SOE2024.bib

@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.},
	language = {en},
	number = {11},
	urldate = {2020-05-18},
	journal = {Journal of Geophysical Research: Oceans},
	author = {Chen, Zhuomin and Curchitser, Enrique and Chant, Robert and Kang, Dujuan},
	month = nov,
	year = {2018},
	pages = {8203--8226},
	file = {Chen et al. - 2018 - Seasonal Variability of the Cold Pool Over the Mid.pdf:/Users/sarah.gaichas/Zotero/storage/RMRTQTZZ/Chen et al. - 2018 - Seasonal Variability of the Cold Pool Over the Mid.pdf:application/pdf},
}

@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.},
	number = {8},
	urldate = {2020-02-10},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Miller, Timothy J. and Hare, Jonathan A. and Alade, Larry A.},
	month = feb,
	year = {2016},
	pages = {1261--1270},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/HY7V7MFA/Miller et al. - 2016 - A state-space approach to incorporating environmen.pdf:application/pdf;NRC Research Press Snapshot:/Users/sarah.gaichas/Zotero/storage/Y3RJFS5U/cjfas-2015-0339.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/S2NZ8UBY/cjfas-2015-0339.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.},
	language = {en},
	number = {4},
	urldate = {2016-10-14},
	journal = {ICES Journal of Marine Science: Journal du Conseil},
	author = {Large, Scott I. and Fay, Gavin and Friedland, Kevin D. and Link, Jason S.},
	month = jul,
	year = {2013},
	keywords = {Ecosystem-based management, decision criteria, generalized additive model, overfishing, reference points},
	pages = {755--767},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/NKANJHZJ/Large et al. - 2013 - Defining trends and thresholds in responses of eco.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/2A25WVNM/Large et al. - 2013 - Defining trends and thresholds in responses of eco.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/M4RB8SDX/755.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/XABY5GNU/727721.html:text/html},
}

@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},
	shorttitle = {Comparing {Apples} to {Oranges}},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2017.00282/full},
	doi = {10.3389/fmars.2017.00282},
	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.},
	language = {English},
	urldate = {2020-03-09},
	journal = {Frontiers in Marine Science},
	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},
	year = {2017},
	note = {Publisher: Frontiers},
	keywords = {ecosystem-based management, anthropogenic and environmental pressures, comparative analysis, Ecological Indicators, Gradient forest, thresholds-based reference points},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/I9HPM25B/Tam et al. - 2017 - Comparing Apples to Oranges Common Trends and Thr.pdf:application/pdf},
}

@article{ekstrom_vulnerability_2015,
	title = {Vulnerability and adaptation of {US} shellfisheries to ocean acidification},
	volume = {5},
	copyright = {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.},
	language = {en},
	number = {3},
	urldate = {2020-03-06},
	journal = {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},
	month = mar,
	year = {2015},
	note = {Number: 3
Publisher: Nature Publishing Group},
	pages = {207--214},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/7RVRWE6M/nclimate2508.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},
	language = {en},
	number = {7},
	urldate = {2020-02-26},
	journal = {ICES Journal of Marine Science},
	author = {Hardison, Sean and Perretti, Charles T. and DePiper, Geret S. and Beet, Andrew},
	month = dec,
	year = {2019},
	pages = {2060--2069},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/K9VYWULK/Hardison et al. - 2019 - A simulation study of trend detection methods for .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/PXVVQDNK/5512306.html:text/html},
}

@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.},
	language = {en},
	urldate = {2020-02-24},
	journal = {Fisheries Research},
	author = {Thorson, James T.},
	month = feb,
	year = {2019},
	keywords = {Distribution shift, Climate vulnerability analysis, Habitat assessment, Index standardization, Integrated ecosystem assessment, Spatio-temporal model, Stock assessment, VAST},
	pages = {143--161},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/38KBWBLZ/Thorson - 2019 - Guidance for decisions using the Vector Autoregres.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/85BILR75/S0165783618302820.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.},
	journal = {Journal of Northwest Atlantic Fishery Science},
	author = {Steimle, Frank and Terranova, Russell},
	month = dec,
	year = {1985},
	file = {Full Text:/Users/sarah.gaichas/Zotero/storage/YKY3WCL9/Jr and Terranova - 1985 - Energy Equivalents of Marine Organisms from the Co.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},
	shorttitle = {Important prey species of marine vertebrate predators in the northwest {Atlantic}},
	url = {https://www.jstor.org/stable/24825521},
	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.},
	urldate = {2020-02-13},
	journal = {Marine Ecology Progress Series},
	author = {Lawson, John W. and Magalhães, Alexandra M. and Miller, Edward H.},
	year = {1998},
	pages = {13--20},
}

