Biology},
	author = {Johnson, David Samuel},
	urldate = {2022-02-10},
	date = {2015-01-01},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XHPF9TU5\\Johnson - 2015 - The Savory Swimmer Swims North A Northern Range E.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\6A9YDFM4\\2547817.html:text/html},
}

@article{deibel_predictability_2009,
	title = {Predictability of patches of neritic salps and doliolids (Tunicata, Thaliacea)},
	volume = {31},
	issn = {0142-7873, 1464-3774},
	url = {https://academic.oup.com/plankt/article-lookup/doi/10.1093/plankt/fbp091},
	doi = {10.1093/plankt/fbp091},
	pages = {1571--1579},
	number = {12},
	journaltitle = {Journal of Plankton Research},
	shortjournal = {Journal of Plankton Research},
	author = {Deibel, D. and Paffenhofer, G.-A.},
	urldate = {2022-02-10},
	date = {2009-12-01},
	langid = {english},
	file = {Deibel and Paffenhofer - 2009 - Predictability of patches of neritic salps and dol.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\5DQSAXWX\\Deibel and Paffenhofer - 2009 - Predictability of patches of neritic salps and dol.pdf:application/pdf},
}

@article{powell_ocean_2020,
	title = {Ocean quahogs (Arctica islandica) and Atlantic surfclams (Spisula solidissima) on the Mid-Atlantic Bight continental shelf and Georges Bank: The death assemblage as a recorder of climate change and the reorganization of the continental shelf benthos},
	volume = {537},
	issn = {0031-0182},
	url = {https://www.sciencedirect.com/science/article/pii/S0031018218309118},
	doi = {10.1016/j.palaeo.2019.05.027},
	shorttitle = {Ocean quahogs (Arctica islandica) and Atlantic surfclams (Spisula solidissima) on the Mid-Atlantic Bight continental shelf and Georges Bank},
	abstract = {The degree to which evidence of range shifts in shelf biomass dominants, Atlantic surfclams and ocean quahogs, as a function of climate change is examined by comparing the dissimilarity in distribution of the living community and the record of habitation ensconced in the death assemblage. Comparison of the distribution of live animals and dead shells reveals for both species that live animals are rarely found where dead shells were not collected, but dead shells were collected at a substantively larger number of sites than where live animals were found. The geographic footprint resolved by the dead shells was much broader than that of live animals. Extensive spatially-coherent regions exist inshore and offshore of the present-day habitat of occupation where evidence of previous occupation exists. Sites where ocean quahog shells were found without live ocean quahogs included a portion of the continental shelf inshore of the present-day habitable range, an area only habitable under colder climatic conditions than observed today. Surfclam shells were found offshore of the present-day habitable region, in deeper water: additional warming of bottom waters offshore would be necessary for surfclams to occupy the region now occupied solely by dead shells. The death assemblage shows that these biomass dominants have repositioned themselves across the continental shelf during the past and this repositioning certainly is driven by changes in bottom water temperature. Moreover, the distribution of surfclam shells indicates that the death assemblage may provide a possible window into the future, as movement of the present-day population is towards these deeper-water previously-occupied regions. Overall, the death assemblage may provide an important source of information on range shifts sparing the need to carry out extensive and frequent benthic surveys and may permit reconstruction of ongoing shifts in community composition as a product of climate change when adequate survey data are not available.},
	pages = {109205},
	journaltitle = {Palaeogeography, Palaeoclimatology, Palaeoecology},
	shortjournal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
	author = {Powell, Eric N. and Ewing, Anja M. and Kuykendall, Kelsey M.},
	urldate = {2022-02-10},
	date = {2020-01-01},
	langid = {english},
	keywords = {Conservation paleobiology, Geographic distribution, Live-dead comparison, Range shift, Spatial time averaging, Species interaction},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\FVKEAPR5\\S0031018218309118.html:text/html},
}

@article{pace_two-hundred_2018,
	title = {Two-hundred year record of increasing growth rates for ocean quahogs (Arctica islandica) from the northwestern Atlantic Ocean},
	volume = {503},
	issn = {0022-0981},
	url = {https://www.sciencedirect.com/science/article/pii/S0022098117303568},
	doi = {10.1016/j.jembe.2018.01.010},
	abstract = {Ocean quahogs [Arctica islandica (Linnaeus, 1769)] are the longest-lived, non-colonial animal known today, with a maximum life span exceeding 500 years. Ocean quahogs are a commercially important bivalve, inhabiting the continental shelf of the North Atlantic basin. We examined growth rates of ocean quahogs that were fully recruited to the commercial fishery ({\textgreater}80-mm shell length) from four sites covering the range of the stock along the east coast of the U.S. through analysis of annual growth lines in the hinge plate. Both geographic and temporal differences (on a scale of decadal or longer) in growth rates exist throughout the range of the stock. The age at which animals reached 60, 80, and 90 mm decreased significantly, and average growth rates to 60, 80, and 90 mm increased significantly with birth year at a New Jersey and a Long Island site, both located in the southwestern portion of the stock, since the late 1700s/early 1800s, likely in response to increasing bottom water temperatures. That is, growth rates vary temporally with birth date at the southwestern sites, with younger animals growing at a much faster rate in recent decades than those born many decades previously, whereas at the northern sites off southern New England and on Georges Bank, changes in growth rates through time are limited to older adult animals or absent altogether. Thus, at the southern portion of the range, variation in growth rate over time exists in all phases of ocean quahog life, whereas on Georges Bank, little evidence exists for any differential in growth rate over the last {\textasciitilde}200 years. The fact that ocean quahogs record the rise in ocean temperatures after the Little Ice Age in the Mid-Atlantic Bight southeast of southern New England, yet demonstrate little evidence of such a rise in the southern New England and Georges Bank region, would suggest a differential response of ocean circulation and its control of bottom water temperature between the northern and southern portions of the Mid-Atlantic Bight over the last 200+ years.},
	pages = {8--22},
	journaltitle = {Journal of Experimental Marine Biology and Ecology},
	shortjournal = {Journal of Experimental Marine Biology and Ecology},
	author = {Pace, Sara M. and Powell, Eric N. and Mann, Roger},
	urldate = {2022-02-10},
	date = {2018-06-01},
	langid = {english},
	keywords = {Climate change, Growth, Little Ice Age, Ocean quahog},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\IKCT8QWJ\\S0022098117303568.html:text/html},
}

@article{worm_predator_2003,
	title = {Predator diversity hotspots in the blue ocean},
	volume = {100},
	rights = {Copyright © 2003, The National Academy of  Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/100/17/9884},
	doi = {10.1073/pnas.1333941100},
	abstract = {Concentrations of biodiversity, or hotspots, represent conservation priorities in terrestrial ecosystems but remain largely unexplored in marine habitats. In the open ocean, many large predators such as tunas, sharks, billfishes, and sea turtles are of current conservation concern because of their vulnerability to overfishing and ecosystem role. Here we use scientific-observer records from pelagic longline fisheries in the Atlantic and Pacific Oceans to show that oceanic predators concentrate in distinct diversity hotspots. Predator diversity consistently peaks at intermediate latitudes (20–30° N and S), where tropical and temperate species ranges overlap. Individual hotspots are found close to prominent habitat features such as reefs, shelf breaks, or seamounts and often coincide with zooplankton and coral reef hotspots. Closed-area models in the northwest Atlantic predict that protection of hotspots outperforms other area closures in safeguarding threatened pelagic predators from ecological extinction. We conclude that the seemingly monotonous landscape of the open ocean shows rich structure in species diversity and that these features should be used to focus future conservation efforts.},
	pages = {9884--9888},
	number = {17},
	journaltitle = {Proceedings of the National Academy of Sciences},
	shortjournal = {{PNAS}},
	author = {Worm, Boris and Lotze, Heike K. and Myers, Ransom A.},
	urldate = {2022-02-10},
	date = {2003-08-19},
	langid = {english},
	pmid = {12907699},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\RYABUMGF\\Worm et al. - 2003 - Predator diversity hotspots in the blue ocean.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\UM6QF23W\\9884.html:text/html},
}

@article{madin_periodic_2006,
	title = {Periodic swarms of the salp Salpa aspera in the Slope Water off the {NE} United States: Biovolume, vertical migration, grazing, and vertical flux},
	volume = {53},
	issn = {0967-0637},
	url = {https://www.sciencedirect.com/science/article/pii/S0967063706000173},
	doi = {10.1016/j.dsr.2005.12.018},
	shorttitle = {Periodic swarms of the salp Salpa aspera in the Slope Water off the {NE} United States},
	abstract = {Sampling during four summers over a twenty-seven year period has documented dense populations of Salpa aspera in the Slope Water south of New England, northeastern United States. The salps demonstrated a strong pattern of diel vertical migration, moving to depth (mostly 600–800m) during the day and aggregating in the epipelagic ({\textless}100m) at night. Filtration rates determined from both gut pigment analysis and direct feeding experiments indicated that both the aggregate and solitary stages filtered water at rates ranging from 0.5 to 6lh-1ml-1 biovolume. Maximum displacement volumes of salps measured were 5.7lm-2 in 1986 and 1.6lm-2 in 1993. Depending on the year, the sampled salp populations were calculated to clear between 8 and 74\% of the upper 50m during each 8h night. Total fecal output for the same populations was estimated to be between 5 and 91mgCm-2night-1. These results, and other observations, suggest this region is a salp “hot spot”, with swarms of S. aspera developing seasonally on a frequent basis.},
	pages = {804--819},
	number = {5},
	journaltitle = {Deep Sea Research Part I: Oceanographic Research Papers},
	shortjournal = {Deep Sea Research Part I: Oceanographic Research Papers},
	author = {Madin, L. P. and Kremer, P. and Wiebe, P. H. and Purcell, J. E. and Horgan, E. H. and Nemazie, D. A.},
	urldate = {2022-02-10},
	date = {2006-05-01},
	langid = {english},
	keywords = {Atlantic Slope Water, Grazing, Salps, Vertical flux, Vertical migration, Zooplankton},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\76VQA2RT\\S0967063706000173.html:text/html},
}

@article{potter_horizontal_2011,
	title = {Horizontal movement of ocean sunfish, Mola mola, in the northwest Atlantic},
	volume = {158},
	issn = {1432-1793},
	url = {https://doi.org/10.1007/s00227-010-1578-2},
	doi = {10.1007/s00227-010-1578-2},
	abstract = {Data were retrieved from 25 ocean sunfish (Mola mola) that were tagged with pop-up satellite archival tags in the southern Gulf of Maine (n = 6), off Nantucket Island (n = 17), and off the coast of Georgia (n = 2) between September 2005 and March 2008. Tags remained attached from 7 to 242 days, with a mean attachment period of (X ± {SD}) 107.2 ± 80.6 days. Ocean sunfish tagged in the Gulf of Maine and southern New England left those areas in the late summer and early autumn and moved south along the continental shelf break. Fish traveled as far south as the Bahamas and the Gulf of Mexico. By moving south, sunfish experienced similar mean sea surface temperatures throughout the tagging period. The maximum straight-line distance traveled by a tagged Mola mola was 2,520 km in 130 days. Two tagged ocean sunfish entered the Gulf of Mexico, one in the December and one in July. Movements were associated with frontal features created by the Gulf Stream and fish moved farther offshore in 2007 when the Gulf Stream was deflected from the shelf break.},
	pages = {531--540},
	number = {3},
	journaltitle = {Marine Biology},
	shortjournal = {Mar Biol},
	author = {Potter, Inga F. and Galuardi, Benjamin and Howell, W. Huntting},
	urldate = {2022-02-10},
	date = {2011-03-01},
	langid = {english},
	file = {Springer Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\YUG6HGHA\\Potter et al. - 2011 - Horizontal movement of ocean sunfish, Mola mola, i.pdf:application/pdf},
}

@article{caesar_current_2021,
	title = {Current Atlantic Meridional Overturning Circulation weakest in last millennium},
	volume = {14},
	rights = {2021 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {1752-0908},
	url = {https://www.nature.com/articles/s41561-021-00699-z},
	doi = {10.1038/s41561-021-00699-z},
	abstract = {The Atlantic Meridional Overturning Circulation ({AMOC})—one of Earth’s major ocean circulation systems—redistributes heat on our planet and has a major impact on climate. Here, we compare a variety of published proxy records to reconstruct the evolution of the {AMOC} since about ad 400. A fairly consistent picture of the {AMOC} emerges: after a long and relatively stable period, there was an initial weakening starting in the nineteenth century, followed by a second, more rapid, decline in the mid-twentieth century, leading to the weakest state of the {AMOC} occurring in recent decades.},
	pages = {118--120},
	number = {3},
	journaltitle = {Nature Geoscience},
	shortjournal = {Nat. Geosci.},
	author = {Caesar, L. and {McCarthy}, G. D. and Thornalley, D. J. R. and Cahill, N. and Rahmstorf, S.},
	urldate = {2022-02-10},
	date = {2021-03},
	langid = {english},
	note = {Number: 3
Publisher: Nature Publishing Group},
	keywords = {Climate change, Physical oceanography, Palaeoclimate},
	file = {Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\DPJZKDCQ\\s41561-021-00699-z.html:text/html;Submitted Version:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\NNTXSEI2\\Caesar et al. - 2021 - Current Atlantic Meridional Overturning Circulatio.pdf:application/pdf},
}

@article{caesar_observed_2018,
	title = {Observed fingerprint of a weakening Atlantic Ocean overturning circulation},
	volume = {556},
	rights = {2018 Macmillan Publishers Ltd., part of Springer Nature},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/s41586-018-0006-5},
	doi = {10.1038/s41586-018-0006-5},
	abstract = {The Atlantic meridional overturning circulation ({AMOC})—a system of ocean currents in the North Atlantic—has a major impact on climate, yet its evolution during the industrial era is poorly known owing to a lack of direct current measurements. Here we provide evidence for a weakening of the {AMOC} by about 3 ± 1 sverdrups (around 15 per cent) since the mid-twentieth century. This weakening is revealed by a characteristic spatial and seasonal sea-surface temperature ‘fingerprint’—consisting of a pattern of cooling in the subpolar Atlantic Ocean and warming in the Gulf Stream region—and is calibrated through an ensemble of model simulations from the {CMIP}5 project. We find this fingerprint both in a high-resolution climate model in response to increasing atmospheric carbon dioxide concentrations, and in the temperature trends observed since the late nineteenth century. The pattern can be explained by a slowdown in the {AMOC} and reduced northward heat transport, as well as an associated northward shift of the Gulf Stream. Comparisons with recent direct measurements from the {RAPID} project and several other studies provide a consistent depiction of record-low {AMOC} values in recent years.},
	pages = {191--196},
	number = {7700},
	journaltitle = {Nature},
	author = {Caesar, L. and Rahmstorf, S. and Robinson, A. and Feulner, G. and Saba, V.},
	urldate = {2022-02-10},
	date = {2018-04},
	langid = {english},
	note = {Number: 7700
Publisher: Nature Publishing Group},
	keywords = {Physical oceanography, Climate and Earth system modelling, Ocean sciences},
	file = {Accepted Version:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\UEBMA38Z\\Caesar et al. - 2018 - Observed fingerprint of a weakening Atlantic Ocean.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\STMDY3GI\\s41586-018-0006-5.html:text/html},
}

@article{miles_offshore_2021,
	title = {Offshore Wind Energy and the Mid-Atlantic Cold Pool: A Review of Potential Interactions},
	volume = {55},
	doi = {10.4031/MTSJ.55.4.8},
	shorttitle = {Offshore Wind Energy and the Mid-Atlantic Cold Pool},
	abstract = {Abstract
The U.S. East Coast has 1.7 million acres of federal bottom under lease for the development of wind energy installations, with plans for more than 1,500 foundations to be placed. The scale of these wind farms has the potential to alter the unique and delicate oceanographic
conditions along the expansive Atlantic continental shelf, a region characterized by a strong seasonal thermocline that overlies cold bottom water, known as the “Cold Pool.” Strong seasonal stratification traps cold (typically less than 10°C) water above the ocean bottom sustaining
a boreal fauna that represents vast fisheries, including the most lucrative shellfish fisheries in the United States. This paper reviews the existing literature and research pertaining to the ways in which offshore wind farms may alter processes that establish, maintain, and degrade stratification
associated with the Cold Pool through vertical mixing in this seasonally dynamic system. Changes in stratification could have important consequences in Cold Pool setup and degradation, processes fundamental to high fishery productivity of the region. The potential for these multiple wind energy
arrays to alter oceanographic processes and the biological systems that rely on them is possible; however, a great deal of uncertainty remains about the nature and scale of these interactions. Research should be prioritized that identifies stratification thresholds of influence, below which
turbines and wind farm arrays may alter oceanographic processes. These should be examined within context of spatial and seasonal dynamics of the Cold Pool and offshore wind lease areas to identify potential areas of further study.},
	pages = {72--87},
	number = {4},
	journaltitle = {Marine Technology Society Journal},
	shortjournal = {Marine Technology Society Journal},
	author = {Miles, Travis and Murphy, Sarah and Kohut, Josh and Borsetti, Sarah and Munroe, Daphne},
	date = {2021-07-01},
	keywords = {Mid-Atlantic Cold Pool, ocean interactions, offshore wind},
}

@article{gawarkiewicz_characteristics_2019,
	title = {Characteristics of an Advective Marine Heatwave in the Middle Atlantic Bight in Early 2017},
	volume = {6},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00712},
	abstract = {There has been wide interest in Marine Heatwaves and their ecological consequences in recent years. Most analyses have focused on remotely sensed sea surface temperature data due to the temporal and spatial coverage it provides in order to establish the presence and duration of Heatwaves. Using hydrographic data from a variety of sources, we show that an advective Marine Heatwave was initiated by an event in late December of 2016 south of New England, with temperature anomalies measuring up to 6°C and salinity anomalies exceeding 1 {PSU}. Similar features were observed off of New Jersey in February 2017, and are associated with the Shelfbreak Front migrating from its normal position to mid-shelf or further onshore. Shelf water of 34 {PSU} was observed just north of Cape Hatteras at the 30 m isobath and across the continental shelf in late April 2017. These observations reveal that the 2017 Marine Heatwave was associated with a strong positive salinity anomaly, that its total duration was approximately 4 months, and its advective path extended roughly 850 km along the length of the continental shelf in the Middle Atlantic Bight. The southward advective velocity implied by the arrival north of Cape Hatteras is consistent with previous estimates of alongshelf velocity for the region. The origin of this Marine Heatwave is likely related to cross-shelf advection driven by the presence of a Warm Core Ring adjacent to the shelfbreak south of New England.},
	journaltitle = {Frontiers in Marine Science},
	author = {Gawarkiewicz, Glen and Chen, Ke and Forsyth, Jacob and Bahr, Frank and Mercer, Anna M. and Ellertson, Aubrey and Fratantoni, Paula and Seim, Harvey and Haines, Sara and Han, Lu},
	urldate = {2022-02-10},
	date = {2019},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\9VF6DG7F\\Gawarkiewicz et al. - 2019 - Characteristics of an Advective Marine Heatwave in.pdf:application/pdf},
}

@article{chen_mesoscale_2022,
	title = {Mesoscale and Submesoscale Shelf-Ocean Exchanges Initialize an Advective Marine Heatwave},
	volume = {127},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021JC017927},
	doi = {https://doi.org/10.1029/2021JC017927},
	abstract = {Abstract Observations and high-resolution numerical modeling are used to investigate the dynamical processes related to the initiation of an advective Marine Heatwave in the Middle Atlantic Bight of the Northwest Atlantic continental shelf. Both the observations and the model identify two significant cross-shelf intrusions in November 2016 and January 2017, with the latter inducing large-magnitude water mass anomalies across the shelf. Model prognostic fields reveal the importance of the combination of cyclonic eddies or ringlets and upwelling-favorable winds in producing the large-distance cross-shelf penetration and temperature/salinity anomalies. The cyclonic eddies in close proximity to the shelfbreak set up local along-isobath pressure gradients and provide favorable conditions for the intensification of the shelfbreak front, both processes driving cross-isobath intrusions of warm, salty offshore water onto the outer continental shelf. Subsequently, strong and persistent upwelling-favorable winds drive a rapid, bottom intensified cross-shelf penetration in January 2017 composed of the anomalous water mass off the shelfbreak. The along-shelf settings including realistic representation of bathymetric features are essential in the characteristics of the cross-shelf penetration. The results highlight the importance of smaller scale cyclonic eddies and the intricacy of the interplay between multiple processes to drive significant cross-shelf events.},
	pages = {e2021JC017927},
	number = {1},
	journaltitle = {Journal of Geophysical Research: Oceans},
	author = {Chen, Ke and Gawarkiewicz, Glen and Yang, Jiayan},
	date = {2022},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021JC017927},
	keywords = {cross-shelf exchange, drivers of Marine heatwave, pressure gradient setup, shelfbreak front and frontogenesis, warm core rings and cyclonic eddies, wind-driven upwelling and bottom intrusion},
}

@article{friedland_middle_2022,
	title = {The Middle Atlantic Bight Cold Pool is warming and shrinking: Indices from in situ autumn seafloor temperatures},
	volume = {31},
	issn = {1365-2419},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12573},
	doi = {10.1111/fog.12573},
	shorttitle = {The Middle Atlantic Bight Cold Pool is warming and shrinking},
	abstract = {The Cold Pool feature of the Middle Atlantic Bight ({MAB}) is a body of cold bottom water that develops in the spring and persists through the summer-autumn months. It is maintained by northerly currents and can be traced back to Arctic water masses. The Cold Pool provides habitat for many boreal species at latitudes far south of their normal range and plays an important role in the population dynamics of lower and upper trophic level organisms. Here, we describe changes in the extent and thermal properties of the Cold Pool using both observations and models. Two indices are developed based on a gridded, interpolated bottom temperature dataset; the first is a mean temperature indicator, and the second is a spatial extent indicator. The temperature indicator showed a significant increasing trend over the study period 1968–2019 and a single change point in 2008. Similarly, the area indicator declined significantly, also displaying a change point in 2008. Cold Pool maximum temperature and minimum size were observed in 2017, which is also known as a heatwave year in the {MAB}. The indices presented here support the view of a rapidly warming Cold Pool that is being limited in its spatial extent. Changes in Cold Pool hydrography will likely affect boreal species distributions and total ecosystem productivity.},
	pages = {217--223},
	number = {2},
	journaltitle = {Fisheries Oceanography},
	author = {Friedland, Kevin D. and Miles, Travis and Goode, Andrew G. and Powell, Eric N. and Brady, Damian C.},
	urldate = {2022-02-10},
	date = {2022},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/fog.12573},
	keywords = {climate change, Cold Pool, ecosystem, regime shift, temperature},
	file = {Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\JG9MK62Q\\fog.html:text/html},
}