@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.},
	language = {en},
	urldate = {2020-02-10},
	journal = {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},
	month = feb,
	year = {2016},
	pages = {227--238},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/UW3BIFJA/Hobday et al. - 2016 - A hierarchical approach to defining marine heatwav.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/724JB4BP/S0079661116000057.html:text/html},
}

@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},
	shorttitle = {Fisheries {Management} in a {Changing} {Climate}},
	url = {https://tos.org/oceanography/article/fisheries-management-in-a-changing-climate-lessonsfrom-the-2012-ocean-heat-},
	doi = {10.5670/oceanog.2013.27},
	number = {2},
	urldate = {2020-02-10},
	journal = {Oceanography},
	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},
	year = {2013},
	file = {Full Text:/Users/sarah.gaichas/Zotero/storage/JBYYTH8F/Mills et al. - 2013 - Fisheries Management in a Changing Climate Lesson.pdf:application/pdf},
}

@article{gangopadhyay_observed_2019,
	title = {An {Observed} {Regime} {Shift} in the {Formation} of {Warm} {Core} {Rings} from the {Gulf} {Stream}},
	volume = {9},
	copyright = {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.},
	language = {en},
	number = {1},
	urldate = {2020-02-10},
	journal = {Scientific Reports},
	author = {Gangopadhyay, Avijit and Gawarkiewicz, Glen and Silva, E. Nishchitha S. and Monim, M. and Clark, Jenifer},
	month = aug,
	year = {2019},
	pages = {1--9},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/V9GUKHJ2/Gangopadhyay et al. - 2019 - An Observed Regime Shift in the Formation of Warm .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/XKY6AXDH/s41598-019-48661-9.html:text/html},
}

@article{andres_recent_2016,
	title = {On the recent destabilization of the {Gulf} {Stream} path downstream of {Cape} {Hatteras}},
	volume = {43},
	copyright = {©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.},
	language = {en},
	number = {18},
	urldate = {2020-02-10},
	journal = {Geophysical Research Letters},
	author = {Andres, M.},
	year = {2016},
	keywords = {altimetry, Cape Hatteras, Deep Western Boundary Current, Gulf Stream, Line W, Middle Atlantic Bight},
	pages = {9836--9842},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/PVGJKP38/Andres - 2016 - On the recent destabilization of the Gulf Stream p.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/3LWGYCLV/2016GL069966.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},
	number = {1},
	urldate = {2020-02-10},
	journal = {Oceanography},
	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},
	month = mar,
	year = {2018},
	pages = {60--70},
	file = {Full Text:/Users/sarah.gaichas/Zotero/storage/KCUJZ87P/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.},
	language = {en},
	urldate = {2020-02-07},
	journal = {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.},
	month = feb,
	year = {2020},
	keywords = {Biodiversity, Habitat, Niche overlap, Species distribution model, Species interactions},
	pages = {135270},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/UYUTBJLT/S0048969719352623.html:text/html},
}

@article{large_quantifying_2015,
	title = {Quantifying {Patterns} of {Change} in {Marine} {Ecosystem} {Response} to {Multiple} {Pressures}: e0119922},
	volume = {10},
	copyright = {© 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},
	shorttitle = {Quantifying {Patterns} of {Change} in {Marine} {Ecosystem} {Response} to {Multiple} {Pressures}},
	url = {http://search.proquest.com/docview/1664222461/abstract/120C1207C54548BEPQ/1},
	doi = {http://dx.doi.org/10.1371/journal.pone.0119922},
	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.},
	language = {English},
	number = {3},
	urldate = {2016-10-14},
	journal = {PLoS One},
	author = {Large, Scott I. and Fay, Gavin and Friedland, Kevin D. and Link, Jason S.},
	month = mar,
	year = {2015},
	keywords = {fish, Ecosystems, Fisheries management, Decision making, Forests, Medical Sciences, Sciences: Comprehensive Works, Variables},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/AWK68SN8/Large et al. - 2015 - Quantifying Patterns of Change in Marine Ecosystem.pdf:application/pdf},
}

@article{zador_ecosystem_2016,
	title = {Ecosystem considerations in {Alaska}: the value of qualitative assessments},
	copyright = {All rights reserved},
	issn = {1054-3139, 1095-9289},
	shorttitle = {Ecosystem considerations in {Alaska}},
	url = {http://icesjms.oxfordjournals.org/content/early/2016/09/12/icesjms.fsw144},
	doi = {10.1093/icesjms/fsw144},
	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.},
	language = {en},
	urldate = {2016-09-24},
	journal = {ICES Journal of Marine Science: Journal du Conseil},
	author = {Zador, Stephani G. and Holsman, Kirstin K. and Aydin, Kerim Y. and Gaichas, Sarah K.},
	month = aug,
	year = {2016},
	keywords = {ecosystem approach to fisheries, Ecosystem-based fisheries management, Alaska, ecosystem assessment, ecosystem report cards.},
	pages = {fsw144},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/JJZXNRER/Zador et al. - 2016 - Ecosystem considerations in Alaska the value of q.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/X6FWF5F7/icesjms.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.},
	language = {en},
	number = {2},
	urldate = {2016-04-26},
	journal = {Ecological Applications},
	author = {Smith, Laurel A. and Link, Jason S. and Cadrin, Steven X. and Palka, Debra L.},
	month = mar,
	year = {2015},
	keywords = {conservation, competition, ecosystem modeling, Atlantic Ocean, commercial fisheries, consumption estimates, energetics, marine mammal diets, Northeast U.S. shelf, uncertainty estimation},
	pages = {373--389},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/CKAGDWQI/abstract.html:text/html},
}

@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.},
	number = {2},
	urldate = {2016-03-01},
	journal = {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.},
	month = feb,
	year = {2016},
	keywords = {climate change, Fisheries, ocean temperature, Marine ecology, Marine fish, Habitats, Invertebrates, Oceans},
	pages = {e0146756},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/S8WFBK9W/Hare et al. - 2016 - A Vulnerability Assessment of Fish and Invertebrat.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/7UQ3W35C/article.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.},
	language = {en},
	number = {1},
	urldate = {2019-02-14},
	journal = {PLOS ONE},
	author = {Bi, Hongsheng and Ji, Rubao and Liu, Hui and Jo, Young-Heon and Hare, Jonathan A.},
	month = jan,
	year = {2014},
	keywords = {Ecosystems, Maine, Seasons, Copepods, Sea water, Seasonal variations, Time series analysis, Zooplankton},
	pages = {e87720},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/R8SQIEC6/Bi et al. - 2014 - Decadal Changes in Zooplankton of the Northeast U..pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/PSKBJXRV/article.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.},
	language = {en},
	urldate = {2019-02-14},
	journal = {Journal of Marine Systems},
	author = {Morse, R.E. and Friedland, K.D. and Tommasi, D. and Stock, C. and Nye, J.},
	month = jan,
	year = {2017},
	keywords = {Climate, Marine ecology, Seasonal variations, Zooplankton, Community composition, Long-term changes},
	pages = {77--91},
	file = {Morse et al. - 2017 - Distinct zooplankton regime shift patterns across .pdf:/Users/sarah.gaichas/Zotero/storage/TDQERQ57/Morse et al. - 2017 - Distinct zooplankton regime shift patterns across .pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/IYMQRUU7/S0924796316303098.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},
	shorttitle = {Chesapeake {Bay}'s water quality condition has been recovering},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969718316577},
	doi = {10.1016/j.scitotenv.2018.05.025},
	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.},
	urldate = {2019-02-14},
	journal = {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.},
	month = oct,
	year = {2018},
	keywords = {Chesapeake Bay, Chlorophyll-a, Dissolved oxygen, Monitoring and assessment, Trends, Water quality standards},
	pages = {1617--1625},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/CD6GRNSX/S0048969718316577.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.},
	language = {en},
	number = {21},
	urldate = {2019-02-14},
	journal = {Ecology and Evolution},
	author = {Pace, Richard M. and Corkeron, Peter J. and Kraus, Scott D.},
	year = {2017},
	keywords = {Bayesian mark–recapture, Eubalaena glacialis, open population abundance, recovery, survival},
	pages = {8730--8741},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/A4VT9XMR/Pace et al. - 2017 - State–space mark–recapture estimates reveal a rece.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/LWCWLW67/ece3.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.},
	language = {en},
	number = {3},
	urldate = {2019-02-14},
	journal = {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},
	year = {2013},
	pages = {803--816},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/KUWBMTU5/Greene et al. - 2013 - Remote climate forcing of decadal-scale regime shi.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/3ZFCWSAD/lo.2013.58.3.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},
	language = {en},
	number = {1},
	urldate = {2019-02-14},
	journal = {Nature Communications},
	author = {Goddard, Paul B. and Yin, Jianjun and Griffies, Stephen M. and Zhang, Shaoqing},
	month = dec,
	year = {2015},
	file = {Goddard et al. - 2015 - An extreme event of sea-level rise along the North.pdf:/Users/sarah.gaichas/Zotero/storage/B8N7BZRI/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.},
	number = {8},
	urldate = {2019-02-14},
	journal = {Journal of Physical Oceanography},
	author = {Zhang, Rong and Vallis, Geoffrey K.},
	month = aug,
	year = {2007},
	pages = {2053--2080},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/LXHW7PVZ/Zhang and Vallis - 2007 - The Role of Bottom Vortex Stretching on the Path o.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/N3M8DP4V/JPO3102.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.},
	language = {en},
	number = {6},
	urldate = {2018-12-10},
	journal = {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.},
	month = jun,
	year = {2017},
	keywords = {ecosystem-based management, reference points, ecosystem indicator, ecosystem threshold, nonlinear},
	pages = {e01860},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/BJNWDPWU/Samhouri et al. - 2017 - Defining ecosystem thresholds for human activities.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/5JWAFBIJ/ecs2.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},
	urldate = {2021-03-02},
	author = {Drohan, Amy F and Manderson, John P and Packer, David B},
	year = {2007},
	file = {Essential fish habitat source document. Black sea bass, Centropristis striata, life history and habitat characteristics:/Users/sarah.gaichas/Zotero/storage/6GSXHRTS/4038.html:text/html},
}