@article{gangopadhyay_census_2020,
	title = {A Census of the Warm-Core Rings of the Gulf Stream: 1980–2017},
	volume = {125},
	issn = {2169-9291},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2019JC016033},
	doi = {10.1029/2019JC016033},
	shorttitle = {A Census of the Warm-Core Rings of the Gulf Stream},
	abstract = {A census of Gulf Stream ({GS}) warm-core rings ({WCRs}) is presented based on 38 years (1980–2017) of data. The census documents formation and demise times and locations, and formation size for all 961 {WCRs} formed in the study period that live for a week or more. A clear regime shift was observed around the Year 2000 and was reported by a subset of authors (Gangopadhyay et al., 2019, https://doi.org/10.1038/s41598-019-48661-9). The {WCR} formation over the whole region (75–55°W) increased from an average of 18 per year during Regime 1 (1980–1999) to 33 per year during Regime 2 (2000–2017). For geographic analysis formation locations were grouped in four 5° zones between 75°W and 55°W. Seasonally, {WCR} formations show a significant summer maxima and winter minima, a pattern that is consistent through all zones and both temporal regimes. The lifespan and size distribution show progressively more rings with higher longevity and greater size when formed to the east of 70°W. The average lifespan of the {WCRs} in all four zones decreased by 20–40\% depending on zones and/or seasons from Regime 1 to Regime 2, while the size distribution remained unchanged across regimes. The ring footprint index, a first-order signature of impact of the {WCRs} on the slope, increased significantly (26–90\%) for all zones from Regime 1 to Regime 2, with the highest percent increase in Zone 2 (70–65°W). This observational study establishes critical statistical and dynamical benchmarks for validating numerical models and highlights the need for further dynamical understanding of the {GS}-ring formation processes.},
	pages = {e2019JC016033},
	number = {8},
	journaltitle = {Journal of Geophysical Research: Oceans},
	author = {Gangopadhyay, Avijit and Gawarkiewicz, Glen and Silva, E. Nishchitha S. and Silver, Adrienne M. and Monim, M. and Clark, Jenifer},
	urldate = {2022-02-10},
	date = {2020},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2019JC016033},
	keywords = {Gulf Stream, Lifespan of rings, Regime-Shift, Ring Census, size of rings, Warm Core Rings},
	file = {Accepted Version:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\4GAVAJBF\\Gangopadhyay et al. - 2020 - A Census of the Warm-Core Rings of the Gulf Stream.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\8UCSFM2W\\2019JC016033.html:text/html},
}

@article{silver_forecasting_2021,
	title = {Forecasting the Gulf Stream Path Using Buoyancy and Wind Forcing Over the North Atlantic},
	volume = {126},
	issn = {2169-9291},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2021JC017614},
	doi = {10.1029/2021JC017614},
	abstract = {Fluctuations in the path of the Gulf Stream ({GS}) have been previously studied by primarily connecting to either the wind-driven subtropical gyre circulation or buoyancy forcing via the subpolar gyre. Here we present a statistical model for 1 year predictions of the {GS} path (represented by the {GS} northern wall—{GSNW}) between W and W incorporating both mechanisms in a combined framework. An existing model with multiple parameters including the previous year's {GSNW} index, center location, and amplitude of the Icelandic Low and the Southern Oscillation Index was augmented with basin-wide Ekman drift over the Azores High. The addition of the wind is supported by a validation of the simpler two-layer Parsons-Veronis model of {GS} separation over the last 40 years. A multivariate analysis was carried out to compare 1-year-in-advance forecast correlations from four different models. The optimal predictors of the best performing model include: (a) the {GSNW} index from the previous year, (b) gyre-scale integrated Ekman Drift over the past 2 years, and (c) longitude of the Icelandic Low center lagged by 3 years. The forecast correlation over the 27 years (1994–2020) is 0.65, an improvement from the previous multi-parameter model's forecast correlation of 0.52. The improvement is attributed to the addition of the wind-drift component. The sensitivity of forecasting the {GS} path after extreme atmospheric years is quantified. Results indicate the possibility of better understanding and enhanced predictability of the dominant wind-driven variability of the Atlantic Meridional Overturning Circulation and of fisheries management models that use the {GS} path as a metric.},
	pages = {e2021JC017614},
	number = {8},
	journaltitle = {Journal of Geophysical Research: Oceans},
	author = {Silver, Adrienne and Gangopadhyay, Avijit and Gawarkiewicz, Glen and Taylor, Arnold and Sanchez-Franks, Alejandra},
	urldate = {2022-02-10},
	date = {2021},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2021JC017614},
	keywords = {Gulf Stream, {AMOC}, Azores high, forecasting, Icelandic low, North Atlantic},
	file = {Full Text:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\E6A2PALX\\Silver et al. - 2021 - Forecasting the Gulf Stream Path Using Buoyancy an.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\RTB5CUQN\\2021JC017614.html:text/html},
}

@article{silver_interannual_2021,
	title = {Interannual and seasonal asymmetries in Gulf Stream Ring Formations from 1980 to 2019},
	volume = {11},
	rights = {2021 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-021-81827-y},
	doi = {10.1038/s41598-021-81827-y},
	abstract = {As the Gulf Stream separates from the coast, it sheds both Warm and Cold Core Rings between \$\$75{\textasciicircum}{\textbackslash}circ\$\$and \$\$55{\textasciicircum}{\textbackslash}circ {\textbackslash},{\textbackslash}hbox \{W\}\$\$. We present evidence that this ring formation behavior has been asymmetric over both interannual and seasonal time-scales. After a previously reported regime-shift in 2000, 15 more Warm Core Rings have been forming yearly compared to 1980–1999. In contrast, there have been no changes in the annual formation rate of the Cold Core Rings. This increase in Warm Core Ring production leads to an excess heat transfer of 0.10 {PW} to the Slope Sea, amounting to 7.7–12.4\% of the total Gulf Stream heat transport, or 5.4–7.3\% of the global oceanic heat budget at \$\$30{\textasciicircum}{\textbackslash}circ {\textbackslash},{\textbackslash}hbox \{N\}\$\$. Seasonally, more Cold Core Rings are produced in the winter and spring and more Warm Core Rings are produced in the summer and fall leading to more summertime heat transfer to the north of the Stream. The seasonal cycle of relative ring formation numbers is strongly correlated (r = 0.82) with that of the difference in upper layer temperatures between the Sargasso and Slope seas. This quantification motivates future efforts to understand the recent increasing influence of the Gulf Stream on the circulation and ecosystem in the western North Atlantic.},
	pages = {2207},
	number = {1},
	journaltitle = {Scientific Reports},
	shortjournal = {Sci Rep},
	author = {Silver, Adrienne and Gangopadhyay, Avijit and Gawarkiewicz, Glen and Silva, E. Nishchitha S. and Clark, Jenifer},
	urldate = {2022-02-10},
	date = {2021-01-26},
	langid = {english},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Physical oceanography, Attribution},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\6VUHKBAB\\Silver et al. - 2021 - Interannual and seasonal asymmetries in Gulf Strea.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\QDX62JJL\\s41598-021-81827-y.html:text/html},
}

@article{goncalves_neto_changes_2021,
	title = {Changes in the Gulf Stream preceded rapid warming of the Northwest Atlantic Shelf},
	volume = {2},
	rights = {2021 The Author(s)},
	issn = {2662-4435},
	url = {https://www.nature.com/articles/s43247-021-00143-5},
	doi = {10.1038/s43247-021-00143-5},
	abstract = {The Northwest Atlantic Shelf provides ecological and economic benefits along the heavily populated North American coastline and beyond. In 2009-2010, abrupt warming prompted an ecosystem shift with consequences for fisheries, yet the cause of this event is unclear. Here we use satellite altimetry and in situ measurements to show that, in 2008, the Gulf Stream migrated closer to the Tail of the Grand Banks, a shift that has persisted ever since. This change reduced the westward connectivity of the Labrador Current that otherwise supplies cold, fresh, oxygen-rich waters to the shelf. Within one year after the appearance of anomalously warm and saline water at the Tail of Grand Banks, subsurface warming progressed south-westwards. Historical observations suggest a similar sequence of events may have occurred in the 1970s. Therefore, monitoring water properties at the Tail of Grand Banks may offer predictability for shelf properties and ecosystem perturbations with substantial lead time.},
	pages = {1--10},
	number = {1},
	journaltitle = {Communications Earth \& Environment},
	shortjournal = {Commun Earth Environ},
	author = {Gonçalves Neto, Afonso and Langan, Joseph A. and Palter, Jaime B.},
	urldate = {2022-02-10},
	date = {2021-04-20},
	langid = {english},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Physical oceanography, Climate-change impacts, Environmental impact},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\TREA4KKH\\Gonçalves Neto et al. - 2021 - Changes in the Gulf Stream preceded rapid warming .pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\U6672DEQ\\s43247-021-00143-5.html:text/html},
}

@incollection{thunberg_northeast_2021,
	title = {Northeast Region Fisheries Impacts from {COVID}-19},
	url = {https://spo.nmfs.noaa.gov/sites/default/files/TM221.pdf},
	pages = {53--64},
	booktitle = {U.S. Seafood Industry and For-Hire Sector Impacts from {COVID}-19: 2020 in Perspective.  {NOAA} Tech. Memo. {NMFS}-{SPO}-221},
	author = {Thunberg, E.M.},
	date = {2021},
	langid = {english},
	file = {U.S. Seafood Industry and For-Hire Sector Impacts .pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\BYJBLBUB\\U.S. Seafood Industry and For-Hire Sector Impacts .pdf:application/pdf},
}

@article{chen_seasonal_2021,
	title = {Seasonal Prediction of Bottom Temperature on the Northeast U.S. Continental Shelf},
	volume = {126},
	issn = {2169-9291},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2021JC017187},
	doi = {10.1029/2021JC017187},
	abstract = {The Northeast U.S. shelf ({NES}) is an oceanographically dynamic marine ecosystem and supports some of the most valuable demersal fisheries in the world. A reliable prediction of {NES} environmental variables, particularly ocean bottom temperature, could lead to a significant improvement in demersal fisheries management. However, the current generation of climate model-based seasonal-to-interannual predictions exhibits limited prediction skill in this continental shelf environment. Here, we have developed a hierarchy of statistical seasonal predictions for {NES} bottom temperatures using an eddy-resolving ocean reanalysis data set. A simple, damped local persistence prediction model produces significant skill for lead times up to ∼5 months in the Mid-Atlantic Bight and up to ∼10 months in the Gulf of Maine, although the prediction skill varies notably by season. Considering temperature from a nearby or upstream (i.e., more poleward) region as an additional predictor generally improves prediction skill, presumably as a result of advective processes. Large-scale atmospheric and oceanic indices, such as Gulf Stream path indices ({GSIs}) and the North Atlantic Oscillation Index, are also tested as predictors for {NES} bottom temperatures. Only the {GSI} constructed from temperature observed at 200 m depth significantly improves the prediction skill relative to local persistence. However, the prediction skill from this {GSI} is not larger than that gained using models incorporating nearby or upstream shelf/slope temperatures. Based on these results, a simplified statistical model has been developed, which can be tailored to fisheries management for the {NES}.},
	pages = {e2021JC017187},
	number = {5},
	journaltitle = {Journal of Geophysical Research: Oceans},
	author = {Chen, Zhuomin and Kwon, Young-Oh and Chen, Ke and Fratantoni, Paula and Gawarkiewicz, Glen and Joyce, Terrence M. and Miller, Timothy J. and Nye, Janet A. and Saba, Vincent S. and Stock, Brian C.},
	urldate = {2021-10-27},
	date = {2021},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2021JC017187},
	keywords = {bottom temperature, Northeast U.S. shelf, seasonal prediction},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\CZWV2IDZ\\Chen et al. - 2021 - Seasonal Prediction of Bottom Temperature on the N.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\DRQ2UP9S\\Chen et al. - 2021 - Seasonal Prediction of Bottom Temperature on the N.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\M8PC2CQ2\\2021JC017187.html:text/html},
}

@article{lucey_conducting_2020,
	title = {Conducting reproducible ecosystem modeling using the open source mass balance model Rpath},
	volume = {427},
	issn = {0304-3800},
	url = {https://www.sciencedirect.com/science/article/pii/S0304380020301290},
	doi = {10.1016/j.ecolmodel.2020.109057},
	abstract = {Ecosystem models are important tools for conducting ecosystem-based management. A particularly useful method of characterizing the flow of energy through an ecosystem and the subsequent direct and indirect implications of management actions is mass balance modeling. Here we outline the equations as utilized in Rpath, an R implementation of the mass balance algorithms popularized by Ecopath with Ecosim that are designed to work with fisheries data sources. We believe that common practices in R will aid in the reproducibility of conducting analysis using a mass balance model as all of the code is contained within a single script file. This includes the built-in statistical and graphical functions of R. In addition to added reproducibility, R is a coding language with which ecologists are familiar. This familiarity offers greater flexibility for practitioners to tailor the model to their needs. We have made the code available on an open software development platform which should aid in continuous community development of the tool.},
	pages = {109057},
	journaltitle = {Ecological Modelling},
	shortjournal = {Ecological Modelling},
	author = {Lucey, Sean M. and Gaichas, Sarah K. and Aydin, Kerim Y.},
	urldate = {2021-04-16},
	date = {2020-07-01},
	langid = {english},
	keywords = {Ecopath, Ecosim, Mass balance, R, Reproducibility, Rpath},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\GC7K2S7N\\Lucey et al. - 2020 - Conducting reproducible ecosystem modeling using t.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\X3HXPY7R\\Lucey et al. - 2020 - Conducting reproducible ecosystem modeling using t.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\TH28V9A5\\Lucey et al. - 2020 - Conducting reproducible ecosystem modeling using t.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\UFVKGJYL\\S0304380020301290.html:text/html;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\4H8EQEJR\\S0304380020301290.html:text/html},
}

@article{bastille_improving_2021,
	title = {Improving the {IEA} Approach Using Principles of Open Data Science},
	volume = {49},
	issn = {0892-0753},
	url = {https://doi.org/10.1080/08920753.2021.1846155},
	doi = {10.1080/08920753.2021.1846155},
	abstract = {Integrated ecosystem assessments ({IEAs}) compile and use indicators, risk assessments, and other analyses to address regional policy needs at varying spatial scales. Although approaches to implementing {IEAs} are context-specific, challenges in data acquisition, management, processing, analysis, and communication are universal. By embracing open science, in which scientific data, methods, and products are made publicly accessible, along with the ever-expanding tools facilitating open science, {IEA} practitioners will be better equipped to address these challenges. Here, we provide a snapshot of the state of open science practices in {IEAs} on-going across the United States. We show that open science has improved the flexibility, reproducibility, and efficiency of the scientific workflows within the {IEA} framework. Although the initial time investment necessary for developing open science workflows may appear daunting, we show that the subsequent returns provided by the efficient and transparent development of {IEA} products are worth the effort. By improving the implementation of {IEAs}, open science tools and principals have the potential to further Ecosystem Based Management ({EBM}) worldwide.},
	pages = {72--89},
	number = {1},
	journaltitle = {Coastal Management},
	author = {Bastille, Kimberly and Hardison, Sean and {deWitt}, Lynn and Brown, Jennifer and Samhouri, Jameal and Gaichas, Sarah and Lucey, Sean and Kearney, Kelly and Best, Ben and Cross, Scott and Large, Scott and Spooner, Ellen},
	urldate = {2021-04-16},
	date = {2021-01-02},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/08920753.2021.1846155},
	keywords = {{IEA} framwork, open science, reproducilibity},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\SQ23VV28\\Bastille et al. - 2020 - Improving the IEA Approach Using Principles of Ope.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\2TRPDNGD\\Bastille et al. - 2021 - Improving the IEA Approach Using Principles of Ope.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\HAF7YFL7\\08920753.2021.html:text/html;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\LUTHUBQD\\08920753.2021.html:text/html},
}

@article{muffley_there_2021,
	title = {There Is no I in {EAFM} Adapting Integrated Ecosystem Assessment for Mid-Atlantic Fisheries Management},
	volume = {49},
	issn = {0892-0753},
	url = {https://doi.org/10.1080/08920753.2021.1846156},
	doi = {10.1080/08920753.2021.1846156},
	abstract = {Resource managers worldwide are being asked to consider the ecosystem while making management decisions. Integrated Ecosystem Assessment ({IEA}) provides a flexible framework for addressing ecosystem considerations in decision making. The {US} Mid-Atlantic Fishery Management Council (Council) adapted the {IEA} approach and implemented a structured decision framework to address species, fleet, habitat, and climate interactions as part of their Ecosystem Approach to Fisheries Management ({EAFM}) in 2016. The Council’s {EAFM} decision framework first uses risk assessment to prioritize fishery-ecosystem interactions for consideration. The Council’s 2017 {EAFM} risk assessment identified a range of ecological, social, and management objectives or risk elements. Development of a conceptual model to identify key environmental, ecological, social, economic, and management linkages for a high-priority fishery is the second step in the framework. The Council identified summer flounder (Paralichthys dentatus) as a high-risk fishery and finalized an {EAFM} conceptual model that considers high-risk factors and ecosystem elements in 2019. The Council used the conceptual model to identify three priority summer flounder management questions (recreational data uncertainty, recreational discards, and distribution shifts) to be considered for quantitative management strategy evaluation, the third step in the {EAFM} framework and set to begin in 2020. Finally, as strategies are implemented, outcomes are monitored and the process is adjusted, and/or other priorities identified in the risk assessment can be addressed. The Council’s rapid progress in implementing {EAFM} resulted from an extensive, positive, and collaborative process between managers, stakeholders, and scientists. Collaboration helps build trust and buy-in from all participants and is essential to {IEA} and to the success of {EAFM}.},
	pages = {90--106},
	number = {1},
	journaltitle = {Coastal Management},
	author = {Muffley, Brandon and Gaichas, Sarah and {DePiper}, Geret and Seagraves, Richard and Lucey, Sean},
	urldate = {2021-04-16},
	date = {2021-01-02},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/08920753.2021.1846156},
	keywords = {conceptual modeling, economic indicators, ecosystem approach, ecosystem indicators, fisheries, integrated ecosystem assessment, management objectives, risk assessment},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XLDZAXTT\\Muffley et al. - 2020 - There Is no I in EAFM Adapting Integrated Ecosyste.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\42WLVQP7\\Muffley et al. - 2021 - There Is no I in EAFM Adapting Integrated Ecosyste.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\6W6VBQXV\\Muffley et al. - 2021 - There Is no I in EAFM Adapting Integrated Ecosyste.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XZP62S8C\\08920753.2021.html:text/html;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\G82GWCW3\\08920753.2021.html:text/html;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\JXQAMQBG\\08920753.2021.html:text/html;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\5A25PBJX\\08920753.2021.html:text/html},
}

@article{depiper_operationalizing_2017,
	title = {Operationalizing integrated ecosystem assessments within a multidisciplinary team: lessons learned from a worked example},
	volume = {74},
	rights = {All rights reserved},
	issn = {1054-3139},
	url = {https://academic.oup.com/icesjms/article/74/8/2076/3094701},
	doi = {10.1093/icesjms/fsx038},
	shorttitle = {Operationalizing integrated ecosystem assessments within a multidisciplinary team},
	abstract = {Between 2014 and 2016, an interdisciplinary team of researchers including physical oceanographers, biologists, economists and anthropologists developed a working example of an Integrated Ecosystem Assessment ({IEA}) for three ecologically distinct regions of the Northwest Atlantic; Georges Bank, the Gulf of Maine and the Grand Banks, as part of the International Council for the Exploration of the Sea ({ICES}) Working Group on the Northwest Atlantic Regional Sea ({WGNARS}). In this paper, we review the transdisciplinary and collaborative process by which the {IEA} was developed, with a particular focus on the decision points arising from the {IEA} construct itself. The aim is to identify key issues faced in developing any {IEA}, practical decisions made to address these issues within the working group and lessons learned from the process.},
	pages = {2076--2086},
	number = {8},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} J Mar Sci},
	author = {{DePiper}, Geret S. and Gaichas, Sarah K. and Lucey, Sean M. and Pinto da Silva, Patricia and Anderson, M. Robin and Breeze, Heather and Bundy, Alida and Clay, Patricia M. and Fay, Gavin and Gamble, Robert J. and Gregory, Robert S. and Fratantoni, Paula S. and Johnson, Catherine L. and Koen-Alonso, Mariano and Kleisner, Kristin M. and Olson, Julia and Perretti, Charles T. and Pepin, Pierre and Phelan, Fred and Saba, Vincent S. and Smith, Laurel A. and Tam, Jamie C. and Templeman, Nadine D. and Wildermuth, Robert P.},
	urldate = {2018-03-09},
	date = {2017-10-01},
	langid = {english},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\J8TP6MIQ\\DePiper et al. - 2017 - Operationalizing integrated ecosystem assessments .pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XQHQHIGZ\\3094701.html:text/html},
}