@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{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.},
	number = {4},
	urldate = {2021-03-01},
	journal = {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},
	month = apr,
	year = {2016},
	pages = {274--284},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/H4EY9D7E/Kritzer et al. - 2016 - The Importance of Benthic Habitats for Coastal Fis.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/53YSHLZ6/2464081.html:text/html},
}

@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},
	copyright = {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 CO2-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 CO2 levels (partial pressure of CO2 in the seawater {\textasciitilde}0.15 kPa, seawater pH {\textasciitilde} 7.7). Within one month of incubation at elevated PCO2 and 15 °C hemolymph pH fell (pHe = 7.1 ± 0.2 (CO2-group) vs. 7.6 ± 0.1 (control)) and PeCO2 values in hemolymph increased (0.5 ± 0.2 kPa (CO2-group) vs. 0.2 ± 0.04 kPa (control)). Slightly but significantly elevated bicarbonate concentrations in the hemolymph of CO2-incubated oysters ([HCO-3]e = 1.8 ± 0.3 mM (CO2-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 CO2-exposed oysters were similar to controls. Upon acute warming SMR rose in both groups, but displayed a stronger increase in the CO2-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.},
	language = {en},
	number = {8},
	urldate = {2021-03-01},
	journal = {Marine Drugs},
	author = {Lannig, Gisela and Eilers, Silke and Pörtner, Hans O. and Sokolova, Inna M. and Bock, Christian},
	month = aug,
	year = {2010},
	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},
	pages = {2318--2339},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/Y4YTMSLZ/Lannig et al. - 2010 - Impact of Ocean Acidification on Energy Metabolism.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/CL757XXF/htm.html:text/html},
}

@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 CO2 concentrations. In this study, we examined the physiological response of Mytilus edulis from the Baltic Sea, grown for 2 months at 4 seawater pCO2 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 pCO2 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 pCO2 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 pCO2 and the highest rates (+60\%) at 243 Pa. \$\$ \{{\textbackslash}text\{NH\}\}\_\{4\}{\textasciicircum}\{ + \} \$\$excretion rose linearly with increasing pCO2. Decreased O:N ratios at the highest seawater pCO2 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.},
	language = {en},
	number = {12},
	urldate = {2021-03-01},
	journal = {Marine Biology},
	author = {Thomsen, Jörn and Melzner, Frank},
	month = dec,
	year = {2010},
	pages = {2667--2676},
}

@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 ρCO2 concentrations. Every two weeks, individuals were sampled for physiological measurements and scope for growth (SFG). In the high ρCO2 treatment, clearance rate decreased and excretion rate increased relative to the low ρCO2 treatment, resulting in reduced SFG. Moreover, oxygen:nitrogen (O:N) excretion ratio dropped, suggesting that a switch in metabolic strategy occurred. The medium ρCO2 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.},
	language = {en},
	urldate = {2021-03-01},
	journal = {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.},
	month = dec,
	year = {2020},
	keywords = {Bioenergetics, Atlantic surfclams, Ocean acidification, Bivalves, Scope for growth},
	pages = {111740},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/93QCS5XL/S0025326X20308584.html:text/html},
}

@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.},
	language = {en},
	number = {1},
	urldate = {2021-03-01},
	journal = {Journal of Mammalogy},
	author = {Wood, Stephanie A and Murray, Kimberly T and Josephson, Elizabeth and Gilbert, James},
	editor = {Swanson, Bradley},
	month = feb,
	year = {2020},
	pages = {121--128},
	file = {Wood et al. - 2020 - Rates of increase in gray seal (Halichoerus grypus.pdf:/Users/sarah.gaichas/Zotero/storage/9GA46GKJ/Wood et al. - 2020 - Rates of increase in gray seal (Halichoerus grypus.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},
	year = {2018},
}

@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.},
	language = {en},
	number = {2},
	urldate = {2021-03-01},
	journal = {Oceanography},
	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},
	month = jun,
	year = {2019},
	file = {Bigelow Laboratory for Ocean Sciences et al. - 2019 - Rapid Climate-Driven Circulation Changes Threaten .pdf:/Users/sarah.gaichas/Zotero/storage/FIASZHQ9/Bigelow Laboratory for Ocean Sciences et al. - 2019 - Rapid Climate-Driven Circulation Changes Threaten .pdf:application/pdf},
}

@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},
	shorttitle = {North {Atlantic} right whale ({Eubalaena} glacialis) and its food},
	url = {https://doi.org/10.1093/plankt/fbz044},
	doi = {10.1093/plankt/fbz044},
	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.},
	number = {5},
	urldate = {2021-03-01},
	journal = {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},
	month = sep,
	year = {2019},
	pages = {687--708},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/FBSFT4Z8/5583901.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.},
	language = {en},
	journal = {J. Aquat. Plant Manage.},
	author = {Rybicki, Nancy B and Carter, Virginia},
	year = {2002},
	pages = {8},
	file = {Rybicki and Carter - Light and Temperature Effects on the Growth of Wil.pdf:/Users/sarah.gaichas/Zotero/storage/WQA6NPEK/Rybicki and Carter - Light and Temperature Effects on the Growth of Wil.pdf:application/pdf},
}

@article{rome_linking_2005,
	series = {Proceedings of the 2003 {Blue} {Crab} {Symposium}},
	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},
	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.},
	language = {en},
	number = {1},
	urldate = {2021-02-26},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Rome, M. S. and Young-Williams, A. C. and Davis, G. R. and Hines, A. H.},
	month = jun,
	year = {2005},
	keywords = {Blue crab, Salinity tolerance, Temperature tolerance, Winter mortality},
	pages = {129--145},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/YD9N9VAI/S0022098105000249.html:text/html},
}

@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.},
	language = {en},
	urldate = {2021-02-26},
	journal = {Marine Ecology Progress Series},
	author = {North, Ew and Houde, Ed},
	year = {2003},
	pages = {219--236},
	file = {North and Houde - 2003 - Linking ETM physics, zooplankton prey, and fish ea.pdf:/Users/sarah.gaichas/Zotero/storage/ADVSSFV5/North and Houde - 2003 - Linking ETM physics, zooplankton prey, and fish ea.pdf:application/pdf},
}

@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.},
	urldate = {2021-02-26},
	journal = {Estuaries and Coasts},
	author = {Moore, Kenneth A. and Shields, Erin C. and Parrish, David B.},
	year = {2014},
	note = {Publisher: [Coastal and Estuarine Research Federation, Springer]},
	pages = {S20--S30},
}

@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.},
	number = {1},
	urldate = {2021-02-26},
	journal = {ICES Journal of Marine Science},
	author = {Millette, N C and Pierson, J J and North, E W},
	month = jan,
	year = {2020},
	pages = {300--314},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/QM669NKS/Millette et al. - 2020 - Water temperature during winter may control stripe.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/53ZUCJZ7/5638886.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},
	shorttitle = {Recruitment of striped bass in {Chesapeake} {Bay}},
	url = {https://www.jstor.org/stable/24873989},
	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.},
	urldate = {2021-02-26},
	journal = {Marine Ecology Progress Series},
	author = {Martino, E. J. and Houde, E. D.},
	year = {2010},
	note = {Publisher: Inter-Research Science Center},
	pages = {213--228},
}

@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},
	number = {1},
	urldate = {2021-02-26},
	journal = {North American Journal of Fisheries Management},
	author = {Kimmel, David G. and Tarnowski, Mitchell and Newell, Roger I. E.},
	month = jan,
	year = {2014},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/02755947.2013.830999},
	pages = {1--15},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/CKWGEXW3/02755947.2013.html:text/html},
}

@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},
	language = {en},
	urldate = {2021-02-26},
	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.},
	month = apr,
	year = {2011},
	pages = {109--127},
	file = {Hines et al. - 2011 - Predicting Effects of Climate Change on Blue Crabs.pdf:/Users/sarah.gaichas/Zotero/storage/342TSDNP/Hines et al. - 2011 - Predicting Effects of Climate Change on Blue Crabs.pdf:application/pdf},
}