@article{gaichas_implementing_2018,
	title = {Implementing Ecosystem Approaches to Fishery Management: Risk Assessment in the {US} Mid-Atlantic},
	volume = {5},
	rights = {All rights reserved},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2018.00442/abstract},
	doi = {10.3389/fmars.2018.00442},
	shorttitle = {Implementing Ecosystem Approaches to Fishery Management},
	abstract = {Fishery managers worldwide are evaluating methods for incorporating climate, habitat, ecological, social, and economic factors into current operations in order to implement Ecosystem Approaches to Fishery Management ({EAFM}). While this can seem overwhelming, it is possible to take practical steps towards {EAFM} implementation that make use of existing information and provide managers with valuable strategic advice. Here, we describe the process used by the U.S. Mid-Atlantic Fishery Management Council (Council) to develop an ecosystem-level risk assessment, the initial step proposed in their recently adopted {EAFM} guidance document. The Council first defined five types of Risk Elements (ecological, economic, social, food production, management) and identified which management objectives aligned with each element. Based on an existing ecosystem status report for the region and other existing sources (including expert opinion), potential ecological, social, economic, and management indicators were identified for each risk element. Finally, low, low-moderate, moderate-high, and high risk criteria were defined for each indicator, and the indicator data were used to score each risk element using the criteria. The ultimate outcome is a ranked risk assessment in order to focus on the highest risk issues for further evaluation and mitigation. The risk assessment highlights certain species and certain management issues as posing higher cumulative risks to meeting Council management objectives when considering a broad range of ecological, social, and economic factors. Tabular color coded summaries of risk assessment results will be used by the Council to prioritize further {EAFM} analyses as well as research plans over the coming five years. As ecosystem reporting and operational {EAFM} continue to evolve in future years, the Council foresees integrating these efforts so that ecosystem indicators are refined to meet the needs of fishery managers in identifying and managing risks to achieving ecological, social, and economic fishery objectives. Overall, ecosystem indicator-based risk assessment is a method that can be adapted to a wide range of resource management systems and available information, and therefore represent a promising way forward in the implementation of {EAFM}.},
	journaltitle = {Frontiers in Marine Science},
	shortjournal = {Front. Mar. Sci.},
	author = {Gaichas, Sarah Kathleen and {DePiper}, Geret Sean and Seagraves, Richard John and Muffley, Brandon W. and Sabo, Mary and Colburn, Lisa L. and Loftus, Andrew L.},
	urldate = {2018-11-20},
	date = {2018},
	keywords = {Economic indicators, Ecosystem Approach, Ecosystem indicators, Fisheries, Integrated Ecosystem Assessment, Management objectives, natural resource management, Risk Assessment},
}

@article{lentz_seasonal_2017,
	title = {Seasonal warming of the Middle Atlantic Bight Cold Pool},
	volume = {122},
	rights = {© 2017. American Geophysical Union. All Rights Reserved.},
	issn = {2169-9291},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016JC012201},
	doi = {10.1002/2016JC012201},
	abstract = {The Cold Pool is a 20–60 m thick band of cold, near-bottom water that persists from spring to fall over the midshelf and outer shelf of the Middle Atlantic Bight ({MAB}) and Southern Flank of Georges Bank. The Cold Pool is remnant winter water bounded above by the seasonal thermocline and offshore by warmer slope water. Historical temperature profiles are used to characterize the average annual evolution and spatial structure of the Cold Pool. The Cold Pool gradually warms from spring to summer at a rate of order 1°C month−1. The warming rate is faster in shallower water where the Cold Pool is thinner, consistent with a vertical turbulent heat flux from the thermocline to the Cold Pool. The Cold Pool warming rate also varies along the shelf; it is larger over Georges Bank and smaller in the southern {MAB}. The mean turbulent diffusivities at the top of the Cold Pool, estimated from the spring to summer mean heat balance, are an order of magnitude larger over Georges Bank than in the southern {MAB}, consistent with much stronger tidal mixing over Georges Bank than in the southern {MAB}. The stronger tidal mixing causes the Cold Pool to warm more rapidly over Georges Bank and the eastern New England shelf than in the New York Bight or southern {MAB}. Consequently, the coldest Cold Pool water is located in the New York Bight from late spring to summer.},
	pages = {941--954},
	number = {2},
	journaltitle = {Journal of Geophysical Research: Oceans},
	author = {Lentz, S. J.},
	urldate = {2020-05-18},
	date = {2017},
	langid = {english},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2016JC012201},
	keywords = {Cold Pool, continental shelf circulation, Middle Atlantic Bight, seasonal cycle},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\MWQDFXEZ\\Lentz - 2017 - Seasonal warming of the Middle Atlantic Bight Cold.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\A3J8YNHQ\\Lentz - 2017 - Seasonal warming of the Middle Atlantic Bight Cold.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\DUQUAJFH\\2016JC012201.html:text/html;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\KFR9M4QU\\2016JC012201.html:text/html;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\CE787RMC\\2016JC012201.html:text/html},
}

@article{lucey_evaluating_2021,
	title = {Evaluating fishery management strategies using an ecosystem model as an operating model},
	volume = {234},
	rights = {All rights reserved},
	issn = {0165-7836},
	url = {http://www.sciencedirect.com/science/article/pii/S0165783620302976},
	doi = {10.1016/j.fishres.2020.105780},
	abstract = {Management Strategy Evaluation ({MSE}) is an effective tool to gauge the relative performance of fishery management options. For the most part, {MSEs} have been applied to single-species management procedures. However, to be more inclusive of all the biological and technical interactions occurring within a system, ecosystem-based strategies are emerging. In order to test the feasibility of these strategies, a full ecosystem model should be used as an operating model. Mass balance food web models include many features that managers are interested in and therefore can be useful as an operating model. Until recently, full feedback interactions between a management strategy and a mass balance operating model were impractical. However, with the development of Rpath, users now have the ability to fully customize their mass balance models. We developed new functionality for the Rpath modelling framework that allows it to be used as a flexible operating model. Using an example Georges Bank model, we demonstrate how Rpath can now pause the simulation, evaluate an external model, and use the results to modify the parameters of the operating model. This new flexibility will allow users to test a variety of management strategies or couple to other models making Rpath a valuable tool for conducting {MSEs}.},
	pages = {105780},
	journaltitle = {Fisheries Research},
	shortjournal = {Fisheries Research},
	author = {Lucey, Sean M. and Aydin, Kerim Y. and Gaichas, Sarah K. and Cadrin, Steven X. and Fay, Gavin and Fogarty, Michael J. and Punt, André},
	urldate = {2020-12-09},
	date = {2021-02-01},
	langid = {english},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\AVNLHXS4\\Lucey et al. - 2021 - Evaluating fishery management strategies using an .pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\WHZPQ5QN\\Lucey et al. - 2021 - Evaluating fishery management strategies using an .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\NC5YVEXC\\S0165783620302976.html:text/html;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\H45YFIUT\\S0165783620302976.html:text/html},
}

@article{pace_cryptic_2021,
	title = {Cryptic mortality of North Atlantic right whales},
	volume = {n/a},
	rights = {© 2021 The Authors. Conservation Science and Practice published by Wiley Periodicals {LLC}. on behalf of Society for Conservation Biology},
	issn = {2578-4854},
	url = {https://conbio.onlinelibrary.wiley.com/doi/abs/10.1111/csp2.346},
	doi = {https://doi.org/10.1111/csp2.346},
	abstract = {Evaluations of the conservation status of the endangered North Atlantic right whale as well as many other wildlife species often rely extensively on counts and cause-of-death determinations of carcasses found accidentally or during dedicated surveys. Even when survey effort dedicated to a population is extensive, many deaths may go unseen. We used an abundance estimation model to derive estimates of cryptic mortality for North Atlantic right whales and found that observed carcasses accounted for only 36\% of all estimated death during 1990–2017. We found strong evidence that total mortality varied over time, and that observed carcass counts were poor predictors of estimated annual numbers of whales dying. Importantly, there were substantial differences between fractions of deaths determined to be entanglement related during necropsy (49\%) and the fraction of cryptic deaths suffering serious injuries related to entanglement (87\%). Although we concluded that a single year's observations produced poor estimates of carcass detection rates due to the volatility of ratios of small counts, ratio estimates of data pooled over periods of consistent survey may offer better information on detection rates. Additionally, it appears unwise to consider cause of death determinations from detected carcasses as representative of cause-specific mortality rates in right whales given the large number of seriously injured whales from entanglement that are likely part of the unseen mortality.},
	pages = {e346},
	issue = {n/a},
	journaltitle = {Conservation Science and Practice},
	author = {Pace, Richard M. and Williams, Rob and Kraus, Scott D. and Knowlton, Amy R. and Pettis, Heather M.},
	urldate = {2021-02-11},
	date = {2021},
	langid = {english},
	note = {\_eprint: https://conbio.onlinelibrary.wiley.com/doi/pdf/10.1111/csp2.346},
	keywords = {carcass detection, cryptic mortality, detection bias, right whale, total mortality},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\RY2UKF8B\\Pace et al. - Cryptic mortality of North Atlantic right whales.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\4ZMDM74U\\csp2.html:text/html},
}

@article{wrightfairbanks_autonomous_2020,
	title = {Autonomous Observation of Seasonal Carbonate Chemistry Dynamics in the Mid-Atlantic Bight},
	volume = {125},
	rights = {©2020. The Authors.},
	issn = {2169-9291},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JC016505},
	doi = {https://doi.org/10.1029/2020JC016505},
	abstract = {Ocean acidification alters the oceanic carbonate system, increasing potential for ecological, economic, and cultural losses. Historically, productive coastal oceans lack vertically resolved high-resolution carbonate system measurements on time scales relevant to organism ecology and life history. The recent development of a deep ion-sensitive field-effect transistor ({ISFET})-based {pH} sensor system integrated into a Slocum glider has provided a platform for achieving high-resolution carbonate system profiles. From May 2018 to November 2019, seasonal deployments of the {pH} glider were conducted in the central Mid-Atlantic Bight. Simultaneous measurements from the glider's {pH} and salinity sensors enabled the derivation of total alkalinity and calculation of other carbonate system parameters including aragonite saturation state. Carbonate system parameters were then mapped against other variables, such as temperature, dissolved oxygen, and chlorophyll, over space and time. The seasonal dynamics of carbonate chemistry presented here provide a baseline to begin identifying drivers of acidification in this vital economic zone.},
	pages = {e2020JC016505},
	number = {11},
	journaltitle = {Journal of Geophysical Research: Oceans},
	author = {Wright‐Fairbanks, Elizabeth K. and Miles, Travis N. and Cai, Wei-Jun and Chen, Baoshan and Saba, Grace K.},
	urldate = {2021-02-26},
	date = {2020},
	langid = {english},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020JC016505},
	keywords = {ocean acidification, autonomous underwater vehicle, carbonate system, glider, Mid-Atlantic Bight},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\UKLG3CRR\\Wright‐Fairbanks et al. - 2020 - Autonomous Observation of Seasonal Carbonate Chemi.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\V2JQ8US9\\2020JC016505.html:text/html},
}

@article{link_global_2019,
	title = {Global ecosystem overfishing: Clear delineation within real limits to production},
	volume = {5},
	rights = {Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution {NonCommercial} License 4.0 ({CC} {BY}-{NC}).. This is an open-access article distributed under the terms of the Creative Commons Attribution-{NonCommercial} license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.},
	issn = {2375-2548},
	url = {https://advances.sciencemag.org/content/5/6/eaav0474},
	doi = {10.1126/sciadv.aav0474},
	shorttitle = {Global ecosystem overfishing},
	abstract = {The well-documented value of marine fisheries is threatened by overfishing. Management typically focuses on target populations but lacks effective tools to document or restrain overexploitation of marine ecosystems. Here, we present three indices and accompanying thresholds to detect and delineate ecosystem overfishing ({EOF}): the Fogarty, Friedland, and Ryther indices. These are based on widely available and readily interpreted catch and satellite data that link fisheries landings to primary production using known limits of trophic transfer efficiency. We propose theoretically and empirically based thresholds for each of those indices; with these criteria, several ecosystems are fished sustainably, but nearly 40 to 50\% of tropical and temperate ecosystems exceed even extreme thresholds. Applying these criteria to global fisheries data results in strong evidence for two specific instances of {EOF}, increases in both pressure on tropical fish and a climate-mediated polar shift. Here, we show that these two patterns represent evidence for global {EOF}.
Newly derived thresholds show that about half the world’s marine ecosystems are experiencing “ecosystem” overfishing.
Newly derived thresholds show that about half the world’s marine ecosystems are experiencing “ecosystem” overfishing.},
	pages = {eaav0474},
	number = {6},
	journaltitle = {Science Advances},
	author = {Link, Jason S. and Watson, Reg A.},
	urldate = {2021-01-29},
	date = {2019-06-01},
	langid = {english},
	note = {Publisher: American Association for the Advancement of Science
Section: Research Article},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\YG42T8TT\\Link and Watson - 2019 - Global ecosystem overfishing Clear delineation wi.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\VFFABX4W\\eaav0474.html:text/html},
}

@article{le_cren_length-weight_1951,
	title = {The Length-Weight Relationship and Seasonal Cycle in Gonad Weight and Condition in the Perch (Perca fluviatilis)},
	volume = {20},
	issn = {0021-8790},
	url = {https://www.jstor.org/stable/1540},
	doi = {10.2307/1540},
	abstract = {1. The methods of analysing length-weight data from fish are reviewed. Emphasis is laid on empirical formulae of the type W = {aLn}, and the limitations of the conventional condition factor. 2. The length-weight relationship of perch of all sizes was determined from a series of regressions of log weight on log length, and an analysis of covariance. Relative condition factors were calculated for individual fish from smoothed mean weights obtained from the regression lines. 3. In length-weight relationship it was found that the perch could be divided into a series of six groups corresponding with age, sex and maturity. Each group was generally homogeneous within itself throughout the seasons, but usually differed significantly from the other groups. Relative condition was found to vary significantly with the season. 4. At any one season the gonad weight is a constant percentage of the body weight for fish of all sizes. The seasonal changes in gonad weight are described and differ somewhat for the two sexes. Stomach contents weigh up to 2\% of the body weight in summer. 5. There is a regular seasonal cycle in condition which is at its maximum in September and minimum in early spring. The different seasonal changes in condition between mature and immature fish can largely be accounted for by the cycle in gonad weight of the former.},
	pages = {201--219},
	number = {2},
	journaltitle = {Journal of Animal Ecology},
	author = {Le Cren, E. D.},
	urldate = {2021-02-26},
	date = {1951},
	note = {Publisher: [Wiley, British Ecological Society]},
	file = {Submitted Version:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\ZMLBKARD\\Le Cren - 1951 - The Length-Weight Relationship and Seasonal Cycle .pdf:application/pdf},
}

@book{boem_bureau_2021,
	title = {Bureau of Ocean Energy Management ({BOEM}). South Fork Wind Farm and South Fork Export Cable Project Draft Environmental Impact Statement. {OCS} {EIS}/{EA} {BOEM} 2020-057.},
	url = {https://www.boem.gov/sites/default/files/documents/renewable-energy/SFWF-DEIS_0.pdf},
	author = {{BOEM}},
	date = {2021},
}

@article{bauer_temperature-_2010,
	title = {Temperature-, Salinity-, and Size-Dependent Winter Mortality of Juvenile Blue Crabs ( Callinectes sapidus )},
	volume = {33},
	issn = {1559-2723},
	url = {https://www.jstor.org/stable/40663676},
	abstract = {At midlatitudes within its range, overwintering mortality may play an important role in regulating blue crab (Callinectes sapidus) populations. We conducted a 121-day experiment to estimate winter mortality that used realistic temperature acclimation periods prior to and light levels during experiments. A 2×2×2 factorial experimental design was used to test for the effects of temperature (3°C, 5°C), salinity (10, 25), and sediment (sediment, no sediment) on the survival of juvenile crabs (14-68-mm carapace width) of both hatchery and wild origin. The presence of sediment did not significantly alter crab survival, while hatchery-raised crabs experienced significantly lower survivorship than wild-caught crabs. An accelerated failure time model fit to the survival data indicated that time to death increased significantly with increasing temperature, salinity, and crab size. These results suggest that winter survival varies with winter severity, is spatially dynamic, and that small juveniles are more at risk of dying over the winter than larger juveniles.},
	pages = {668--677},
	number = {3},
	journaltitle = {Estuaries and Coasts},
	author = {Bauer, Laurie J. and Miller, Thomas J.},
	urldate = {2021-02-26},
	date = {2010},
	note = {Publisher: Coastal and Estuarine Research Federation},
}

@inproceedings{hines_predicting_2011,
	title = {Predicting Effects of Climate Change on Blue Crabs in Chesapeake Bay},
	isbn = {978-1-56612-154-5},
	url = {http://www.alaskaseagrant.org/bookstore/pubs/AK-SG-10-01.html},
	doi = {10.4027/bmecpcc.2010.22},
	eventtitle = {Biology and Management of Exploited Crab Populations under Climate Change},
	pages = {109--127},
	booktitle = {Biology and Management of Exploited Crab Populations under Climate Change},
	publisher = {Alaska Sea Grant, University of Alaska Fairbanks},
	author = {Hines, A.H. and Johnson, E.G. and Darnell, M.Z. and Rittschof, D. and Miller, T.J. and Bauer, L.J. and Rodgers, P. and Aguilar, R.},
	urldate = {2021-02-26},
	date = {2011-04-27},
	langid = {english},
	file = {Hines et al. - 2011 - Predicting Effects of Climate Change on Blue Crabs.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\2ANKMV3U\\Hines et al. - 2011 - Predicting Effects of Climate Change on Blue Crabs.pdf:application/pdf},
}

@article{kimmel_relationship_2014,
	title = {The Relationship between Interannual Climate Variability and Juvenile Eastern Oyster Abundance at a Regional Scale in Chesapeake Bay},
	volume = {34},
	issn = {0275-5947},
	url = {https://doi.org/10.1080/02755947.2013.830999},
	doi = {10.1080/02755947.2013.830999},
	abstract = {The eastern oyster, Crassostrea virginica, is an important ecological and commercial species along the Eastern Seaboard of North America, although its abundance in Chesapeake Bay (Maryland and Virginia) has declined precipitously since the mid-1800s. Management activities, including efforts to enhance larval settlement, to rebuild the Chesapeake Bay eastern oyster population have met with limited success. Since 1939, juvenile oyster abundance has been measured at oyster bars in the northern portion of Chesapeake Bay. Prior analyses of those data indicate that juvenile oyster abundance is influenced by environmental conditions, which are related to regional climate. We quantified a regional scale (1,000 km2) climate signal using a synoptic climatology approach by identifying predominant weather patterns. We related these weather patterns to Susquehanna River freshwater discharge, a major influencing factor on Chesapeake Bay salinity, and the Palmer Hydrological Drought Index ({PHDI}), an indicator of the overall wetness or dryness of a given region. We developed path analysis models that linked weather patterns to Susquehanna River discharge and thence to either the {PHDI} or ambient salinity and water temperature and finally to juvenile oyster abundance in one of four preidentified spatial groupings. The path models indicated that weather patterns that produce wet conditions, leading to a higher {PHDI} and lower salinity, resulted in reduced juvenile oyster abundance; weather patterns that produce dry conditions that decreased the {PHDI} and increased salinity resulted in higher juvenile oyster abundance. Our results indicate that regions of higher juvenile oyster abundance may be predicted several months in advance using the path model. These predictions can be used to increase the effectiveness of oyster restoration efforts by indicating where hard substrate added to oyster bars in the four regions is likely to result in greater than average numbers of juvenile oysters.Received January 16, 2013; accepted July 24, 2013Published online December 3, 2013},
	pages = {1--15},
	number = {1},
	journaltitle = {North American Journal of Fisheries Management},
	author = {Kimmel, David G. and Tarnowski, Mitchell and Newell, Roger I. E.},
	urldate = {2021-02-26},
	date = {2014-01-02},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/02755947.2013.830999},
	file = {Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\ZJFCEYCC\\02755947.2013.html:text/html},
}

@article{martino_recruitment_2010,
	title = {Recruitment of striped bass in Chesapeake Bay:: spatial and temporal environmental variability and availability of zooplankton prey},
	volume = {409},
	issn = {0171-8630},
	url = {https://www.jstor.org/stable/24873989},
	shorttitle = {Recruitment of striped bass in Chesapeake Bay},
	abstract = {{ABSTRACT}: Causes of recruitment variability in young-of-the-year ({YOY}) striped bass Morone saxatilis from Chesapeake Bay were investigated based on (1) surveys from 2001 to 2003 to document spatio-temporal variability in abundance of larval striped bass, zooplankton prey, and feeding success of larvae; (2) a synthetic analysis (1996, 1998, 1999, 2001 to 2003) to describe how environmental factors and prey affect recruitment success; and (3) a 10 yr analysis (1993 to 2002) of inter-annual differences in spatial and temporal patterns of copepods and cladocera eaten by striped bass larvae. Striped bass {YOY} recruitment levels varied {\textgreater}11-fold in the 6 years examined. In those years, mean daily freshwater flows from the Susquehanna River to the bay in March and April varied {\textgreater}2-fold and controlled distribution and apparent survival of striped bass larvae. Strong recruitments of {YOY} striped bass were associated with matches in space and time of larval striped bass and high concentrations of zooplankton prey, especially the copepod Eurytemora affinis and cladoceran Bosmina longirostris. The strongest year classes (1996, 2003) were produced in years of high freshwater flow, characterized by a high abundance of feeding-stage larvae and a spatio-temporal match between peak abundance of larvae and zooplankton prey. Enhanced feeding opportunities were most pronounced in high freshwater-flow years (1996, 1998, 2003), when larvae and zooplankton prey were strongly associated with, and apparently retained near, the estuarine turbidity maximum. First-feeding larvae fed more successfully in a high-flow year (2003; prey incidence 91\%) than in a drier year (2001; prey incidence 35\%). A regression model that may have forecasting potential was developed to describe recruitment of {YOY} striped bass for the years from 1985 to 2006. The model includes spring freshwater flow and air temperatures to predict age-0 striped bass recruitment strength (R² = 0.65). Flow and temperature control environmental and hydrographic conditions that strongly influence spatio-temporal overlap of larval striped bass and zooplankton. The model provided accurate recruitment forecasts for 2007 and 2009, but was less successful in 2008, a year of exceptionally low recruitment.},
	pages = {213--228},
	journaltitle = {Marine Ecology Progress Series},
	author = {Martino, E. J. and Houde, E. D.},
	urldate = {2021-02-26},
	date = {2010},
	note = {Publisher: Inter-Research Science Center},
}