@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.},
	number = {3},
	urldate = {2021-02-26},
	journal = {Estuaries and Coasts},
	author = {Bauer, Laurie J. and Miller, Thomas J.},
	year = {2010},
	note = {Publisher: Coastal and Estuarine Research Federation},
	pages = {668--677},
}

@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},
	year = {2021},
}

@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.},
	number = {2},
	urldate = {2021-02-26},
	journal = {Journal of Animal Ecology},
	author = {Le Cren, E. D.},
	year = {1951},
	note = {Publisher: [Wiley, British Ecological Society]},
	pages = {201--219},
	file = {Submitted Version:/Users/sarah.gaichas/Zotero/storage/5U3WNDCQ/Le Cren - 1951 - The Length-Weight Relationship and Seasonal Cycle .pdf:application/pdf},
}

@article{wrightfairbanks_autonomous_2020,
	title = {Autonomous {Observation} of {Seasonal} {Carbonate} {Chemistry} {Dynamics} in the {Mid}-{Atlantic} {Bight}},
	volume = {125},
	copyright = {©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.},
	language = {en},
	number = {11},
	urldate = {2021-02-26},
	journal = {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.},
	year = {2020},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020JC016505},
	keywords = {ocean acidification, autonomous underwater vehicle, carbonate system, glider, Mid-Atlantic Bight},
	pages = {e2020JC016505},
	annote = {e2020JC016505 2020JC016505},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/GGCVHT6T/Wright‐Fairbanks et al. - 2020 - Autonomous Observation of Seasonal Carbonate Chemi.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/RGXH5X2V/2020JC016505.html:text/html},
}

@article{pace_cryptic_2021,
	title = {Cryptic mortality of {North} {Atlantic} right whales},
	volume = {n/a},
	copyright = {© 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.},
	language = {en},
	number = {n/a},
	urldate = {2021-02-11},
	journal = {Conservation Science and Practice},
	author = {Pace, Richard M. and Williams, Rob and Kraus, Scott D. and Knowlton, Amy R. and Pettis, Heather M.},
	year = {2021},
	note = {\_eprint: https://conbio.onlinelibrary.wiley.com/doi/pdf/10.1111/csp2.346},
	keywords = {carcass detection, cryptic mortality, detection bias, right whale, total mortality},
	pages = {e346},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/KEYWRLI5/Pace et al. - Cryptic mortality of North Atlantic right whales.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/FT9UKRAA/csp2.html:text/html},
}

@article{link_global_2019,
	title = {Global ecosystem overfishing: {Clear} delineation within real limits to production},
	volume = {5},
	copyright = {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},
	shorttitle = {Global ecosystem overfishing},
	url = {https://advances.sciencemag.org/content/5/6/eaav0474},
	doi = {10.1126/sciadv.aav0474},
	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.},
	language = {en},
	number = {6},
	urldate = {2021-01-29},
	journal = {Science Advances},
	author = {Link, Jason S. and Watson, Reg A.},
	month = jun,
	year = {2019},
	note = {Publisher: American Association for the Advancement of Science
Section: Research Article},
	pages = {eaav0474},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/UIR8MFQU/Link and Watson - 2019 - Global ecosystem overfishing Clear delineation wi.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/J2I5GBKW/eaav0474.html:text/html},
}

@article{lucey_evaluating_2021,
	title = {Evaluating fishery management strategies using an ecosystem model as an operating model},
	volume = {234},
	copyright = {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.},
	language = {en},
	urldate = {2020-12-09},
	journal = {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},
	month = feb,
	year = {2021},
	pages = {105780},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/UE78XPGW/Lucey et al. - 2021 - Evaluating fishery management strategies using an .pdf:application/pdf;ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/3PKE6BVJ/Lucey et al. - 2021 - Evaluating fishery management strategies using an .pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/UJVBJ76E/S0165783620302976.html:text/html;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/FA8IQPMJ/S0165783620302976.html:text/html},
}

@article{lentz_seasonal_2017,
	title = {Seasonal warming of the {Middle} {Atlantic} {Bight} {Cold} {Pool}},
	volume = {122},
	copyright = {© 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.},
	language = {en},
	number = {2},
	urldate = {2020-05-18},
	journal = {Journal of Geophysical Research: Oceans},
	author = {Lentz, S. J.},
	year = {2017},
	note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2016JC012201},
	keywords = {Middle Atlantic Bight, Cold Pool, continental shelf circulation, seasonal cycle},
	pages = {941--954},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/FPC5VTLM/Lentz - 2017 - Seasonal warming of the Middle Atlantic Bight Cold.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/LU3YDZGX/Lentz - 2017 - Seasonal warming of the Middle Atlantic Bight Cold.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/ZCRWNJKN/2016JC012201.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/V86D682V/2016JC012201.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/DZ3PLK3V/2016JC012201.html:text/html},
}