@article{moore_impacts_2014,
	title = {Impacts of Varying Estuarine Temperature and Light Conditions on Zostera marina (Eelgrass) and its Interactions With Ruppia maritima (Widgeongrass)},
	volume = {37},
	issn = {1559-2723},
	url = {https://www.jstor.org/stable/44851580},
	abstract = {Seagrass populations have been declining globally, with changes attributed to anthropogenic stresses and, more recently, negative effects of global climate change. We examined the distribution of Zostera marina (eelgrass) dominated beds in the York River, Chesapeake Bay, {VA} over an 8-year time period. Using a temperature-dependent light model, declines in upriver areas were associated with higher light attenuation, resulting in lower light availability relative to compensating light requirements of Z. marina compared with downriver areas. An inverse relationship was observed between {SAV} growth and temperature with a change between net bed cover increases and decreases for the period of 2004-2011 observed at approximately 23 °C. Z. marina-dominated beds in the lower river have been recovering from a die-off event in 2005 and experienced another near complete decline in 2010, losing an average of 97 \% of coverage of Z. marina from June to October. These 2010 declines were attributed to an early summer heat event in which daily mean water temperatures increased from 25 to 30 °C over a 2-week time period, considerably higher than previous years when complete die-offs were not observed. Z. marina recovery from this event was minimal, while Ruppia maritima (widgeongrass) expanded its abundance. Water temperatures are projected to continue to increase in the Chesapeake Bay and elsewhere. These results suggest that short-term exposures to rapidly increasing temperatures by 4—5 °C above normal during summer months can result in widespread diebacks that may lead to Z. marina extirpation from historically vegetated areas, with the potential replacement by other species.},
	pages = {S20--S30},
	journaltitle = {Estuaries and Coasts},
	author = {Moore, Kenneth A. and Shields, Erin C. and Parrish, David B.},
	urldate = {2021-02-26},
	date = {2014},
	note = {Publisher: [Coastal and Estuarine Research Federation, Springer]},
}

@article{north_linking_2003,
	title = {Linking {ETM} physics, zooplankton prey, and fish early-life histories to striped bass Morone saxatilis and white perch M. americana recruitment},
	volume = {260},
	issn = {0171-8630, 1616-1599},
	url = {http://www.int-res.com/abstracts/meps/v260/p219-236/},
	doi = {10.3354/meps260219},
	abstract = {Transport to and retention of early-life history stages within the estuarine turbidity maximum ({ETM}) region may be an important component of recruitment success of the anadromous striped bass Morone saxatilis and the white perch M. americana. This hypothesis was evaluated with spatially resolved surveys of the physical and biological characteristics of the upper Chesapeake Bay estuary during 5 cruises, 3 in May 1998 and 2 in May 1999. Gradients in depth-specific patterns of larval abundance and zooplankton prey were evaluated with respect to salinity, temperature and total suspended solids ({TSS}). Although physical conditions in the upper estuary differed between cruises and years, the spatial patterns in distribution of larvae and potential prey were consistent and tracked changes in salt front and {ETM} locations. A statistical analysis suggested that location relative to the {ETM} explained a significant amount of variability in concentrations of eggs, yolk-sac larvae, and larval prey, and that prey concentrations accounted for a significant amount of variability in concentrations of feeding larvae. Transport to the {ETM} region probably occurs during the egg (striped bass) and yolk-sac larva (white perch) stages and results in retention of early-stage feeding larvae in a zone of high prey concentrations. Physical conditions in the {ETM} region differed markedly between a low freshwater-flow year (1999) and a high flow year (1998), and abundances of striped bass and white perch post-yolk-sac larvae were significantly lower in 1999. Recruitment variability was poorly correlated with spawning stock biomass, but spawner-recruitment models that incorporated spring freshwater discharge explained an additional 41\% (striped bass) and 30\% (white perch) of the variability in recruitment. Annual changes in freshwater flow could control larval survival and recruitment by modifying the physical and biological characteristics of the {ETM} region.},
	pages = {219--236},
	journaltitle = {Marine Ecology Progress Series},
	shortjournal = {Mar. Ecol. Prog. Ser.},
	author = {North, Ew and Houde, Ed},
	urldate = {2021-02-26},
	date = {2003},
	langid = {english},
	file = {North and Houde - 2003 - Linking ETM physics, zooplankton prey, and fish ea.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\SKWLG5HP\\North and Houde - 2003 - Linking ETM physics, zooplankton prey, and fish ea.pdf:application/pdf},
}

@article{millette_water_2020,
	title = {Water temperature during winter may control striped bass recruitment during spring by affecting the development time of copepod nauplii},
	volume = {77},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsz203},
	doi = {10.1093/icesjms/fsz203},
	abstract = {Striped bass (Morone saxatilis) are anadromous fish that support an important fishery along the east coast of North America. In Chesapeake Bay, strong juvenile recruitment of striped bass can occur when larvae overlap with high concentrations of their zooplankton prey, but the mechanisms fostering the temporal overlap are unknown. Here, the influence of winter temperature on the peak abundances of a key prey, Eurytemora carolleeae, was estimated with a temperature-dependent developmental model. The role of these peaks in regulating striped bass recruitment was explored in three nursery areas: upper Chesapeake Bay, Choptank River, and Patuxent River. Model results indicated that cold winters delay the timing and increase the size of peak E. carolleeae spring abundance. When the model output was used in regression relationships with striped bass juvenile recruitment and freshwater discharge, the regression models explained up to 78\% of annual recruitment variability. Results suggests that cold, wet winters could increase the chance of a match between striped bass larvae and high concentrations of their prey. This mechanistic link between winter temperatures and striped bass production, acting through prey dynamics, could further understanding of fish recruitment variability and indicates that warmer winters could negatively affect some striped bass populations.},
	pages = {300--314},
	number = {1},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} Journal of Marine Science},
	author = {Millette, N C and Pierson, J J and North, E W},
	urldate = {2021-02-26},
	date = {2020-01-01},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\G2LJDACB\\Millette et al. - 2020 - Water temperature during winter may control stripe.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\RB7SALYL\\5638886.html:text/html},
}

@article{rome_linking_2005,
	title = {Linking temperature and salinity tolerance to winter mortality of Chesapeake Bay blue crabs (Callinectes sapidus)},
	volume = {319},
	issn = {0022-0981},
	url = {https://www.sciencedirect.com/science/article/pii/S0022098105000249},
	doi = {10.1016/j.jembe.2004.06.014},
	series = {Proceedings of the 2003 Blue Crab Symposium},
	abstract = {Blue crabs (Callinectes sapidus) form one of the most important and largest commercial fisheries in Chesapeake Bay. Blue crabs have evolutionary origins in the tropics, although they currently inhabit temperature estuaries that exhibit major fluctuations in diurnal, monthly, and seasonal environmental conditions. Therefore, harsh winter conditions in Chesapeake Bay are a potentially important source of blue crab stock loss. However, this variable has been largely unexamined. To assess the effects of variation in winter environmental conditions on blue crab survival, we measured winter morality of crabs in the field and conducted laboratory experiments to test the interactive effects of low temperature, salinity, and blue crab life stage. Field studies indicated that blue crabs suffered relatively low winter morality rates (≤3\%) during five out of eight winters, when bottom water temperature in February was at or above the 8-year average (3.4 °C). However, in years when bottom water temperature fell below the February average, annual mortality rates rose to 6.0–14.5\%. Mortality rates were highest in the coldest regions of Chesapeake Bay, and larger crabs and female crabs were most vulnerable to these stressful conditions. Similarly, in the laboratory, mortality was highest in the lowest temperature (1 °C) and salinity (8 ppt) treatments. Mature females were more sensitive to winter conditions than juvenile crabs. Of the juvenile life stages, recruits ({\textless}15 mm carapace width) were least tolerant to winter conditions. These results indicate that temperature, salinity, and blue crab life stage are important variables in predicting survivorship over winter months. Because winter mortality may be a significant source of stock loss for blue crabs, especially during severe winters and in low salinity areas of Chesapeake Bay, these predictions can be used to improve management estimates of stock size prior to each summer fishing season.},
	pages = {129--145},
	number = {1},
	journaltitle = {Journal of Experimental Marine Biology and Ecology},
	shortjournal = {Journal of Experimental Marine Biology and Ecology},
	author = {Rome, M. S. and Young-Williams, A. C. and Davis, G. R. and Hines, A. H.},
	urldate = {2021-02-26},
	date = {2005-06-01},
	langid = {english},
	keywords = {Blue crab, Salinity tolerance, Temperature tolerance, Winter mortality},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\C5XNRUSR\\S0022098105000249.html:text/html},
}

@article{rybicki_light_2002,
	title = {Light and Temperature Effects on the Growth of Wild Celery and Hydrilla},
	abstract = {Wild celery (Vallisneria americana L.) has coexisted with the dominant species hydrilla (Hydrilla verticillata (L.f.) Royle) since the resurgence of submersed aquatic vegetation in the tidal Potomac River in 1983. In 1989, particularly turbid, cool, and cloudy spring conditions were associated with a substantial decrease in hydrilla coverage. We measured growth and elongation potential of wild celery and hydrilla propagules under various temperature and irradiance conditions to compare these two species and in part explain the stable persistence of wild celery and the variability in hydrilla coverage. A plant growth experiment was conducted to simulate actual temperatures in the Potomac River during spring of 1986 (plant coverage increased) and 1989 (plant coverage decreased). In the 1989 temperature treatment, final heights of hydrilla and wild celery were unaffected by a 6-C decrease in temperature 2 weeks following tuber germination. Heights of wild celery, however, were more than twice that of hydrilla, and elongation rates of wild celery were greater than those of hydrilla when temperatures reached 17 to 22C. Laboratory studies conducted in complete darkness showed that wild celery tubers germinate at 13C, whereas hydrilla tubers germinate at 15C, and that wild celery elongated to heights twice those of hydrilla. Heights were positively correlated to tuber length. If irradiance is diminished at incipience, differences in tuber reserves and elongation potential may be sufficient to ensure that wild celery can survive when hydrilla is not successful.},
	pages = {8},
	journaltitle = {J. Aquat. Plant Manage.},
	author = {Rybicki, Nancy B and Carter, Virginia},
	date = {2002},
	langid = {english},
	file = {Rybicki and Carter - Light and Temperature Effects on the Growth of Wil.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\GANUDBQD\\Rybicki and Carter - Light and Temperature Effects on the Growth of Wil.pdf:application/pdf},
}

@article{wood_rates_2020,
	title = {Rates of increase in gray seal (Halichoerus grypus atlantica) pupping at recolonized sites in the United States, 1988–2019},
	volume = {101},
	issn = {0022-2372, 1545-1542},
	url = {https://academic.oup.com/jmammal/article/101/1/121/5675096},
	doi = {10.1093/jmammal/gyz184},
	abstract = {Abstract
            Gray seals were historically distributed along the northeastern coast of the United States, but bounties and lack of protection reduced numbers and they were rarely observed for most of the 20th century. Once protections were enacted, the population started to rebound. Here, we describe the recolonization and recovery of gray seals in the United States, focusing on the re-establishment of pupping sites. We fit individual generalized linear models to various time series (1988–2019) to estimate rates of increase in observed pup counts at four of the more data-rich sites. Annual rate of increase at individual sites ranged from −0.2\% (95\% {CI}: −2.3–1.9\%) to 26.3\% (95\% {CI}: 21.6–31.4\%). The increase in sites and number of pups born in the United States is driven by population growth and immigration from Canadian colonies and is part of a larger recovery of the Northwest Atlantic population. Wildlife protection, a healthy source population, habitat availability, and species traits that allow for dispersal and high productivity were all important factors in this recovery.},
	pages = {121--128},
	number = {1},
	journaltitle = {Journal of Mammalogy},
	author = {Wood, Stephanie A and Murray, Kimberly T and Josephson, Elizabeth and Gilbert, James},
	editor = {Swanson, Bradley},
	urldate = {2021-03-01},
	date = {2020-02-21},
	langid = {english},
	file = {Wood et al. - 2020 - Rates of increase in gray seal (Halichoerus grypus.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\L2KSKFJ9\\Wood et al. - 2020 - Rates of increase in gray seal (Halichoerus grypus.pdf:application/pdf},
}

@article{pousse_energetic_2020,
	title = {Energetic response of Atlantic surfclam Spisula solidissima to ocean acidification},
	volume = {161},
	issn = {0025-326X},
	url = {https://www.sciencedirect.com/science/article/pii/S0025326X20308584},
	doi = {10.1016/j.marpolbul.2020.111740},
	abstract = {In this study, we assessed the Atlantic surfclam (Spisula solidissima) energy budget under different ocean acidification conditions ({OA}). During 12 weeks, 126 individuals were maintained at three different ρ{CO}2 concentrations. Every two weeks, individuals were sampled for physiological measurements and scope for growth ({SFG}). In the high ρ{CO}2 treatment, clearance rate decreased and excretion rate increased relative to the low ρ{CO}2 treatment, resulting in reduced {SFG}. Moreover, oxygen:nitrogen (O:N) excretion ratio dropped, suggesting that a switch in metabolic strategy occurred. The medium ρ{CO}2 treatment had no significant effects upon {SFG}; however, metabolic loss increased, suggesting a rise in energy expenditure. In addition, a significant increase in food selection efficiency was observed in the medium treatment, which could be a compensatory reaction to the metabolic over-costs. Results showed that surfclams are particularly sensitive to {OA}; however, the different compensatory mechanisms observed indicate that they are capable of some temporary resilience.},
	pages = {111740},
	journaltitle = {Marine Pollution Bulletin},
	shortjournal = {Marine Pollution Bulletin},
	author = {Pousse, Emilien and Poach, Matthew E. and Redman, Dylan H. and Sennefelder, George and White, Lauren E. and Lindsay, Jessica M. and Munroe, Daphne and Hart, Deborah and Hennen, Daniel and Dixon, Mark S. and Li, Yaqin and Wikfors, Gary H. and Meseck, Shannon L.},
	urldate = {2021-03-01},
	date = {2020-12-01},
	langid = {english},
	keywords = {Ocean acidification, Atlantic surfclams, Bioenergetics, Bivalves, Scope for growth},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\IEWPC7FQ\\S0025326X20308584.html:text/html},
}

@article{sorochan_north_2019,
	title = {North Atlantic right whale (Eubalaena glacialis) and its food: ({II}) interannual variations in biomass of Calanus spp. on western North Atlantic shelves},
	volume = {41},
	issn = {0142-7873},
	url = {https://doi.org/10.1093/plankt/fbz044},
	doi = {10.1093/plankt/fbz044},
	shorttitle = {North Atlantic right whale (Eubalaena glacialis) and its food},
	abstract = {The North Atlantic right whale ({NARW}), Eubalaena glacialis, feeds on zooplankton, particularly copepods of the genus Calanus. We quantified interannual variation in anomalies of abundance and biomass of Calanus spp. and near-surface and near-bottom ocean temperature and salinity from 19 subregions spanning the Gulf of Maine–Georges Bank ({GoM}–{GBK}), Scotian Shelf ({SS}), Gulf of St. Lawrence ({GSL}) and Newfoundland and Labrador Shelves. We analyzed time series from 1977 to 2016 in {GoM}–{GBK}, 1982 to 2016 in southwest {GSL} and 1999 to 2016 in remaining areas. Calanus finmarchicus dominated abundance and biomass, except in the {GSL} where Calanus hyperboreus was abundant. The biomass of Calanus spp. declined in many subregions over years 1999–2016 and was negatively correlated with sea surface temperature in {GoM}–{GBK} and on the {SS}. We detected ``regime shifts” to lower biomass of Calanus spp. in the {GoM}–{GBK} in 2010 and on the {SS} in 2011. In the {GoM}–{GBK}, shifts to lower biomass of C. finmarchicus coincided with shifts to warmer ocean temperature and with published reports of changes in spatial distribution and reduced calving rate of {NARW}. We hypothesize that warming has negatively impacted population levels of Calanus spp. near their southern range limit, reducing the availability of prey to {NARW}.},
	pages = {687--708},
	number = {5},
	journaltitle = {Journal of Plankton Research},
	shortjournal = {Journal of Plankton Research},
	author = {Sorochan, Kevin A and Plourde, {StÉphane} and Morse, Ryan and Pepin, Pierre and Runge, Jeffrey and Thompson, Cameron and Johnson, Catherine L},
	urldate = {2021-03-01},
	date = {2019-09-27},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\MMBNNE9F\\Sorochan et al. - 2019 - North Atlantic right whale (Eubalaena glacialis) a.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\C3TQ2WUJ\\5583901.html:text/html},
}

@article{record_rapid_2019,
	title = {Rapid Climate-Driven Circulation Changes Threaten Conservation of Endangered North Atlantic Right Whales},
	volume = {32},
	issn = {10428275},
	url = {https://tos.org/oceanography/article/rapid-climate-driven-circulation-changes-threaten-conservation-of-endangere},
	doi = {10.5670/oceanog.2019.201},
	abstract = {As climate trends accelerate, ecosystems will be pushed rapidly into new states, reducing the potential efficacy of conservation strategies based on historical patterns. In the Gulf of Maine, climate-driven changes have restructured the ecosystem rapidly over the past decade. Changes in the Atlantic meridional overturning circulation have altered deepwater dynamics, driving warming rates twice as high as the fastest surface rates. This has had implications for the copepod Calanus finmarchicus, a critical food supply for the endangered North Atlantic right whale (Eubalaena glacialis). The oceanographic changes have driven a deviation in the seasonal foraging patterns of E. glacialis upon which conservation strategies depend, making the whales more vulnerable to ship strikes and gear entanglements. The effects of rapid climate-driven changes on a species at risk undermine current management approaches.},
	number = {2},
	journaltitle = {Oceanography},
	shortjournal = {Oceanog},
	author = {Record, Nicholas and Runge, Jeffrey and Pendleton, Daniel and Balch, William and Davies, Kimberley and Pershing, Andrew and Johnson, Catherine and Stamieszkin, Karen and Ji, Rubao and Feng, Zhixuan and Kraus, Scott and Kenney, Robert and Hudak, Christy and Mayo, Charles and Chen, Changsheng and Salisbury, Joseph and Thompson, Cameron},
	urldate = {2021-03-01},
	date = {2019-06-01},
	langid = {english},
	file = {Bigelow Laboratory for Ocean Sciences et al. - 2019 - Rapid Climate-Driven Circulation Changes Threaten .pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XZ9NLG7Z\\Bigelow Laboratory for Ocean Sciences et al. - 2019 - Rapid Climate-Driven Circulation Changes Threaten .pdf:application/pdf;JSTOR Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\EJGWY8WD\\Record et al. - 2019 - Rapid Climate-Driven Circulation Changes Threaten .pdf:application/pdf},
}

@book{hayes_north_2018,
	title = {North Atlantic Right Whales-Evaluating Their Recovery Challenges in 2018. {NOAA} Tech Memo {NMFS} {NEFSC} 247.},
	author = {Hayes, Sean and Gardner, S and Garrison, Lance P. and Henry, A and Leandro, L},
	date = {2018},
}

@article{thomsen_moderate_2010,
	title = {Moderate seawater acidification does not elicit long-term metabolic depression in the blue mussel Mytilus edulis},
	volume = {157},
	issn = {1432-1793},
	url = {https://doi.org/10.1007/s00227-010-1527-0},
	doi = {10.1007/s00227-010-1527-0},
	abstract = {Marine organisms are exposed to increasingly acidic oceans, as a result of equilibration of surface ocean water with rising atmospheric {CO}2 concentrations. In this study, we examined the physiological response of Mytilus edulis from the Baltic Sea, grown for 2 months at 4 seawater {pCO}2 levels (39, 113, 243 and 405 Pa/385, 1,120, 2,400 and 4,000 μatm). Shell and somatic growth, calcification, oxygen consumption and \$\$ \{{\textbackslash}text\{{NH}\}\}\_\{4\}{\textasciicircum}\{ + \} \$\$excretion rates were measured in order to test the hypothesis whether exposure to elevated seawater {pCO}2 is causally related to metabolic depression. During the experimental period, mussel shell mass and shell-free dry mass ({SFDM}) increased at least by a factor of two and three, respectively. However, shell length and shell mass growth decreased linearly with increasing {pCO}2 by 6–20 and 10–34\%, while {SFDM} growth was not significantly affected by hypercapnia. We observed a parabolic change in routine metabolic rates with increasing {pCO}2 and the highest rates (+60\%) at 243 Pa. \$\$ \{{\textbackslash}text\{{NH}\}\}\_\{4\}{\textasciicircum}\{ + \} \$\$excretion rose linearly with increasing {pCO}2. Decreased O:N ratios at the highest seawater {pCO}2 indicate enhanced protein metabolism which may contribute to intracellular {pH} regulation. We suggest that reduced shell growth under severe acidification is not caused by (global) metabolic depression but is potentially due to synergistic effects of increased cellular energy demand and nitrogen loss.},
	pages = {2667--2676},
	number = {12},
	journaltitle = {Marine Biology},
	shortjournal = {Mar Biol},
	author = {Thomsen, Jörn and Melzner, Frank},
	urldate = {2021-03-01},
	date = {2010-12-01},
	langid = {english},
}

@book{johnson_vulnerability_nodate,
	title = {A Vulnerability Assessment of Habitats to Climate Change in the Northeast U.S.},
	author = {Johnson, M and Farr, E and Nelson, M and et al.},
}

@article{lannig_impact_2010,
	title = {Impact of Ocean Acidification on Energy Metabolism of Oyster, Crassostrea gigas—Changes in Metabolic Pathways and Thermal Response},
	volume = {8},
	rights = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1660-3397/8/8/2318},
	doi = {10.3390/md8082318},
	abstract = {Climate change with increasing temperature and ocean acidification ({OA}) poses risks for marine ecosystems. According to Pörtner and Farrell [1], synergistic effects of elevated temperature and {CO}2-induced {OA} on energy metabolism will narrow the thermal tolerance window of marine ectothermal animals. To test this hypothesis, we investigated the effect of an acute temperature rise on energy metabolism of the oyster, Crassostrea gigas chronically exposed to elevated {CO}2 levels (partial pressure of {CO}2 in the seawater {\textasciitilde}0.15 {kPa}, seawater {pH} {\textasciitilde} 7.7). Within one month of incubation at elevated {PCO}2 and 15 °C hemolymph {pH} fell ({pHe} = 7.1 ± 0.2 ({CO}2-group) vs. 7.6 ± 0.1 (control)) and {PeCO}2 values in hemolymph increased (0.5 ± 0.2 {kPa} ({CO}2-group) vs. 0.2 ± 0.04 {kPa} (control)). Slightly but significantly elevated bicarbonate concentrations in the hemolymph of {CO}2-incubated oysters ([{HCO}-3]e = 1.8 ± 0.3 {mM} ({CO}2-group) vs. 1.3 ± 0.1 {mM} (control)) indicate only minimal regulation of extracellular acid-base status. At the acclimation temperature of 15 °C the {OA}-induced decrease in {pHe} did not lead to metabolic depression in oysters as standard metabolism rates ({SMR}) of {CO}2-exposed oysters were similar to controls. Upon acute warming {SMR} rose in both groups, but displayed a stronger increase in the {CO}2-incubated group. Investigation in isolated gill cells revealed a similar temperature-dependence of respiration between groups. Furthermore, the fraction of cellular energy demand for ion regulation via Na+/K+-{ATPase} was not affected by chronic hypercapnia or temperature. Metabolic profiling using 1H-{NMR} spectroscopy revealed substantial changes in some tissues following {OA} exposure at 15 °C. In mantle tissue alanine and {ATP} levels decreased significantly whereas an increase in succinate levels was observed in gill tissue. These findings suggest shifts in metabolic pathways following {OA}-exposure. Our study confirms that {OA} affects energy metabolism in oysters and suggests that climate change may affect populations of sessile coastal invertebrates such as mollusks.},
	pages = {2318--2339},
	number = {8},
	journaltitle = {Marine Drugs},
	author = {Lannig, Gisela and Eilers, Silke and Pörtner, Hans O. and Sokolova, Inna M. and Bock, Christian},
	urldate = {2021-03-01},
	date = {2010-08},
	langid = {english},
	note = {Number: 8
Publisher: Molecular Diversity Preservation International},
	keywords = {$^{\textrm{1}}$H-{NMR} spectroscopy, acid-base status, acute warming, long-term hypercapnia, metabolic profiling, Na$^{\textrm{+}}$/K$^{\textrm{+}}$-{ATPase}},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\TZ6C8NJD\\Lannig et al. - 2010 - Impact of Ocean Acidification on Energy Metabolism.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\MHF9CVXI\\htm.html:text/html},
}

@article{kritzer_importance_2016,
	title = {The Importance of Benthic Habitats for Coastal Fisheries},
	volume = {66},
	issn = {0006-3568},
	url = {https://doi.org/10.1093/biosci/biw014},
	doi = {10.1093/biosci/biw014},
	abstract = {Ecosystem-based management requires greater attention to habitat conservation. We evaluate the importance of benthic habitats as space for shelter, feeding, and breeding by coastal fishes and motile invertebrates in four biogeographic regions of the eastern United States. The importance of different habitats changed with latitude. Soft sediments and riverine systems scored higher in northern regions, and marshes and coral reefs scored higher in the south. The importance of soft sediments is notable because environmental assessments often assume their ecological value is lower. Submerged aquatic vegetation was a key nursery habitat coast-wide. An important consideration is that anthropogenic impacts have altered habitat availability and use, and climate change is causing ongoing disturbance. Furthermore, distinct habitats should not be managed in isolation but rather as interconnected mosaics. Our approach, combined with information on status, vulnerability, and other ecological functions, can be used to evaluate trade-offs and develop habitat-management strategies.},
	pages = {274--284},
	number = {4},
	journaltitle = {{BioScience}},
	shortjournal = {{BioScience}},
	author = {Kritzer, Jacob P. and {DeLucia}, Mari-Beth and Greene, Emily and Shumway, Caroly and Topolski, Marek F. and Thomas-Blate, Jessie and Chiarella, Louis A. and Davy, Kay B. and Smith, Kent},
	urldate = {2021-03-01},
	date = {2016-04-01},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\DTYZTVY8\\Kritzer et al. - 2016 - The Importance of Benthic Habitats for Coastal Fis.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\W5FNNCQT\\2464081.html:text/html},
}

@book{drohan_essential_2007,
	title = {Essential fish habitat source document. Black sea bass, Centropristis striata, life history and habitat characteristics. {NOAA} Technical Memorandum {NMFS}-{NE}-200},
	url = {https://repository.library.noaa.gov/view/noaa/4038},
	author = {Drohan, Amy F and Manderson, John P and Packer, David B},
	urldate = {2021-03-02},
	date = {2007},
	file = {Essential fish habitat source document. Black sea bass, Centropristis striata, life history and habitat characteristics:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\K5FTJ597\\4038.html:text/html},
}

@article{samhouri_defining_2017,
	title = {Defining ecosystem thresholds for human activities and environmental pressures in the California Current},
	volume = {8},
	issn = {2150-8925},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.1860},
	doi = {10.1002/ecs2.1860},
	abstract = {The oceans are changing more rapidly than ever before. Unprecedented climatic variability is interacting with unmistakable long-term trends, all against a backdrop of intensifying human activities. What remains unclear, however, is how to evaluate whether conditions have changed sufficiently to provoke major responses of species, habitats, and communities. We developed a framework based on multimodel inference to define ecosystem-based thresholds for human and environmental pressures in the California Current marine ecosystem. To demonstrate how to apply the framework, we explored two decades of data using gradient forest and generalized additive model analyses, screening for nonlinearities and potential threshold responses of ecosystem states (n = 9) across environmental (n = 6) and human (n = 10) pressures. These analyses identified the existence of threshold responses of five ecosystem states to four environmental and two human pressures. Both methods agreed on threshold relationships in two cases: (1) the winter copepod anomaly and habitat modification, and (2) sea lion pup production and the summer mode of the Pacific Decadal Oscillation ({PDO}). Considered collectively, however, these alternative analytical approaches imply that as many as five of the nine ecosystem states may exhibit threshold changes in response to negative {PDO} values in the summer (copepods, scavengers, groundfish, and marine mammals). This result is consistent with the idea that the influence of the {PDO} extends across multiple trophic levels, but extends current knowledge by defining the nonlinear nature of these responses. This research provides a new way to interpret changes in the intensities of human and environmental pressures as they relate to the ecological integrity of the California Current ecosystem. These insights can be used to make more informed assessments of when and under what conditions intervention, preparation, and mitigation may enhance progress toward ecosystem-based management goals.},
	pages = {e01860},
	number = {6},
	journaltitle = {Ecosphere},
	author = {Samhouri, Jameal F. and Andrews, Kelly S. and Fay, Gavin and Harvey, Chris J. and Hazen, Elliott L. and Hennessey, Shannon M. and Holsman, Kirstin and Hunsicker, Mary E. and Large, Scott I. and Marshall, Kristin N. and Stier, Adrian C. and Tam, Jamie C. and Zador, Stephani G.},
	urldate = {2018-12-10},
	date = {2017-06-01},
	langid = {english},
	keywords = {ecosystem-based management, reference points, ecosystem indicator, ecosystem threshold, nonlinear},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\83CJQHRK\\Samhouri et al. - 2017 - Defining ecosystem thresholds for human activities.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\PBVDAQ3P\\ecs2.html:text/html},
}

@article{goddard_extreme_2015,
	title = {An extreme event of sea-level rise along the Northeast coast of North America in 2009–2010},
	volume = {6},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms7346},
	doi = {10.1038/ncomms7346},
	number = {1},
	journaltitle = {Nature Communications},
	author = {Goddard, Paul B. and Yin, Jianjun and Griffies, Stephen M. and Zhang, Shaoqing},
	urldate = {2019-02-14},
	date = {2015-12},
	langid = {english},
	file = {Goddard et al. - 2015 - An extreme event of sea-level rise along the North.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\G73TKV2E\\Goddard et al. - 2015 - An extreme event of sea-level rise along the North.pdf:application/pdf},
}

@article{zhang_role_2007,
	title = {The Role of Bottom Vortex Stretching on the Path of the North Atlantic Western Boundary Current and on the Northern Recirculation Gyre},
	volume = {37},
	issn = {0022-3670},
	url = {https://journals.ametsoc.org/doi/10.1175/JPO3102.1},
	doi = {10.1175/JPO3102.1},
	abstract = {The mechanisms affecting the path of the depth-integrated North Atlantic western boundary current and the formation of the northern recirculation gyre are investigated using a hierarchy of models, namely, a robust diagnostic model, a prognostic model using a global 1° ocean general circulation model coupled to a two-dimensional atmospheric energy balance model with a hydrological cycle, a simple numerical barotropic model, and an analytic model. The results herein suggest that the path of this boundary current and the formation of the northern recirculation gyre are sensitive to both the magnitude of lateral viscosity and the strength of the deep western boundary current ({DWBC}). In particular, it is shown that bottom vortex stretching induced by a downslope {DWBC} near the south of the Grand Banks leads to the formation of a cyclonic northern recirculation gyre and keeps the path of the depth-integrated western boundary current downstream of Cape Hatteras separated from the North American coast. Both south of the Grand Banks and at the crossover region of the {DWBC} and Gulf Stream, the downslope {DWBC} induces strong bottom downwelling over the steep continental slope, and the magnitude of the bottom downwelling is locally stronger than surface Ekman pumping velocity, providing strong positive vorticity through bottom vortex-stretching effects. The bottom vortex-stretching effect is also present in an extensive area in the North Atlantic, and the contribution to the North Atlantic subpolar and subtropical gyres is on the same order as the local surface wind stress curl. Analytic solutions show that the bottom vortex stretching is important near the western boundary only when the continental slope is wider than the Munk frictional layer scale.},
	pages = {2053--2080},
	number = {8},
	journaltitle = {Journal of Physical Oceanography},
	shortjournal = {J. Phys. Oceanogr.},
	author = {Zhang, Rong and Vallis, Geoffrey K.},
	urldate = {2019-02-14},
	date = {2007-08-01},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\F4H2XV23\\Zhang and Vallis - 2007 - The Role of Bottom Vortex Stretching on the Path o.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\LY6VRJAF\\JPO3102.html:text/html},
}

@article{greene_remote_2013,
	title = {Remote climate forcing of decadal-scale regime shifts in Northwest Atlantic shelf ecosystems},
	volume = {58},
	issn = {1939-5590},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2013.58.3.0803},
	doi = {10.4319/lo.2013.58.3.0803},
	abstract = {Decadal-scale regime shifts in Northwest Atlantic shelf ecosystems can be remotely forced by climate-associated atmosphere-ocean interactions in the North Atlantic and Arctic Ocean Basins. This remote climate forcing is mediated primarily by basin- and hemispheric-scale changes in ocean circulation. We review and synthesize results from process-oriented field studies and retrospective analyses of time-series data to document the linkages between climate, ocean circulation, and ecosystem dynamics. Bottom-up forcing associated with climate plays a prominent role in the dynamics of these ecosystems, comparable in importance to that of top-down forcing associated with commercial fishing. A broad perspective, one encompassing the effects of basin- and hemispheric-scale climate processes on marine ecosystems, will be critical to the sustainable management of marine living resources in the Northwest Atlantic.},
	pages = {803--816},
	number = {3},
	journaltitle = {Limnology and Oceanography},
	author = {Greene, Charles H. and Meyer-Gutbrod, Erin and Monger, Bruce C. and {McGarry}, Louise P. and Pershing, Andrew J. and Belkin, Igor M. and Fratantoni, Paula S. and Mountain, David G. and Pickart, Robert S. and Proshutinsky, Andrey and Ji, Rubao and Bisagni, James J. and Hakkinen, Sirpa M. A. and Haidvogel, Dale B. and Wang, Jia and Head, Erica and Smith, Peter and Reid, Philip C. and Conversi, Alessandra},
	urldate = {2019-02-14},
	date = {2013},
	langid = {english},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\V9LSLIS2\\Greene et al. - 2013 - Remote climate forcing of decadal-scale regime shi.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\3UFWZQV3\\lo.2013.58.3.html:text/html},
}

@article{bi_decadal_2014,
	title = {Decadal Changes in Zooplankton of the Northeast U.S. Continental Shelf},
	volume = {9},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087720},
	doi = {10.1371/journal.pone.0087720},
	abstract = {The abundance of the subarctic copepod, Calanus finmarchicus, and temperate, shelf copepod, Centropages typicus, was estimated from samples collected bi-monthly over the Northeast U.S. continental shelf ({NEUS}) from 1977–2010. Latitudinal variation in long term trends and seasonal patterns for the two copepod species were examined for four sub-regions: the Gulf of Maine ({GOM}), Georges Bank ({GB}), Southern New England ({SNE}), and Mid-Atlantic Bight ({MAB}). Results suggested that there was significant difference in long term variation between northern region ({GOM} and {GB}), and the {MAB} for both species. C. finmarchicus generally peaked in May – June throughout the entire study region and Cen. typicus had a more complex seasonal pattern. Time series analysis revealed that the peak time for Cen. typicus switched from November – December to January - March after 1985 in the {MAB}. The long term abundance of C. finmarchicus showed more fluctuation in the {MAB} than the {GOM} and {GB}, whereas the long term abundance of Cen. typicus was more variable in the {GB} than other sub-regions. Alongshore transport was significantly correlated with the abundance of C. finmarchicus, i.e., more water from north, higher abundance for C. finmarchicus. The abundance of Cen. typicus showed positive relationship with the Gulf Stream north wall index ({GSNWI}) in the {GOM} and {GB}, but the {GSNWI} only explained 12–15\% of variation in Cen. typicus abundance. In general, the alongshore current was negatively correlated with the {GSNWI}, suggesting that Cen. typicus is more abundant when advection from the north is less. However, the relationship between Cen. typicus and alongshore transport was not significant. The present study highlights the importance of spatial scales in the study of marine populations: observed long term changes in the northern region were different from the south for both species.},
	pages = {e87720},
	number = {1},
	journaltitle = {{PLOS} {ONE}},
	shortjournal = {{PLOS} {ONE}},
	author = {Bi, Hongsheng and Ji, Rubao and Liu, Hui and Jo, Young-Heon and Hare, Jonathan A.},
	urldate = {2019-02-14},
	date = {2014-01-31},
	langid = {english},
	keywords = {Zooplankton, Copepods, Ecosystems, Maine, Sea water, Seasonal variations, Seasons, Time series analysis},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\JKT8A44M\\Bi et al. - 2014 - Decadal Changes in Zooplankton of the Northeast U..pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\SY2YSGT4\\article.html:text/html},
}

@article{pace_statespace_2017,
	title = {State–space mark–recapture estimates reveal a recent decline in abundance of North Atlantic right whales},
	volume = {7},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.3406},
	doi = {10.1002/ece3.3406},
	abstract = {North Atlantic right whales (Eubalaena glacialis Müller 1776) present an interesting problem for abundance and trend estimation in marine wildlife conservation. They are long lived, individually identifiable, highly mobile, and one of the rarest of cetaceans. Individuals are annually resighted at different rates, primarily due to varying stay durations among several principal habitats within a large geographic range. To date, characterizations of abundance have been produced that use simple accounting procedures with differing assumptions about mortality. To better characterize changing abundance of North Atlantic right whales between 1990 and 2015, we adapted a state–space formulation with Jolly-Seber assumptions about population entry (birth and immigration) to individual resighting histories and fit it using empirical Bayes methodology. This hierarchical model included accommodation for the effect of the substantial individual capture heterogeneity. Estimates from this approach were only slightly higher than published accounting procedures, except for the most recent years (when recapture rates had declined substantially). North Atlantic right whales' abundance increased at about 2.8\% per annum from median point estimates of 270 individuals in 1990 to 483 in 2010, and then declined to 2015, when the final estimate was 458 individuals (95\% credible intervals 444–471). The probability that the population's trajectory post-2010 was a decline was estimated at 99.99\%. Of special concern was the finding that reduced survival rates of adult females relative to adult males have produced diverging abundance trends between sexes. Despite constraints in recent years, both biological (whales' distribution changing) and logistical (fewer resources available to collect individual photo-identifications), it is still possible to detect this relatively recent, small change in the population's trajectory. This is thanks to the massive dataset of individual North Atlantic right whale identifications accrued over the past three decades. Photo-identification data provide biological information that allows more informed inference on the status of this species.},
	pages = {8730--8741},
	number = {21},
	journaltitle = {Ecology and Evolution},
	author = {Pace, Richard M. and Corkeron, Peter J. and Kraus, Scott D.},
	urldate = {2019-02-14},
	date = {2017},
	langid = {english},
	keywords = {Bayesian mark–recapture, Eubalaena glacialis, open population abundance, recovery, survival},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\2C2WU392\\Pace et al. - 2017 - State–space mark–recapture estimates reveal a rece.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\X3AR35R8\\ece3.html:text/html},
}

@article{zhang_chesapeake_2018,
	title = {Chesapeake Bay's water quality condition has been recovering: Insights from a multimetric indicator assessment of thirty years of tidal monitoring data},
	volume = {637-638},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969718316577},
	doi = {10.1016/j.scitotenv.2018.05.025},
	shorttitle = {Chesapeake Bay's water quality condition has been recovering},
	abstract = {To protect the aquatic living resources of Chesapeake Bay, the Chesapeake Bay Program partnership has developed guidance for state water quality standards, which include ambient water quality criteria to protect designated uses ({DUs}), and associated assessment procedures for dissolved oxygen ({DO}), water clarity/underwater bay grasses, and chlorophyll-a. For measuring progress toward meeting the respective states' water quality standards, a multimetric attainment indicator approach was developed to estimate combined standards attainment. We applied this approach to three decades of monitoring data of {DO}, water clarity/underwater bay grasses, and chlorophyll-a data on annually updated moving 3-year periods to track the progress in all 92 management segments of tidal waters in Chesapeake Bay. In 2014–2016, 40\% of tidal water segment-{DU}-criterion combinations in the Bay (n = 291) are estimated to meet thresholds for attainment of their water quality criteria. This index score marks the best 3-year status in the entire record. Since 1985–1987, the indicator has followed a nonlinear trajectory, consistent with impacts from extreme weather events and subsequent recoveries. Over the period of record (1985–2016), the indicator exhibited a positive and statistically significant trend (p {\textless} 0.05), indicating that the Bay has been recovering since 1985. Patterns of attainment of individual {DUs} are variable, but improvements in open water {DO}, deep channel {DO}, and water clarity/submerged aquatic vegetation have combined to drive the improvement in the Baywide indicator in 2014–2016 relative to its long-term median. Finally, the improvement in estimated Baywide attainment was statistically linked to the decline of total nitrogen, indicating responsiveness of attainment status to the reduction of nutrient load through various management actions since at least the 1980s.},
	pages = {1617--1625},
	journaltitle = {Science of The Total Environment},
	shortjournal = {Science of The Total Environment},
	author = {Zhang, Qian and Murphy, Rebecca R. and Tian, Richard and Forsyth, Melinda K. and Trentacoste, Emily M. and Keisman, Jennifer and Tango, Peter J.},
	urldate = {2019-02-14},
	date = {2018-10-01},
	keywords = {Chesapeake Bay, Chlorophyll-a, Dissolved oxygen, Monitoring and assessment, Trends, Water quality standards},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\Z6LATKQH\\S0048969718316577.html:text/html},
}

@article{morse_distinct_2017,
	title = {Distinct zooplankton regime shift patterns across ecoregions of the U.S. Northeast continental shelf Large Marine Ecosystem},
	volume = {165},
	issn = {09247963},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0924796316303098},
	doi = {10.1016/j.jmarsys.2016.09.011},
	abstract = {We investigated regime shifts in seasonal zooplankton communities of the Northeast continental shelf Large Marine Ecosystem ({NES}) and its subcomponent ecoregions over a multi-decadal period (1977–2013). Our cross ecoregion analysis shows that regime shifts in different ecoregions often exhibited very distinct characteristics, emphasizing more granular fluctuations in {NES} plankton communities relative to previous work. Shifts early in the time series generally reflected an increase in abundance levels. The response of zooplankton abundance within fall communities was more similar among ecoregions than for spring communities. The Gulf of Maine exhibited highly distinct patterns from other ecoregions, with regime shifts identified in the early 1980s, early 2000s, and mid-2000s for spring communities. Regime shifts were identified in the early to mid-1990s for the {NES}, Georges Bank, and the Mid-Atlantic Bight ecoregions, while the fall communities experienced shifts in the early 1990s and late 1980s for the {NES} and Georges Bank, but in the late 1990s in the Mid-Atlantic Bight. A constrained correspondence analysis of zooplankton community against local and basin-scale climatological indices suggests that water temperature, stratification, and the Atlantic multidecadal oscillation ({AMO}) were the predominant factors in driving the zooplankton community composition.},
	pages = {77--91},
	journaltitle = {Journal of Marine Systems},
	author = {Morse, R.E. and Friedland, K.D. and Tommasi, D. and Stock, C. and Nye, J.},
	urldate = {2019-02-14},
	date = {2017-01},
	langid = {english},
	keywords = {Zooplankton, Seasonal variations, Climate, Community composition, Long-term changes, Marine ecology},
	file = {Morse et al. - 2017 - Distinct zooplankton regime shift patterns across .pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\4529XXYW\\Morse et al. - 2017 - Distinct zooplankton regime shift patterns across .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\3SREYWET\\S0924796316303098.html:text/html},
}

@article{large_quantifying_2015,
	title = {Quantifying Patterns of Change in Marine Ecosystem Response to Multiple Pressures: e0119922},
	volume = {10},
	rights = {© 2015 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited:  Citation: Large {SI}, Fay G, Friedland {KD}, Link {JS} (2015) Quantifying Patterns of Change in Marine Ecosystem Response to Multiple Pressures. {PLoS} {ONE} 10(3): e0119922. doi:10.1371/journal.pone.0119922},
	url = {http://search.proquest.com/docview/1664222461/abstract/120C1207C54548BEPQ/1},
	doi = {http://dx.doi.org/10.1371/journal.pone.0119922},
	shorttitle = {Quantifying Patterns of Change in Marine Ecosystem Response to Multiple Pressures},
	abstract = {The ability to understand and ultimately predict ecosystem response to multiple pressures is paramount to successfully implement ecosystem-based management. Thresholds shifts and nonlinear patterns in ecosystem responses can be used to determine reference points that identify levels of a pressure that may drastically alter ecosystem status, which can inform management action. However, quantifying ecosystem reference points has proven elusive due in large part to the multi-dimensional nature of both ecosystem pressures and ecosystem responses. We used ecological indicators, synthetic measures of ecosystem status and functioning, to enumerate important ecosystem attributes and to reduce the complexity of the Northeast Shelf Large Marine Ecosystem ({NES} {LME}). Random forests were used to quantify the importance of four environmental and four anthropogenic pressure variables to the value of ecological indicators, and to quantify shifts in aggregate ecological indicator response along pressure gradients. Anthropogenic pressure variables were critical defining features and were able to predict an average of 8-13\% (up to 25-66\% for individual ecological indicators) of the variation in ecological indicator values, whereas environmental pressures were able to predict an average of 1-5 \% (up to 9-26\% for individual ecological indicators) of ecological indicator variation. Each pressure variable predicted a different suite of ecological indicator's variation and the shapes of ecological indicator responses along pressure gradients were generally nonlinear. Threshold shifts in ecosystem response to exploitation, the most important pressure variable, occurred when commercial landings were 20 and 60\% of total surveyed biomass. Although present, threshold shifts in ecosystem response to environmental pressures were much less important, which suggests that anthropogenic pressures have significantly altered the ecosystem structure and functioning of the {NES} {LME}. Gradient response curves provide ecologically informed transformations of pressure variables to explain patterns of ecosystem structure and functioning. By concurrently identifying thresholds for a suite of ecological indicator responses to multiple pressures, we demonstrate that ecosystem reference points can be evaluated and used to support ecosystem-based management.},
	number = {3},
	journaltitle = {{PLoS} One},
	author = {Large, Scott I. and Fay, Gavin and Friedland, Kevin D. and Link, Jason S.},
	urldate = {2016-10-14},
	date = {2015-03},
	keywords = {Ecosystems, Decision making, fish, Fisheries management, Forests, Medical Sciences, Sciences: Comprehensive Works, Variables},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\FCU7JZHL\\Large et al. - 2015 - Quantifying Patterns of Change in Marine Ecosystem.pdf:application/pdf},
}