@article{gaichas_implementing_2018,
	title = {Implementing {Ecosystem} {Approaches} to {Fishery} {Management}: {Risk} {Assessment} in the {US} {Mid}-{Atlantic}},
	volume = {5},
	copyright = {All rights reserved},
	issn = {2296-7745},
	shorttitle = {Implementing {Ecosystem} {Approaches} to {Fishery} {Management}},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2018.00442/abstract},
	doi = {10.3389/fmars.2018.00442},
	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.},
	language = {English},
	urldate = {2018-11-20},
	journal = {Frontiers in Marine Science},
	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.},
	year = {2018},
	keywords = {Fisheries, Ecosystem Approach, Risk Assessment, Economic indicators, Ecosystem indicators, Integrated Ecosystem Assessment, Management objectives, natural resource management},
	annote = {Publisher: Frontiers},
}

@article{depiper_operationalizing_2017,
	title = {Operationalizing integrated ecosystem assessments within a multidisciplinary team: lessons learned from a worked example},
	volume = {74},
	copyright = {All rights reserved},
	issn = {1054-3139},
	shorttitle = {Operationalizing integrated ecosystem assessments within a multidisciplinary team},
	url = {https://academic.oup.com/icesjms/article/74/8/2076/3094701},
	doi = {10.1093/icesjms/fsx038},
	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.},
	language = {en},
	number = {8},
	urldate = {2018-03-09},
	journal = {ICES Journal of Marine Science},
	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.},
	month = oct,
	year = {2017},
	pages = {2076--2086},
	annote = {Publisher: Oxford Academic},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/GXTCRDUK/DePiper et al. - 2017 - Operationalizing integrated ecosystem assessments .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/P7LIQAI9/3094701.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.},
	number = {1},
	urldate = {2021-04-16},
	journal = {Coastal Management},
	author = {Muffley, Brandon and Gaichas, Sarah and DePiper, Geret and Seagraves, Richard and Lucey, Sean},
	month = jan,
	year = {2021},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/08920753.2021.1846156},
	keywords = {integrated ecosystem assessment, fisheries, ecosystem indicators, ecosystem approach, risk assessment, conceptual modeling, economic indicators, management objectives},
	pages = {90--106},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/ESFUDR64/Muffley et al. - 2020 - There Is no I in EAFM Adapting Integrated Ecosyste.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/2P68VR5M/Muffley et al. - 2021 - There Is no I in EAFM Adapting Integrated Ecosyste.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/VF4GGSFW/Muffley et al. - 2021 - There Is no I in EAFM Adapting Integrated Ecosyste.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/VG86GU76/08920753.2021.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/LP9WGACM/08920753.2021.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/DGGMLV2B/08920753.2021.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/ZZDPZEK8/08920753.2021.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.},
	number = {1},
	urldate = {2021-04-16},
	journal = {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},
	month = jan,
	year = {2021},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/08920753.2021.1846155},
	keywords = {open science, IEA framwork, reproducilibity},
	pages = {72--89},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/A26QHF3L/Bastille et al. - 2020 - Improving the IEA Approach Using Principles of Ope.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/7SP7NEEF/Bastille et al. - 2021 - Improving the IEA Approach Using Principles of Ope.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/B8H6FHGA/08920753.2021.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/424UEWKL/08920753.2021.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.},
	language = {en},
	urldate = {2021-04-16},
	journal = {Ecological Modelling},
	author = {Lucey, Sean M. and Gaichas, Sarah K. and Aydin, Kerim Y.},
	month = jul,
	year = {2020},
	keywords = {Reproducibility, Ecosim, Rpath, Ecopath, R, Mass balance},
	pages = {109057},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/FFPCH5ZW/Lucey et al. - 2020 - Conducting reproducible ecosystem modeling using t.pdf:application/pdf;ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/AI3CQ579/Lucey et al. - 2020 - Conducting reproducible ecosystem modeling using t.pdf:application/pdf;ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/SDQ64VU7/Lucey et al. - 2020 - Conducting reproducible ecosystem modeling using t.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/WQXFX7KZ/S0304380020301290.html:text/html;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/P28ZCPZR/S0304380020301290.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},
	language = {en},
	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.},
	year = {2021},
	pages = {53--64},
	file = {U.S. Seafood Industry and For-Hire Sector Impacts .pdf:/Users/sarah.gaichas/Zotero/storage/8C5GASKX/U.S. Seafood Industry and For-Hire Sector Impacts .pdf:application/pdf},
}