@article{hare_vulnerability_2016,
	title = {A Vulnerability Assessment of Fish and Invertebrates to Climate Change on the Northeast U.S. Continental Shelf},
	volume = {11},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146756},
	doi = {10.1371/journal.pone.0146756},
	abstract = {Climate change and decadal variability are impacting marine fish and invertebrate species worldwide and these impacts will continue for the foreseeable future. Quantitative approaches have been developed to examine climate impacts on productivity, abundance, and distribution of various marine fish and invertebrate species. However, it is difficult to apply these approaches to large numbers of species owing to the lack of mechanistic understanding sufficient for quantitative analyses, as well as the lack of scientific infrastructure to support these more detailed studies. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species with existing information. These methods combine the exposure of a species to a stressor (climate change and decadal variability) and the sensitivity of species to the stressor. These two components are then combined to estimate an overall vulnerability. Quantitative data are used when available, but qualitative information and expert opinion are used when quantitative data is lacking. Here we conduct a climate vulnerability assessment on 82 fish and invertebrate species in the Northeast U.S. Shelf including exploited, forage, and protected species. We define climate vulnerability as the extent to which abundance or productivity of a species in the region could be impacted by climate change and decadal variability. We find that the overall climate vulnerability is high to very high for approximately half the species assessed; diadromous and benthic invertebrate species exhibit the greatest vulnerability. In addition, the majority of species included in the assessment have a high potential for a change in distribution in response to projected changes in climate. Negative effects of climate change are expected for approximately half of the species assessed, but some species are expected to be positively affected (e.g., increase in productivity or move into the region). These results will inform research and management activities related to understanding and adapting marine fisheries management and conservation to climate change and decadal variability.},
	pages = {e0146756},
	number = {2},
	journaltitle = {{PLOS} {ONE}},
	shortjournal = {{PLOS} {ONE}},
	author = {Hare, Jonathan A. and Morrison, Wendy E. and Nelson, Mark W. and Stachura, Megan M. and Teeters, Eric J. and Griffis, Roger B. and Alexander, Michael A. and Scott, James D. and Alade, Larry and Bell, Richard J. and Chute, Antonie S. and Curti, Kiersten L. and Curtis, Tobey H. and Kircheis, Daniel and Kocik, John F. and Lucey, Sean M. and {McCandless}, Camilla T. and Milke, Lisa M. and Richardson, David E. and Robillard, Eric and Walsh, Harvey J. and {McManus}, M. Conor and Marancik, Katrin E. and Griswold, Carolyn A.},
	urldate = {2016-03-01},
	date = {2016-02-03},
	keywords = {climate change, Habitats, Marine fish, Fisheries, Marine ecology, Invertebrates, ocean temperature, Oceans},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\PWLSV283\\Hare et al. - 2016 - A Vulnerability Assessment of Fish and Invertebrat.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\IUN3JGZ7\\article.html:text/html},
}

@article{smith_consumption_2015,
	title = {Consumption by marine mammals on the Northeast U.S. continental shelf},
	volume = {25},
	issn = {1939-5582},
	url = {http://onlinelibrary.wiley.com/doi/10.1890/13-1656.1/abstract},
	doi = {10.1890/13-1656.1},
	abstract = {The economic and ecological impacts of fish consumption by marine mammals, the associated interactions with commercial fish stocks, and the forage demands of these marine mammal populations are largely unknown. Consumption estimates are often either data deficient or not fully evaluated in a rigorous, quantitative manner. Although consumption estimates exist for the Northeast United States ({NEUS}) Large Marine Ecosystem, there is considerable uncertainty in those estimates. We examined consumption estimates for 12 marine mammal species inhabiting the regional ecosystem. We used sensitivity analyses to examine metabolically driven daily individual consumption rates, resulting in a suite of feasible parameter-pair ranges for each of three taxonomic groups: mysticetes, odontocetes, and pinnipeds. We expanded daily individual consumption to annual consumption based on abundance estimates of marine mammals found on the {NEUS} continental shelf coupled with estimates of annual residence time for each species. To examine consumptive removals for specific prey, diet compositions were summarized into major prey categories, and predatory removals by marine mammal species as well as for total marine mammal consumption were estimated for each prey taxa. Bounds on consumption estimates for each marine mammal species were determined using Monte Carlo resampling simulations. Our results suggest that consumption for these 12 marine mammal species combined may be similar in magnitude to commercial fishery landings for small pelagic and groundfish prey groups. Consumption by marine mammals warrants consideration both as a source of mortality in assessments of prey stocks, and to determine marine mammal forage demands in ecosystem assessment models. The approach that we present represents a rigorous, quantitative method to scope the bounds of the biomass that marine mammals are expected to consume, and is appropriate for use in other ecosystems where the interaction between marine mammals and commercial fisheries is thought to be prominent.},
	pages = {373--389},
	number = {2},
	journaltitle = {Ecological Applications},
	author = {Smith, Laurel A. and Link, Jason S. and Cadrin, Steven X. and Palka, Debra L.},
	urldate = {2016-04-26},
	date = {2015-03-01},
	langid = {english},
	keywords = {Northeast U.S. shelf, Atlantic Ocean, commercial fisheries, competition, conservation, consumption estimates, ecosystem modeling, energetics, marine mammal diets, uncertainty estimation},
	file = {Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\B4PVYBPE\\abstract.html:text/html},
}

@article{zador_ecosystem_2016,
	title = {Ecosystem considerations in Alaska: the value of qualitative assessments},
	rights = {All rights reserved},
	issn = {1054-3139, 1095-9289},
	url = {http://icesjms.oxfordjournals.org/content/early/2016/09/12/icesjms.fsw144},
	doi = {10.1093/icesjms/fsw144},
	shorttitle = {Ecosystem considerations in Alaska},
	abstract = {The application of ecosystem considerations, and in particular ecosystem report cards, in federal groundfish fisheries management in Alaska can be described as an ecosystem approach to fisheries management ({EAFM}). Ecosystem information is provided to managers to establish an ecosystem context within which deliberations of fisheries quota occur. Our goal is to make the case for the need for qualitative ecosystem assessments in {EAFM}, specifically that qualitative synthesis has advantages worthy to keep a permanent place at the fisheries management table. These advantages include flexibility and speed in responding to and synthesizing new information from a variety of sources. First, we use the development of indicator-based ecosystem report cards as an example of adapting ecosystem information to management needs. Second, we review lessons learned and provide suggestions for best practices for applying {EAFM} to large and diverse fisheries in multiple marine ecosystems. Adapting ecosystem indicator information to better suit the needs of fisheries managers resulted in succinct report cards that summarize ecosystem trends, complementing more detailed ecosystem information to provide context for {EAFM}. There were several lessons learned in the process of developing the ecosystem report cards. The selection of indicators for each region was influenced by geography, the extent of scientific knowledge/data, and the particular expertise of the selection teams. Optimizing the opportunity to qualitatively incorporate ecosystem information into management decisions requires a good understanding of the management system in question. We found that frequent dialogue with managers and other stakeholders leads to adaptive products. We believe that there will always be a need for qualitative ecosystem assessment because it allows for rapid incorporation of new ideas and data and unexpected events. As we build modelling and predictive capacity, we will still need qualitative synthesis to capture events outside the bounds of current models and to detect impacts of the unexpected.},
	pages = {fsw144},
	journaltitle = {{ICES} Journal of Marine Science: Journal du Conseil},
	shortjournal = {{ICES} J. Mar. Sci.},
	author = {Zador, Stephani G. and Holsman, Kirstin K. and Aydin, Kerim Y. and Gaichas, Sarah K.},
	urldate = {2016-09-24},
	date = {2016-08-22},
	langid = {english},
	keywords = {Alaska, ecosystem approach to fisheries, ecosystem assessment, ecosystem report cards., Ecosystem-based fisheries management},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\J8TGK3YC\\Zador et al. - 2016 - Ecosystem considerations in Alaska the value of q.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\T3INLMFK\\icesjms.html:text/html},
}

@article{gawarkiewicz_changing_2018,
	title = {The Changing Nature of Shelf-Break Exchange Revealed by the {OOI} Pioneer Array},
	volume = {31},
	issn = {10428275},
	url = {https://tos.org/oceanography/article/the-changing-nature-of-shelf-break-exchange-revealed-by-the-ooi-pioneer-arr},
	doi = {10.5670/oceanog.2018.110},
	pages = {60--70},
	number = {1},
	journaltitle = {Oceanography},
	shortjournal = {Oceanog},
	author = {Gawarkiewicz, Glen and Todd, Robert and Zhang, Weifeng and Partida, Jacob and Gangopadhyay, Avijit and Monim, Mahmud-Ul-Hasan and Fratantoni, Paula and Malek Mercer, Anna and Dent, Margaret},
	urldate = {2020-02-10},
	date = {2018-03-01},
	file = {Full Text:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XJCTJY7Z\\Gawarkiewicz et al. - 2018 - The Changing Nature of Shelf-Break Exchange Reveal.pdf:application/pdf},
}

@article{friedland_changes_2020,
	title = {Changes in higher trophic level productivity, diversity and niche space in a rapidly warming continental shelf ecosystem},
	volume = {704},
	issn = {0048-9697},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969719352623},
	doi = {10.1016/j.scitotenv.2019.135270},
	abstract = {There is long-standing ecological and socioeconomic interest in what controls the diversity and productivity of ecosystems. That focus has intensified with shifting environmental conditions associated with accelerating climate change. The U.S. Northeast Shelf ({NES}) is a well-studied continental shelf marine ecosystem that is among the more rapidly warming marine systems worldwide. Furthermore, many constituent species have experienced significant distributional shifts. However, the system response of the {NES} to climate change goes beyond simple shifts in species distribution. The fish and macroinvertebrate communities of the {NES} have increased in species diversity and overall productivity in recent decades, despite no significant decline in fishing pressure. Species distribution models constructed using random forest classification and regression trees were fit for the dominant species in the system. Over time, the areal distribution of occupancy habitat has increased for approximately 80\% of the modeled taxa, suggesting most species have significantly increased their range and niche space. These niche spaces were analyzed to determine the area of niche overlap between species pairs. For the vast majority of species pairs, interaction has increased over time suggesting greater niche overlap and the increased probability for more intense species interactions, such as between competitors or predators and prey. Furthermore, the species taxonomic composition and size structure indicate a potential tropicalization of the fish community. The system and community changes are consistent with the view that the {NES} may be transitioning from a cold temperate or boreal ecoregion to one more consistent with the composition of a warm temperate or Carolinian system.},
	pages = {135270},
	journaltitle = {Science of The Total Environment},
	shortjournal = {Science of The Total Environment},
	author = {Friedland, Kevin D. and Langan, Joseph A. and Large, Scott I. and Selden, Rebecca L. and Link, Jason S. and Watson, Reg A. and Collie, Jeremy S.},
	urldate = {2020-02-07},
	date = {2020-02-20},
	langid = {english},
	keywords = {Biodiversity, Habitat, Niche overlap, Species distribution model, Species interactions},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\LU6932BM\\S0048969719352623.html:text/html},
}

@article{andres_recent_2016,
	title = {On the recent destabilization of the Gulf Stream path downstream of Cape Hatteras},
	volume = {43},
	rights = {©2016. American Geophysical Union. All Rights Reserved.},
	issn = {1944-8007},
	url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016GL069966},
	doi = {10.1002/2016GL069966},
	abstract = {Mapped satellite altimetry reveals interannual variability in the position of initiation of Gulf Stream meanders downstream of Cape Hatteras. The longitude where the Gulf Stream begins meandering varies by 1500 km. There has been a general trend for the destabilization point to shift west, and 5 of the last 6 years had a Gulf Stream destabilization point upstream of the New England Seamounts. Independent in situ data suggest that this shift has increased both upper-ocean/deep-ocean interaction events at Line W and open-ocean/shelf interactions across the Middle Atlantic Bight ({MAB}) shelf break. Mooring data and along-track altimetry indicate a recent increase in the number of deep cyclones that stir Deep Western Boundary Current waters from the {MAB} slope into the deep interior. Temperature profiles from the Oleander Program suggest that recent enhanced warming of the {MAB} shelf may be related to shifts in the Gulf Stream's destabilization point.},
	pages = {9836--9842},
	number = {18},
	journaltitle = {Geophysical Research Letters},
	author = {Andres, M.},
	urldate = {2020-02-10},
	date = {2016},
	langid = {english},
	keywords = {Gulf Stream, Middle Atlantic Bight, altimetry, Cape Hatteras, Deep Western Boundary Current, Line W},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\CF2LBGAU\\Andres - 2016 - On the recent destabilization of the Gulf Stream p.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\8TKG8B66\\2016GL069966.html:text/html},
}

@article{gangopadhyay_observed_2019,
	title = {An Observed Regime Shift in the Formation of Warm Core Rings from the Gulf Stream},
	volume = {9},
	rights = {2019 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-019-48661-9},
	doi = {10.1038/s41598-019-48661-9},
	abstract = {We present observational evidence that a significant regime change occurred around the year 2000 in the formation of Warm Core Rings ({WCRs}) from the Gulf Stream ({GS}) between 75° and 55°W. The dataset for this study is a set of synoptic oceanographic charts available over the thirty-eight-year period of 1980–2017. The upward regime change shows an increase to 33 {WCRs} per year during 2000–2017 from an average of 18 {WCRs} during 1980 to 1999. A seasonal analysis confirms May-June-July as the peak time for {WCR} births in agreement with earlier studies. The westernmost region (75°-70°W) is least ring-productive, while the region from 65°W to 60°W is most productive. This regime shift around 2000 is detected in {WCR} formation for all of the four 5-degree wide sub-regions and the whole region (75°-55°W). This might be related to a reduction of the deformation radius for ring formation, allowing unstable meanders to shed more frequent rings in recent years. A number of possible factors resulting in such a regime shift related to the possible changes in reduced gravity, instability, transport of the {GS}, large-scale changes in the wind system and atmospheric fluxes are outlined, which suggest new research directions. The increase in {WCRs} has likely had an impact on the marine ecosystem since 2000, a topic worthy for future studies.},
	pages = {1--9},
	number = {1},
	journaltitle = {Scientific Reports},
	shortjournal = {Sci Rep},
	author = {Gangopadhyay, Avijit and Gawarkiewicz, Glen and Silva, E. Nishchitha S. and Monim, M. and Clark, Jenifer},
	urldate = {2020-02-10},
	date = {2019-08-23},
	langid = {english},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\YN8GHAWK\\Gangopadhyay et al. - 2019 - An Observed Regime Shift in the Formation of Warm .pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\JHFINVB3\\s41598-019-48661-9.html:text/html},
}

@article{lettrich_vulnerability_2023,
	title = {Vulnerability to climate change of United States marine mammal stocks in the western North Atlantic, Gulf of Mexico, and Caribbean},
	volume = {18},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0290643},
	doi = {10.1371/journal.pone.0290643},
	abstract = {Climate change and climate variability are affecting marine mammal species and these impacts are projected to continue in the coming decades. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species using currently available information. We conducted a trait-based climate vulnerability assessment using expert elicitation for 108 marine mammal stocks and stock groups in the western North Atlantic, Gulf of Mexico, and Caribbean Sea. Our approach combined the exposure (projected change in environmental conditions) and sensitivity (ability to tolerate and adapt to changing conditions) of marine mammal stocks to estimate vulnerability to climate change, and categorize stocks with a vulnerability index. The climate vulnerability score was very high for 44\% (n = 47) of these stocks, high for 29\% (n = 31), moderate for 20\% (n = 22), and low for 7\% (n = 8). The majority of stocks (n = 78; 72\%) scored very high exposure, whereas 24\% (n = 26) scored high, and 4\% (n = 4) scored moderate. The sensitivity score was very high for 33\% (n = 36) of these stocks, high for 18\% (n = 19), moderate for 34\% (n = 37), and low for 15\% (n = 16). Vulnerability results were summarized for stocks in five taxonomic groups: pinnipeds (n = 4; 25\% high, 75\% moderate), mysticetes (n = 7; 29\% very high, 57\% high, 14\% moderate), ziphiids (n = 8; 13\% very high, 50\% high, 38\% moderate), delphinids (n = 84; 52\% very high, 23\% high, 15\% moderate, 10\% low), and other odontocetes (n = 5; 60\% high, 40\% moderate). Factors including temperature, ocean {pH}, and dissolved oxygen were the primary drivers of high climate exposure, with effects mediated through prey and habitat parameters. We quantified sources of uncertainty by bootstrapping vulnerability scores, conducting leave-one-out analyses of individual attributes and individual scorers, and through scoring data quality for each attribute. These results provide information for researchers, managers, and the public on marine mammal responses to climate change to enhance the development of more effective marine mammal management, restoration, and conservation activities that address current and future environmental variation and biological responses due to climate change.},
	pages = {e0290643},
	number = {9},
	journaltitle = {{PLOS} {ONE}},
	shortjournal = {{PLOS} {ONE}},
	author = {Lettrich, Matthew D. and Asaro, Michael J. and Borggaard, Diane L. and Dick, Dorothy M. and Griffis, Roger B. and Litz, Jenny A. and Orphanides, Christopher D. and Palka, Debra L. and Soldevilla, Melissa S. and Balmer, Brian and Chavez, Samuel and Cholewiak, Danielle and Claridge, Diane and Ewing, Ruth Y. and Fazioli, Kristi L. and Fertl, Dagmar and Fougeres, Erin M. and Gannon, Damon and Garrison, Lance and Gilbert, James and Gorgone, Annie and Hohn, Aleta and Horstman, Stacey and Josephson, Beth and Kenney, Robert D. and Kiszka, Jeremy J. and Maze-Foley, Katherine and {McFee}, Wayne and Mullin, Keith D. and Murray, Kimberly and Pendleton, Daniel E. and Robbins, Jooke and Roberts, Jason J. and Ferrer, Grisel Rodriguez- and Ronje, Errol I. and Rosel, Patricia E. and Speakman, Todd and Stanistreet, Joy E. and Stevens, Tara and Stolen, Megan and Moore, Reny Tyson and Vollmer, Nicole L. and Wells, Randall and Whitehead, Heidi R. and Whitt, Amy},
	urldate = {2024-02-05},
	date = {2023-09-20},
	langid = {english},
	note = {Publisher: Public Library of Science},
	keywords = {Climate change, Anthropogenic climate change, Animal migration, Ocean temperature, Caribbean, Dolphins, Marine mammals, Sea level rise},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\J7RIM3FD\\Lettrich et al. - 2023 - Vulnerability to climate change of United States m.pdf:application/pdf},
}

@article{staudinger_its_2019,
	title = {It’s about time: A synthesis of changing phenology in the Gulf of Maine ecosystem},
	volume = {28},
	rights = {© 2019 The Authors. Fisheries Oceanography Published by John Wiley \& Sons Ltd},
	issn = {1365-2419},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12429},
	doi = {10.1111/fog.12429},
	shorttitle = {It’s about time},
	abstract = {The timing of recurring biological and seasonal environmental events is changing on a global scale relative to temperature and other climate drivers. This study considers the Gulf of Maine ecosystem, a region of high social and ecological importance in the Northwest Atlantic Ocean and synthesizes current knowledge of (a) key seasonal processes, patterns, and events; (b) direct evidence for shifts in timing; (c) implications of phenological responses for linked ecological-human systems; and (d) potential phenology-focused adaptation strategies and actions. Twenty studies demonstrated shifts in timing of regional marine organisms and seasonal environmental events. The most common response was earlier timing, observed in spring onset, spring and winter hydrology, zooplankton abundance, occurrence of several larval fishes, and diadromous fish migrations. Later timing was documented for fall onset, reproduction and fledging in Atlantic puffins, spring and fall phytoplankton blooms, and occurrence of additional larval fishes. Changes in event duration generally increased and were detected in zooplankton peak abundance, early life history periods of macro-invertebrates, and lobster fishery landings. Reduced duration was observed in winter–spring ice-affected stream flows. Two studies projected phenological changes, both finding diapause duration would decrease in zooplankton under future climate scenarios. Phenological responses were species-specific and varied depending on the environmental driver, spatial, and temporal scales evaluated. Overall, a wide range of baseline phenology and relevant modeling studies exist, yet surprisingly few document long-term shifts. Results reveal a need for increased emphasis on phenological shifts in the Gulf of Maine and identify opportunities for future research and consideration of phenological changes in adaptation efforts.},
	pages = {532--566},
	number = {5},
	journaltitle = {Fisheries Oceanography},
	author = {Staudinger, Michelle D. and Mills, Katherine E. and Stamieszkin, Karen and Record, Nicholas R. and Hudak, Christine A. and Allyn, Andrew and Diamond, Antony and Friedland, Kevin D. and Golet, Walt and Henderson, Meghan Elisabeth and Hernandez, Christina M. and Huntington, Thomas G. and Ji, Rubao and Johnson, Catherine L. and Johnson, David Samuel and Jordaan, Adrian and Kocik, John and Li, Yun and Liebman, Matthew and Nichols, Owen C. and Pendleton, Daniel and Richards, R. Anne and Robben, Thomas and Thomas, Andrew C. and Walsh, Harvey J. and Yakola, Keenan},
	urldate = {2024-02-05},
	date = {2019},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/fog.12429},
	keywords = {Gulf of Maine, phenology, fish, coastal, life cycle, marine, marine invertebrates, marine mammals, migration, phytoplankton, seabirds, seasonal, timing, zooplankton},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\X26EBHB6\\Staudinger et al. - 2019 - It’s about time A synthesis of changing phenology.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\NSLLYQJE\\fog.html:text/html},
}

@article{crear_climate-influenced_2023,
	title = {Climate-influenced shifts in a highly migratory species recreational fishery},
	volume = {32},
	rights = {© 2023 John Wiley \& Sons Ltd.},
	issn = {1365-2419},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12632},
	doi = {10.1111/fog.12632},
	abstract = {The distribution of marine species is changing as a direct result of climate change. Large pelagic highly migratory species ({HMS}), like tunas, billfishes, and sharks, are particularly sensitive to environmental change due to their migratory nature and use of large-scale ocean features. These temporal and spatial shifts are likely reflected in the Atlantic {HMS} recreational fishery and could have downstream effects on coastal communities. We utilized dockside intercept data from the Large Pelagics Survey ({LPS}) from 2002 to 2019, which conducts sampling from June to October and spans Maine to Virginia, {USA}. We assessed how species catch composition has changed and developed spatiotemporal models to understand latitudinal and temporal shifts in the recreational catch of 12 {HMS} groups. Latitudinal shifts were significantly affected by Northeast Shelf {SST} for 11 of the 12 {HMS} groups and ranged from 3 ± 1 km°C−1 for the large bluefin tuna to 40 ± 1 km°C−1 for the blue shark. In addition, the estimated day of the year when the first 25\% of bigeye tuna intercepts occurred, happened over 50 days earlier in 2019 compared to 2002, suggesting the initial catch is happening earlier in recent years. These results suggest that changes in species distribution and phenology are affecting where and when {HMS} recreational catch occurs. Understanding these shifts would allow managers to be more responsive and flexible and also help communities prepare for changes, whether it would be a switch to a new species or shifts in the fishing season.},
	pages = {327--340},
	number = {4},
	journaltitle = {Fisheries Oceanography},
	author = {Crear, Daniel P. and Curtis, Tobey H. and Hutt, Cliff P. and Lee, Yong-Woo},
	urldate = {2024-02-06},
	date = {2023},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/fog.12632},
	keywords = {climate change, billfishes, fisheries management, Large Pelagics Survey, pelagic sharks, spatiotemporal models, tunas},
	file = {Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\9IPF4TBA\\fog.html:text/html;Submitted Version:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\487LDGYG\\Crear et al. - 2023 - Climate-influenced shifts in a highly migratory sp.pdf:application/pdf},
}

@article{grieve_projecting_2017,
	title = {Projecting the effects of climate change on Calanus finmarchicus distribution within the U.S. Northeast Continental Shelf},
	volume = {7},
	rights = {2017 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-017-06524-1},
	doi = {10.1038/s41598-017-06524-1},
	abstract = {Calanus finmarchicus is vital to pelagic ecosystems in the North Atlantic Ocean. Previous studies suggest the species is vulnerable to the effects of global warming, particularly on the Northeast U.S. Shelf, which is in the southern portion of its range. In this study, we evaluate an ensemble of six different downscaled climate models and a high-resolution global climate model, and create a generalized additive model ({GAM}) to examine how future changes in temperature and salinity could affect the distribution and density of C. finmarchicus. By 2081–2100, we project average C. finmarchicus density will decrease by as much as 50\% under a high greenhouse gas emissions scenario. These decreases are particularly pronounced in the spring and summer in the Gulf of Maine and Georges Bank. When compared to a high-resolution global climate model, the ensemble showed a more uniform change throughout the Northeast U.S. Shelf, while the high-resolution model showed larger decreases in the Northeast Channel, Shelf Break, and Central Gulf of Maine. C. finmarchicus is an important link between primary production and higher trophic levels, and the decrease projected here could be detrimental to the North Atlantic Right Whale and a host of important fishery species.},
	pages = {6264},
	number = {1},
	journaltitle = {Scientific Reports},
	shortjournal = {Sci Rep},
	author = {Grieve, Brian D. and Hare, Jon A. and Saba, Vincent S.},
	urldate = {2024-02-06},
	date = {2017-07-24},
	langid = {english},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Biooceanography, Climate-change ecology, Marine biology, Ocean sciences},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\LAL7J7VB\\Grieve et al. - 2017 - Projecting the effects of climate change on Calanu.pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\ZD5G4FW4\\Grieve et al. - 2017 - Projecting the effects of climate change on Calanu.pdf:application/pdf},
}

@article{stevens_modeling_2019,
	title = {Modeling the impacts of dams and stocking practices on an endangered Atlantic salmon (Salmo salar) population in the Penobscot River, Maine, {USA}},
	volume = {76},
	issn = {0706-652X},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/cjfas-2018-0225},
	doi = {10.1139/cjfas-2018-0225},
	abstract = {Dams challenge Atlantic salmon (Salmo salar) conservation, while hatcheries are a common but poorly evaluated recovery tool. We developed a spatially explicit smolt survival model for the Penobscot River, Maine, {USA}, population. By partitioning survival through dams (with flow dependency), free-flowing river reaches, and the estuary (with dam dependency), the model quantified how these factors influenced the number of fish entering the ocean. Given historical impounded conditions, 74\%–22\% of hatchery smolts released entered the ocean annually from 1970 to 2012. Of 19.7 million smolts stocked, 7.7 million entered the ocean (39\%). Survival was most variable at dams (range 95\% to 63\%), followed by in-river (range 98\% to 70\%) and estuary (range 88\% to 82\%). Overall, lower-river stocking sites resulted in significantly higher numbers at ocean entry because of fewer dam encounters and shorter migrations. Higher flows also resulted in reduced losses. By reconstructing these freshwater and estuary dynamics, the model provides a more accurate estimate of ocean recruitment annually and can be used for scenario planning of future stocking locations relative to predicted flows while being adaptable to new survival rates.},
	pages = {1795--1807},
	number = {10},
	journaltitle = {Canadian Journal of Fisheries and Aquatic Sciences},
	shortjournal = {Can. J. Fish. Aquat. Sci.},
	author = {Stevens, Justin R. and Kocik, John F. and Sheehan, Timothy F.},
	urldate = {2024-02-07},
	date = {2019-10},
	note = {Publisher: {NRC} Research Press},
}

@article{mountain_volume_1991,
	title = {The volume of Shelf Water in the Middle Atlantic Bight: seasonal and interannual variability, 1977–1987},
	volume = {11},
	issn = {0278-4343},
	url = {https://www.sciencedirect.com/science/article/pii/027843439190068H},
	doi = {10.1016/0278-4343(91)90068-H},
	shorttitle = {The volume of Shelf Water in the Middle Atlantic Bight},
	abstract = {The volume of Shelf Water (salinity {\textless}34psu) is determined for three regions in the Middle Atlantic Bight ({MAB}) and for Georges Bank from a combination of hydrographic data and shelf/slope front positions derived from satellite imagery. The hydrographic data were obtained on 49 surveys of the shelf between 1977 and 1987. In each region the shelf water volume exhibits a significant annual cycle with a range of 50–80\% of the mean volume. The annual volume cycle appears to be advected southwestward from Georges Bank through the {MAB} with the mean circulation. Large interannual changes in volume are observed which have a range comparable to the mean volume of Shelf Water in the {MAB}. Both the seasonal and interannual changes in volume appear to be related to changes in the inflow to the Gulf of Maine through Northeast Channel and from the Scotian Shelf.},
	pages = {251--267},
	number = {3},
	journaltitle = {Continental Shelf Research},
	shortjournal = {Continental Shelf Research},
	author = {Mountain, David G.},
	urldate = {2024-02-07},
	date = {1991-03-01},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\FWDR7722\\027843439190068H.html:text/html},
}

@article{mountain_labrador_2012,
	title = {Labrador slope water entering the Gulf of Maine—response to the North Atlantic Oscillation},
	volume = {47},
	issn = {0278-4343},
	url = {https://www.sciencedirect.com/science/article/pii/S0278434312001938},
	doi = {10.1016/j.csr.2012.07.008},
	abstract = {The percent of Labrador Slope Water (\%{LSW}) in the waters entering the Gulf of Maine at depth (150–200m) through the Northeast Channel is estimated from temperature/salinity measurements for the period 1964–2008. Comparison of the annual average \%{LSW} with the North Atlantic Oscillation ({NAO}) lagged two years shows that both series have very similar, but opposite, long term trends. High \%{LSW} in the 1960s decreased to low values in the 1990s as the {NAO} increased from low to high values over the same period. A regression of the residuals of the two series from their long term trends also is significant at the 5\% level, indicating that the \%{LSW} at the Northeast Channel has a persistent relationship on a year-to-year basis with the {NAO} over the full range of variation in the {NAO}. The response of the \%{LSW} to the {NAO}, however, appeared substantially reduced after about 1990. Changes in the potential nutrient flux into the Gulf of Maine/Georges Bank system associated with changes in the \%{LSW} cannot account for changes in chlorophyll a concentrations estimated for three multi-year stanzas during the sampling period.},
	pages = {150--155},
	journaltitle = {Continental Shelf Research},
	shortjournal = {Continental Shelf Research},
	author = {Mountain, David G.},
	urldate = {2024-02-07},
	date = {2012-09-15},
	keywords = {Gulf of Maine, Labrador slope water, North Atlantic Oscillation},
	file = {ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\79KAYHBV\\S0278434312001938.html:text/html},
}

@article{northeast_fisheries_science_center_us_fall_2022,
	title = {Fall Management Track Assessments 2020},
	url = {https://repository.library.noaa.gov/view/noaa/39404},
	doi = {10.25923/8N72-Q136},
	author = {{Northeast Fisheries Science Center (U.S.)}},
	urldate = {2024-02-07},
	date = {2022},
	note = {Publisher: Northeast Fisheries Science Center (U.S.)},
}

@article{benjamin_visualizing_2018,
	title = {Visualizing Fishing Data as Rasters},
	url = {https://repository.library.noaa.gov/view/noaa/23030},
	doi = {10.25923/C14D-G218},
	author = {Benjamin, Sharon and Lee, Min-Yang A. and {DePiper}, Geret Sean},
	urldate = {2024-02-07},
	date = {2018},
	note = {Publisher: Northeast Fisheries Science Center (U.S.)},
}

@online{palka_atlantic_2021,
	title = {Atlantic Marine Assessment Program for Protected Species: {FY}15-{FY}19},
	url = {https://repository.library.noaa.gov/view/noaa/47287},
	author = {Palka, D and Aichinger Dias,, L and Broughton, E and Chavez-Rosales, S and Cholewiak, D and Davis, G and {DeAngelis}, A and Garrison, L and Haas, H and Hatch, J and Hyde, K and Jech, M and Josephson, E and Mueller-Brennan, L and Orphanides, C and Pegg,, N and Sasso, C and Sigourney, D and Soldevilla, M and Walsh, H},
	urldate = {2024-02-07},
	date = {2021},
	file = {Atlantic Marine Assessment Program for Protected Species\: FY15-FY19:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\N27ZDQJ7\\47287.html:text/html},
}

@article{petrenko_evaluation_2014,
	title = {Evaluation and selection of {SST} regression algorithms for {JPSS} {VIIRS}},
	volume = {119},
	rights = {©2014. American Geophysical Union. All Rights Reserved.},
	issn = {2169-8996},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/2013JD020637},
	doi = {10.1002/2013JD020637},
	abstract = {{AbstractTwo} global level 2 sea surface temperature ({SST}) products are generated at {NOAA} from the Suomi National Polar-Orbiting Partnership Visible Infrared Imaging Radiometer Suite ({VIIRS}) sensor data records (L1) with two independent processing systems, the Joint Polar Satellite System ({JPSS}) Interface Data Processing Segment ({IDPS}) and the {NOAA} heritage Advanced Clear-Sky Processor for Oceans ({ACSPO}). The two systems use different {SST} retrieval and cloud masking algorithms. Validation against in situ and L4 analyses has shown suboptimal performance of the {IDPS} product. In this context, existing operational and proposed {SST} algorithms have been evaluated for their potential implementation in {IDPS}. This paper documents the evaluation methodology and results. The performance of {SST} retrievals is characterized with bias and standard deviation with respect to in situ {SSTs} and sensitivity to true {SST}. Given three retrieval metrics, all being variable in space and with observational conditions, an additional integral metric is needed to evaluate the overall performance of {SST} algorithms. Therefore, we introduce the Quality Retrieval Domain ({QRD}) as a part of the global ocean, where the retrieval characteristics meet predefined specifications. Based on the {QRDs} analyses for all tested algorithms over a representative range of specifications for accuracy, precision, and sensitivity, we have selected the algorithms developed at the {EUMETSAT} Ocean and Sea Ice Satellite Application Facility ({OSI}-{SAF}) for implementation in {IDPS} and {ACSPO}. Testing the {OSI}-{SAF} algorithms with {ACSPO} and {IDPS} products shows the improved consistency between {VIIRS} {SST} and Reynolds L4 daily analysis. Further improvement of the {IDPS} {SST} product requires adjustment of the {VIIRS} cloud and ice masks.},
	pages = {4580--4599},
	number = {8},
	journaltitle = {Journal of Geophysical Research: Atmospheres},
	author = {Petrenko, Boris and Ignatov, Alexander and Kihai, Yury and Stroup, John and Dash, Prasanjit},
	urldate = {2024-02-07},
	date = {2014},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/2013JD020637},
	keywords = {accuracy, algorithm, precision, regression, sea surface temperature, sensitivity},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\CM93WUCS\\Petrenko et al. - 2014 - Evaluation and selection of SST regression algorit.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\B4UKL23F\\2013JD020637.html:text/html},
}

@article{petrenko_sensor-specific_2016,
	title = {Sensor-Specific Error Statistics for {SST} in the Advanced Clear-Sky Processor for Oceans},
	volume = {33},
	issn = {0739-0572, 1520-0426},
	url = {https://journals.ametsoc.org/view/journals/atot/33/2/jtech-d-15-0166_1.xml},
	doi = {10.1175/JTECH-D-15-0166.1},
	abstract = {Abstract The formulation of the sensor-specific error statistics ({SSES}) has been redesigned in the latest implementation of the {NOAA} Advanced Clear-Sky Processor for Oceans ({ACSPO}) to enable efficient use of {SSES} for assimilation of the {ACSPO} baseline regression {SST} ({BSST}) into level 4 (L4) analyses. The {SSES} algorithm employs segmentation of the {SST} domain in the space of regressors and derives the segmentation parameter from the statistics of regressors within the global dataset of matchups. For each segment, local regression coefficients and standard deviations ({SDs}) of {BSST} minus in situ {SST} are calculated from the corresponding subset of matchups. The local regression coefficients are used to generate an auxiliary product—piecewise regression ({PWR}) {SST}—and {SSES} biases are estimated as differences between {BSST} and {PWR} {SST}. Correction of {SSES} biases, which transforms {BSST} back into {PWR} {SST}, reduces the effects of residual cloud; variations in view zenith angle; and, during the daytime, diurnal surface warming. This results in significant reduction in the global {SD} of fitting in situ {SST}, making it comparable with {SD} for the Canadian Meteorological Centre ({CMC}) L4 {SST}. Unlike the foundation {CMC} {SST} (which is consistent with in situ {SST} at night but biased cold during the daytime), the {PWR} {SST} is consistent with in situ data during both day and night and thus may be viewed as an estimate of “depth” in situ {SST}. The {PWR} {SST} is expected to be a useful input into L4 {SST} analyses, especially for foundation {SST} products, such as the {CMC} L4.},
	pages = {345--359},
	number = {2},
	journaltitle = {Journal of Atmospheric and Oceanic Technology},
	author = {Petrenko, B. and Ignatov, A. and Kihai, Y. and Dash, P.},
	urldate = {2024-02-07},
	date = {2016-02-01},
	note = {Publisher: American Meteorological Society
Section: Journal of Atmospheric and Oceanic Technology},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XAEUF4JQ\\Petrenko et al. - 2016 - Sensor-Specific Error Statistics for SST in the Ad.pdf:application/pdf},
}

@article{ji_drivers_2022,
	title = {Drivers of variability of Calanus finmarchicus in the Gulf of Maine: roles of internal production and external exchange},
	volume = {79},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsab147},
	doi = {10.1093/icesjms/fsab147},
	shorttitle = {Drivers of variability of Calanus finmarchicus in the Gulf of Maine},
	abstract = {The lipid-rich calanoid copepod, Calanus finmarchicus, plays a critical role in the Gulf of Maine pelagic food web. Despite numerous studies over the last several decades, a clear picture of variability patterns and links with key environmental drivers remains elusive. This study applies model-based scaling and sensitivity analyses to a regional plankton dataset collected over the last four decades (1977–2017). The focus is to describe the gulf-wide spatio-temporal patterns across three major basins, and to assess the relative roles of internal population dynamics and external exchanges. For the spring stock, there is strong synchrony of interannual variability among three basins. This variability is largely driven by internal population dynamics rather than external exchanges, and the internal population dynamics are more sensitive to the change of top-down mortality regime than the bottom-up forcings. For the fall stock, the synchrony among basins weakens, and the variability is influenced by both internal mortality and external dilution loss. There appears to be no direct connection between the spring stock with either the preceding or subsequent fall stock, suggesting seasonal or sub-seasonal scales of population variability and associated drivers. The results highlight seasonally varying drivers responsible for population variability, including previously less recognized top-down control.},
	pages = {775--784},
	number = {3},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} Journal of Marine Science},
	author = {Ji, Rubao and Runge, Jeffrey A and Davis, Cabell S and Wiebe, Peter H},
	urldate = {2024-02-07},
	date = {2022-04-01},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\M6HYRJ4U\\Ji et al. - 2022 - Drivers of variability of Calanus finmarchicus in .pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\ZTTCEYGY\\Ji et al. - 2022 - Drivers of variability of Calanus finmarchicus in .pdf:application/pdf;Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\8GF2LJ5T\\Ji et al. - 2022 - Drivers of variability of Calanus finmarchicus in .pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\FMJMVE6E\\6350837.html:text/html},
}

@article{melle_north_2014,
	title = {The North Atlantic Ocean as habitat for Calanus finmarchicus: Environmental factors and life history traits},
	volume = {129},
	issn = {0079-6611},
	url = {https://www.sciencedirect.com/science/article/pii/S0079661114000743},
	doi = {10.1016/j.pocean.2014.04.026},
	series = {North Atlantic Ecosystems, the role of climate and anthropogenic forcing on their structure and function},
	shorttitle = {The North Atlantic Ocean as habitat for Calanus finmarchicus},
	abstract = {Here we present a new, pan-Atlantic compilation and analysis of data on Calanus finmarchicus abundance, demography, dormancy, egg production and mortality in relation to basin-scale patterns of temperature, phytoplankton biomass, circulation and other environmental characteristics in the context of understanding factors determining the distribution and abundance of C. finmarchicus across its North Atlantic habitat. A number of themes emerge: (1) the south-to-north transport of plankton in the northeast Atlantic contrasts with north-to-south transport in the western North Atlantic, which has implications for understanding population responses of C. finmarchicus to climate forcing, (2) recruitment to the youngest copepodite stages occurs during or just after the phytoplankton bloom in the east whereas it occurs after the bloom at many western sites, with up to 3.5months difference in recruitment timing, (3) the deep basin and gyre of the southern Norwegian Sea is the centre of production and overwintering of C. finmarchicus, upon which the surrounding waters depend, whereas, in the Labrador/Irminger Seas production mainly occurs along the margins, such that the deep basins serve as collection areas and refugia for the overwintering populations, rather than as centres of production, (4) the western North Atlantic marginal seas have an important role in sustaining high C. finmarchicus abundance on the nearby coastal shelves, (5) differences in mean temperature and chlorophyll concentration between the western and eastern North Atlantic are reflected in regional differences in female body size and egg production, (6) regional differences in functional responses of egg production rate may reflect genetic differences between western and eastern populations, (7) dormancy duration is generally shorter in the deep waters adjacent to the lower latitude western North Atlantic shelves than in the east, (8) there are differences in stage-specific daily mortality rates between eastern and western shelves and basins, but the survival trajectories for cohort development from {CI} to {CV} are similar, and (9) early life stage survival is much lower in regions where C. finmarchicus is found with its congeners, C. glacialis and/or C. hyperboreus. This compilation and analysis provides new knowledge for evaluation and parameterisation of population models of C. finmarchicus and their responses to climate change in the North Atlantic. The strengths and weaknesses of modeling approaches, including a statistical approach based on ecological niche theory and a dynamical approach based on knowledge of spatial population dynamics and life history, are discussed, as well as needs for further research.},
	pages = {244--284},
	journaltitle = {Progress in Oceanography},
	shortjournal = {Progress in Oceanography},
	author = {Melle, Webjørn and Runge, Jeffrey and Head, Erica and Plourde, Stéphane and Castellani, Claudia and Licandro, Priscilla and Pierson, James and Jonasdottir, Sigrun and Johnson, Catherine and Broms, Cecilie and Debes, Høgni and Falkenhaug, Tone and Gaard, Eilif and Gislason, Astthor and Heath, Michael and Niehoff, Barbara and Nielsen, Torkel Gissel and Pepin, Pierre and Stenevik, Erling Kaare and Chust, Guillem},
	urldate = {2024-02-07},
	date = {2014-12-01},
	file = {Full Text:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\U7UFWQF6\\Melle et al. - 2014 - The North Atlantic Ocean as habitat for Calanus fi.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\BI4NGCXD\\S0079661114000743.html:text/html},
}

@article{skjoldal_size-fractioned_2022,
	title = {Size-fractioned zooplankton biomass in the Barents Sea: Spatial patterns and temporal variations during three decades of warming and strong fluctuations of the capelin stock (1989–2020)},
	volume = {206},
	issn = {0079-6611},
	url = {https://www.sciencedirect.com/science/article/pii/S0079661122001112},
	doi = {10.1016/j.pocean.2022.102852},
	shorttitle = {Size-fractioned zooplankton biomass in the Barents Sea},
	abstract = {Zooplankton biomass has been monitored on joint Norwegian-Russian surveys in late summer and autumn since the 1980s. We report here on zooplankton biomass in three size fractions ({\textless}1, 1–2, and {\textgreater} 2 mm in screen mesh opening) obtained with {WP}-2 plankton net (180 μm mesh size) hauled vertically over the water column from near bottom to the surface for the period 1989–2020. The number of samples (stations) collected each year has been about 100–200, with a total number of 4543 stations for the whole data set. The size composition of zooplankton reflected by the three fractions has shown remarkable stability, with about 50\% of biomass contained in the medium fraction (made up largely of Calanus species), about 1/3 in the small fraction (36\%), and 16\% in the large fraction. The depth integrated biomass was generally larger in basins compared to shallower bank areas. The temporal (interannual) pattern of change was characterized by a marked peak in biomass in 1994 and 1995 with values up to {\textgreater}20 g dry weight (dw) m−2, driven to large extent by the small size fraction. Subsequently the biomass decreased to lower values but with a divergence of relatively high values (10–15 g dw m−2) in the inflow area of Atlantic water in southwest, and low values (2–6 g dw m−2) in the central area. The difference is interpreted to reflect an increase in a second summer generation of Calanus finmarchicus in the Atlantic water and a decrease of C. glacialis in the central area. The zooplankton biomass fluctuated inversely with the biomass of the Barents Sea capelin (Mallotus villosus) stock, reflecting a top-down predation effect. However, biomass was also negatively correlated with temperature of the Atlantic water, suggesting an additional and confounding effect of climate variability and change. The decrease in biomass of the central area used as a forage area by capelin, was associated with a shift to dominance by the small size fraction. This is likely an effect of predation and could be associated with a lower trophic conversion efficiency from phytoplankton to planktivorous fish and higher trophic levels by smaller zooplankton (smaller copepods such as Pseudocalanus and others) compared to the larger Calanus species.},
	pages = {102852},
	journaltitle = {Progress in Oceanography},
	shortjournal = {Progress in Oceanography},
	author = {Skjoldal, Hein Rune and Eriksen, Elena and Gjøsæter, Harald},
	urldate = {2024-02-07},
	date = {2022-08-01},
	keywords = {Climate, Fish predation, Top-down, Trait-based},
	file = {Full Text:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\3AK2DKRE\\Skjoldal et al. - 2022 - Size-fractioned zooplankton biomass in the Barents.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\F2VZ6U8Z\\S0079661122001112.html:text/html},
}

@article{friedland_event_2019,
	title = {Event scale and persistent drivers of fish and macroinvertebrate distributions on the Northeast {US} Shelf},
	volume = {76},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsy167},
	doi = {10.1093/icesjms/fsy167},
	abstract = {The Northeast {US} Continental Shelf Large Marine Ecosystem is experiencing warming at a rate exceeding that of many other large marine ecosystems and has undergone significant climate-related changes. We examined the effect of thermal events and shifting patterns of primary and secondary productivity on the distribution of fish and macroinvertebrate species during the period 1968–2016. Though subject to inter-annual change, the along-shelf centre of gravity of chlorophyll concentration lacked a trend. Similarly, zooplankton bio-volume and total abundance along-shelf distance were also found to be without trend. However, the trend in the centre of gravity of copepod taxa diverged from the trends in bio-volume and non-copepod zooplankton abundance, suggesting most of these taxa had shifted in distribution to the northeast. The centres of gravity of fish and macroinvertebrate species have trended significantly to the northeast, suggesting copepods may play a key role in the distribution of higher trophic levels. Analysis of thermal events suggest that abrupt change in temperature can actuate persistent change in the distribution of fish and macroinvertebrate species. In aggregate, these broad trophic level patterns imply that distributional changes affecting upper trophic levels were dominated by thermal mechanisms, whereas lower trophic productivity, although subject to the same thermal conditions, exhibited less of a response. We hypothesize this lack of distributional response at lower trophic levels is due to their higher rates of production and turnover, and hence reflect a capacity to better integrate seasonal thermal changes. Furthermore, distributional changes of upper trophic levels may also be significantly impacted by feeding interactions at specific life history stages, where temperature affects both predator and prey.},
	pages = {1316--1334},
	number = {5},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} Journal of Marine Science},
	author = {Friedland, Kevin D and {McManus}, M Conor and Morse, Ryan E and Link, Jason S},
	urldate = {2024-02-07},
	date = {2019-09-01},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\SNWW4K7P\\Friedland et al. - 2019 - Event scale and persistent drivers of fish and mac.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\HH8P2JLP\\5197071.html:text/html},
}

@article{dupontavice_ocean_2022,
	title = {Ocean model-based covariates improve a marine fish stock assessment when observations are limited},
	volume = {79},
	issn = {1054-3139, 1095-9289},
	url = {https://academic.oup.com/icesjms/article/79/4/1259/6567589},
	doi = {10.1093/icesjms/fsac050},
	abstract = {The productivity of many fish populations is influenced by the environment, but developing environment-linked stock assessments remain challenging and current management of most commercial species assumes that stock productivity is time-invariant. In the Northeast United States, previous studies suggest that the recruitment of Southern New England-Mid Atlantic yellowtail flounder is closely related to the strength of the Cold Pool, a seasonally formed cold water mass on the continental shelf. Here, we developed three new indices that enhance the characterization of Cold Pool interannual variations using bottom temperature from a regional hindcast ocean model and a global ocean data assimilated hindcast. We associated these new indices to yellowtail flounder recruitment in a state–space, age-structured stock assessment framework using the Woods Hole Assessment Model. We demonstrate that incorporating Cold Pool effects on yellowtail flounder recruitment reduces the retrospective patterns and may improve the predictive skill of recruitment and, to a lesser extent, spawning stock biomass. We also show that the performance of the assessment models that incorporated ocean model-based indices is improved compared to the model using only the observation-based index. Instead of relying on limited subsurface observations, using validated ocean model products as environmental covariates in stock assessments may both improve predictions and facilitate operationalization.},
	pages = {1259--1273},
	number = {4},
	journaltitle = {{ICES} Journal of Marine Science},
	author = {du Pontavice, Hubert and Miller, Timothy J and Stock, Brian C and Chen, Zhuomin and Saba, Vincent S},
	editor = {Hidalgo, Manuel},
	urldate = {2024-02-07},
	date = {2022-05-23},
	langid = {english},
	file = {du Pontavice et al. - 2022 - Ocean model-based covariates improve a marine fish.pdf:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\NEB85ACU\\du Pontavice et al. - 2022 - Ocean model-based covariates improve a marine fish.pdf:application/pdf},
}

@article{griffin_warming_2019,
	title = {Warming seas increase cold-stunning events for Kemp’s ridley sea turtles in the northwest Atlantic},
	volume = {14},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0211503},
	doi = {10.1371/journal.pone.0211503},
	abstract = {Since the 1970s, the magnitude of turtle cold-stun strandings have increased dramatically within the northwestern Atlantic. Here, we examine oceanic, atmospheric, and biological factors that may affect the increasing trend of cold-stunned Kemp’s ridleys in Cape Cod Bay, Massachusetts, United States of America. Using machine learning and Bayesian inference modeling techniques, we demonstrate higher cold-stunning years occur when the Gulf of Maine has warmer sea surface temperatures in late October through early November. Surprisingly, hatchling numbers in Mexico, a proxy for population abundance, was not identified as an important factor. Further, using our Bayesian count model and forecasted sea surface temperature projections, we predict more than 2,300 Kemp’s ridley turtles may cold-stun annually by 2031 as sea surface temperatures continue to increase within the Gulf of Maine. We suggest warmer sea surface temperatures may have modified the northerly distribution of Kemp’s ridleys and act as an ecological bridge between the Gulf Stream and nearshore waters. While cold-stunning may currently account for a minor proportion of juvenile mortality, we recommend continuing efforts to rehabilitate cold-stunned individuals to maintain population resiliency for this critically endangered species in the face of a changing climate and continuing anthropogenic threats.},
	pages = {e0211503},
	number = {1},
	journaltitle = {{PLOS} {ONE}},
	shortjournal = {{PLOS} {ONE}},
	author = {Griffin, Lucas P. and Griffin, Curtice R. and Finn, John T. and Prescott, Robert L. and Faherty, Mark and Still, Brett M. and Danylchuk, Andy J.},
	urldate = {2024-02-07},
	date = {2019-01-29},
	langid = {english},
	note = {Publisher: Public Library of Science},
	keywords = {Animal migration, Beaches, Gulf of Mexico, Maine, Ocean temperature, Sea water, Surface temperature, Turtles},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\VXN9D7IX\\Griffin et al. - 2019 - Warming seas increase cold-stunning events for Kem.pdf:application/pdf},
}

@article{noauthor_notitle_nodate,
}

@article{wigley_length-weight_2003,
	title = {Length-weight relationships for 74 fish species collected during {NEFSC} research vessel bottom trawl surveys, 1992-99},
	url = {https://repository.library.noaa.gov/view/noaa/3346},
	author = {Wigley, {SE} and {McBride}, {NJ} and {McHugh}, {NJ}},
	date = {2003},
}

@article{meyer-gutbrod_ocean_2021,
	title = {Ocean Regime Shift Is Driving Collapse of the North Atlantic Right Whale Population},
	volume = {34},
	issn = {1042-8275},
	url = {https://www.jstor.org/stable/27051387},
	abstract = {Ocean warming linked to anthropogenic climate change is impacting the ecology of marine species around the world. In 2010, the Gulf of Maine and Scotian Shelf regions of the Northwest Atlantic underwent an unprecedented regime shift. Forced by climate-driven changes in the Gulf Stream, warm slope waters entered the region and created a less favorable foraging environment for the endangered North Atlantic right whale population. By mid-decade, right whales had shifted their late spring/summer foraging grounds from the Gulf of Maine and the western Scotian Shelf to the Gulf of St. Lawrence. The population also began exhibiting unusually high mortality in 2017. Here, we report that climate-driven changes in ocean circulation have altered the foraging environment and habitat use of right whales, reducing the population’s calving rate and exposing it to greater mortality risks from ship strikes and fishing gear entanglement. The case of the North Atlantic right whale provides a cautionary tale for the management of protected species in a changing ocean.},
	pages = {22--31},
	number = {3},
	journaltitle = {Oceanography},
	author = {Meyer-Gutbrod, Erin L. and Greene, Charles H. and Davies, Kimberley T.A. and Johns, David G.},
	urldate = {2024-02-08},
	date = {2021},
	note = {Publisher: Oceanography Society},
	file = {JSTOR Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\8WH9XZD3\\Meyer-Gutbrod et al. - 2021 - Ocean Regime Shift Is Driving Collapse of the Nort.pdf:application/pdf},
}

@thesis{dullaert_response_2023,
	title = {The Response of the Zooplankton Community in the Western Gulf of Maine to a Shift in Oceanographic Conditions: 2005-2017 - {ProQuest}},
	url = {https://www.proquest.com/openview/94bd0ad57c25a1623c75df0c0d4f5d82/1?pq-origsite=gscholar&cbl=18750&diss=y},
	shorttitle = {The Response of the Zooplankton Community in the Western Gulf of Maine to a Shift in Oceanographic Conditions},
	abstract = {Explore millions of resources from scholarly journals, books, newspapers, videos and more, on the {ProQuest} Platform.},
	type = {phdthesis},
	author = {Dullaert, Emma Cecile},
	urldate = {2024-02-08},
	date = {2023},
	langid = {english},
	file = {Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\7TTA5E25\\1.html:text/html},
}

@article{pershing_decadal_2023,
	title = {Decadal comparisons identify the drivers of persistent changes in the zooplankton community structure in the northwest Atlantic},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsad198},
	doi = {10.1093/icesjms/fsad198},
	abstract = {Plankton community structure changes seasonally in response to the annual cycles of stratification, temperature, and primary productivity. These communities also change from year-to-year, in some cases exhibiting persistent regime shifts. How changes in physical conditions structure the plankton community and why conditions persist is a fundamental question in oceanography. Continuous plankton recorders have been used to sample the plankton community across the Gulf of Maine since 1961. Historically, this community has had a classic subarctic structure dominated by Calanus finmarchicus. However, during the 1990s, C. finmarchicus became less prominent, and a more diverse community of smaller copepods emerged. This shift was related to an influx of cold, low-salinity water. We show that a similar community shift occurred around 2012. We use high-resolution hydrographic data to link the shift to an influx of saltier water and warmer conditions. By comparing the 1990s with the recent decade, we develop a synthesis for how physical changes lead to community shifts. Our synthesis suggests that the link between the 1990s and 2010s is enhanced water column stratification. We further propose that ecological interactions link declines in C. finmarchicus with the emergence of the more diverse community, drawing parallels with classic food web ecology.},
	pages = {fsad198},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} Journal of Marine Science},
	author = {Pershing, Andrew J and Kemberling, Adam},
	urldate = {2024-02-08},
	date = {2023-12-15},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XKH4EDIQ\\Pershing and Kemberling - 2023 - Decadal comparisons identify the drivers of persis.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\VBMNFDQ2\\7475010.html:text/html},
}

@online{noauthor_sensitivity_nodate,
	title = {Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast {US} shelf forage fish complex {\textbar} {ICES} Journal of Marine Science {\textbar} Oxford Academic},
	url = {https://academic.oup.com/icesjms/article/78/3/1023/6120244},
	urldate = {2024-02-08},
	file = {Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex | ICES Journal of Marine Science | Oxford Academic:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\LHUVY5EX\\6120244.html:text/html},
}

@article{suca_sensitivity_2021,
	title = {Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast {US} shelf forage fish complex},
	volume = {78},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsaa251},
	doi = {10.1093/icesjms/fsaa251},
	abstract = {Northern sand lance (Ammodytes dubius) and Atlantic herring (Clupea harengus) represent the dominant lipid-rich forage fish species throughout the Northeast {US} shelf and are critical prey for numerous top predators. However, unlike Atlantic herring, there is little research on sand lance or information about drivers of their abundance. We use intra-annual measurements of sand lance diet, growth, and condition to explain annual variability in sand lance abundance on the Northeast {US} Shelf. Our observations indicate that northern sand lance feed, grow, and accumulate lipids in the late winter through summer, predominantly consuming the copepod Calanus finmarchicus. Sand lance then cease feeding, utilize lipids, and begin gonad development in the fall. We show that the abundance of C. finmarchicus influences sand lance parental condition and recruitment. Atlantic herring can mute this effect through intra-guild predation. Hydrography further impacts sand lance abundance as increases in warm slope water decrease overwinter survival of reproductive adults. The predicted changes to these drivers indicate that sand lance will no longer be able to fill the role of lipid-rich forage during times of low Atlantic herring abundance—changing the Northeast {US} shelf forage fish complex by the end of the century.},
	pages = {1023--1037},
	number = {3},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} Journal of Marine Science},
	author = {Suca, Justin J and Wiley, David N and Silva, Tammy L and Robuck, Anna R and Richardson, David E and Glancy, Sarah G and Clancey, Emily and Giandonato, Teresa and Solow, Andrew R and Thompson, Michael A and Hong, Peter and Baumann, Hannes and Kaufman, Les and Llopiz, Joel K},
	urldate = {2024-02-08},
	date = {2021-07-01},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\CHMZMZ8E\\Suca et al. - 2021 - Sensitivity of sand lance to shifting prey and hyd.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\RHWNANFC\\6120244.html:text/html},
}

@article{white_spatial_2020,
	title = {Spatial ecology of long-tailed ducks and white-winged scoters wintering on Nantucket Shoals},
	volume = {11},
	rights = {© 2020 The Authors.},
	issn = {2150-8925},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.3002},
	doi = {10.1002/ecs2.3002},
	abstract = {We examine the long-term co-occurrence of long-tailed ducks (Clangula hyemalis) and white-winged scoters (Melanitta fusca) wintering at the Nantucket Shoals off Massachusetts, {USA}, and ask: (1) What oceanographic features attract these aggregations? (2) How are distributions of prey and sea ducks related to one another? and (3) What is the explanation for the spatial association between these two species? A winter concentration of long-tailed ducks on the order of 3 × 105 birds have been present near Nantucket Island and the Nantucket Shoals since the 1970s, and there is evidence of some concentration there since the late 1800s. Despite the difference in diet, the two duck species overlap in spatial distribution in relation to a prominent tidal front on the west side of Nantucket Shoals where nested swarms of pelagic amphipods and massive clam beds occur in persistent broadscale concentrations. Gammarid amphipods were collected seasonally by bongo tows over 39 yr (1977–2016), and Atlantic surf clams and ocean quahogs were collected by hydraulic dredge over a 34-yr timescale (1982–2016). Long-tailed ducks and white-winged scoters were counted during systematic low-level aerial surveys. Both long-tailed ducks and white-winged scoters associated with amphipod and clam aggregations at similar scales, and tracked amphipod and clam concentrations at larger spatial scales, up to 30 km. These multi-scalar nested associations suggest that the sea ducks foraged within a hierarchical patch system structured by the tidal regime, and concentrated in areas of spatially anchored recurring prey, with highest densities in southwest areas. Enhanced concentrations of prey within a relatively narrow zone on Nantucket Shoals provide a predictable food resource to wintering sea ducks whose populations are in decline. As supported by our generalized additive models, we propose that the positive spatial associations among these species are at least partly explained by local enhancement or facilitation, whereby each species of duck derives foraging benefit from noting the location of aggregations of the other. This interaction will be important to the designation of marine protected areas.},
	pages = {e03002},
	number = {1},
	journaltitle = {Ecosphere},
	author = {White, Timothy P. and Veit, Richard R.},
	urldate = {2024-02-08},
	date = {2020},
	langid = {english},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3002},
	keywords = {aerial surveys, Atlantic Ocean, ecotone, feeding ecology, local enhancement, long-tailed duck, Nantucket Shoals, sea duck, spatial anchor, spatial synchrony, white-winged scoter},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\LV4G6RYG\\White and Veit - 2020 - Spatial ecology of long-tailed ducks and white-win.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\G7NMQQJE\\ecs2.html:text/html},
}

@article{friedland_spatial_2023,
	title = {The spatial correlation between trawl surveys and planned wind energy infrastructure on the {US} Northeast Continental Shelf},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsad167},
	doi = {10.1093/icesjms/fsad167},
	abstract = {The development of wind energy on the {US} Northeast Continental Shelf ({NES}) may preclude resource-monitoring programmes from continuing in their original study designs. We considered the spatial requirements of energy developers and the spatial autocorrelation of resident species as a means to inform survey mitigation. The spatial requirements of the {NES} wind industry were considered in respect to the delineation of settled lease areas. We suggest access metrics ranging from 8 to 21 km representing the interquartile range of chord distances across the settled lease areas. Using survey data and concentrating on commercial species with stock assessment requirements, we computed indices of spatial autocorrelation. Tests of spatial autocorrelation using Moran’s I and join counts statistics were significant (p \< 0.05) for most species, suggesting a high level of spatial correlation in their distributions. To characterize a scalar extent of spatial correlation, variograms were fit to estimate the physical range of correlated catches. These data suggest most species were spatially correlated well beyond the distance metrics derived from the lease area shapes. Sampling by a range of gears has the potential of producing spatially accurate depictions of species distributions and abundance despite the restrictions wind lease areas may place on sampling designs.},
	pages = {fsad167},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} Journal of Marine Science},
	author = {Friedland, K D and Boucher, J M and Jones, A W and Methratta, E T and Morse, R E and Foley, C and Rago, P J},
	urldate = {2024-02-08},
	date = {2023-11-02},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\XWCCSMF7\\Friedland et al. - 2023 - The spatial correlation between trawl surveys and .pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\5A6ZY3WU\\7337020.html:text/html},
}

@online{casault_optical_2002,
	title = {Optical, chemical, and biological oceanographic conditions on the Scotian Shelf and in the eastern Gulf of Maine during 2020 / B. Casault, C. Johnson, E. Devred, E. Head, L. Beazley, and J. Spry.: Fs70-5/2022-018E-{PDF} - Government of Canada Publications - Canada.ca},
	url = {https://publications.gc.ca/site/eng/9.909043/publication.html},
	shorttitle = {Optical, chemical, and biological oceanographic conditions on the Scotian Shelf and in the eastern Gulf of Maine during 2020 / B. Casault, C. Johnson, E. Devred, E. Head, L. Beazley, and J. Spry.},
	abstract = {Publication information / bibliographic Record.},
	author = {Casault, B and Johnson, C and Devred, E and Head, E and Beazley, L and Spry, J},
	urldate = {2024-02-08},
	date = {2002-07-01},
	note = {Last Modified: 2013-04-03},
	file = {Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\E8JS4SVF\\publication.html:text/html},
}

@article{pershing_interdecadal_2005,
	title = {Interdecadal variability in the Gulf of Maine zooplankton community, with potential impacts on fish recruitment},
	volume = {62},
	issn = {1054-3139},
	url = {https://doi.org/10.1016/j.icesjms.2005.04.025},
	doi = {10.1016/j.icesjms.2005.04.025},
	abstract = {We used principal component analysis ({PCA}) to explore interannual changes in a time-series lasting more than 40 years of zooplankton abundance from {NOAA}'s Continuous Plankton Recorder ({CPR}) survey. This analysis identified a complex of taxa, including Centropages typicus, Oithona spp., Pseudocalanus spp., and Metridia lucens that followed a common pattern of interdecadal variability characterized by a dramatic increase in these taxa around 1990, followed by a rapid decline in 2002. All of these taxa showed a large proportional increase in winter abundance between the 1980s and 1990s. These changes could be driven by increased primary productivity during winter, caused by a large-scale freshening of the Northwest Atlantic Shelf. In addition to the “community shift” mode, the analysis found a strong mode of interannual variability attributed to previously described changes in the abundance of late-stage Calanus finmarchicus. To explore the impact of these modes on higher trophic levels, we correlated the zooplankton modes with recruitment time-series from 12 fish stocks from the Gulf of Maine region. Several significant correlations were found, suggesting that the changes in the zooplankton modes may reflect broad changes in the Gulf of Maine ecosystem.},
	pages = {1511--1523},
	number = {7},
	journaltitle = {{ICES} Journal of Marine Science},
	shortjournal = {{ICES} Journal of Marine Science},
	author = {Pershing, Andrew J. and Greene, Charles H. and Jossi, Jack W. and O'Brien, Loretta and Brodziak, Jon K.T. and Bailey, Barbara A.},
	urldate = {2024-02-08},
	date = {2005-01-01},
	file = {Full Text PDF:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\7YXWS5R5\\Pershing et al. - 2005 - Interdecadal variability in the Gulf of Maine zoop.pdf:application/pdf;Snapshot:C\:\\Users\\joseph.caracappa\\Zotero\\storage\\KQTELFTV\\661385.html:text/html},
}