@article{goncalves_neto_changes_2021,
	title = {Changes in the {Gulf} {Stream} preceded rapid warming of the {Northwest} {Atlantic} {Shelf}},
	volume = {2},
	copyright = {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.},
	language = {en},
	number = {1},
	urldate = {2022-02-10},
	journal = {Communications Earth \& Environment},
	author = {Gonçalves Neto, Afonso and Langan, Joseph A. and Palter, Jaime B.},
	month = apr,
	year = {2021},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Climate-change impacts, Environmental impact, Physical oceanography},
	pages = {1--10},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/4QQQBVAB/Gonçalves Neto et al. - 2021 - Changes in the Gulf Stream preceded rapid warming .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/FN7STBTP/s43247-021-00143-5.html:text/html},
}

@article{silver_interannual_2021,
	title = {Interannual and seasonal asymmetries in {Gulf} {Stream} {Ring} {Formations} from 1980 to 2019},
	volume = {11},
	copyright = {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.},
	language = {en},
	number = {1},
	urldate = {2022-02-10},
	journal = {Scientific Reports},
	author = {Silver, Adrienne and Gangopadhyay, Avijit and Gawarkiewicz, Glen and Silva, E. Nishchitha S. and Clark, Jenifer},
	month = jan,
	year = {2021},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Physical oceanography, Attribution},
	pages = {2207},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/56AU8VHG/Silver et al. - 2021 - Interannual and seasonal asymmetries in Gulf Strea.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/C3U6RB8I/s41598-021-81827-y.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.},
	language = {en},
	number = {8},
	urldate = {2022-02-10},
	journal = {Journal of Geophysical Research: Oceans},
	author = {Silver, Adrienne and Gangopadhyay, Avijit and Gawarkiewicz, Glen and Taylor, Arnold and Sanchez-Franks, Alejandra},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2021JC017614},
	keywords = {Gulf Stream, forecasting, AMOC, Azores high, Icelandic low, North Atlantic},
	pages = {e2021JC017614},
	annote = {e2021JC017614 2021JC017614},
	file = {Full Text:/Users/sarah.gaichas/Zotero/storage/9IKNAIDG/Silver et al. - 2021 - Forecasting the Gulf Stream Path Using Buoyancy an.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/SCCGAZII/2021JC017614.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},
	shorttitle = {A {Census} of the {Warm}-{Core} {Rings} of the {Gulf} {Stream}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2019JC016033},
	doi = {10.1029/2019JC016033},
	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.},
	language = {en},
	number = {8},
	urldate = {2022-02-10},
	journal = {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},
	year = {2020},
	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},
	pages = {e2019JC016033},
	annote = {e2019JC016033 2019JC016033},
	file = {Accepted Version:/Users/sarah.gaichas/Zotero/storage/TKJI5EP7/Gangopadhyay et al. - 2020 - A Census of the Warm-Core Rings of the Gulf Stream.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/KUTQ86RB/2019JC016033.html:text/html},
}

@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},
	shorttitle = {The {Middle} {Atlantic} {Bight} {Cold} {Pool} is warming and shrinking},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12573},
	doi = {10.1111/fog.12573},
	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.},
	language = {en},
	number = {2},
	urldate = {2022-02-10},
	journal = {Fisheries Oceanography},
	author = {Friedland, Kevin D. and Miles, Travis and Goode, Andrew G. and Powell, Eric N. and Brady, Damian C.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/fog.12573},
	keywords = {ecosystem, climate change, regime shift, Cold Pool, temperature},
	pages = {217--223},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/A4RBZN9P/fog.html:text/html},
}

@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.},
	number = {1},
	journal = {Journal of Geophysical Research: Oceans},
	author = {Chen, Ke and Gawarkiewicz, Glen and Yang, Jiayan},
	year = {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},
	pages = {e2021JC017927},
	annote = {e2021JC017927 2021JC017927},
}

@article{miles_offshore_2021,
	title = {Offshore {Wind} {Energy} and the {Mid}-{Atlantic} {Cold} {Pool}: {A} {Review} of {Potential} {Interactions}},
	volume = {55},
	shorttitle = {Offshore {Wind} {Energy} and the {Mid}-{Atlantic} {Cold} {Pool}},
	doi = {10.4031/MTSJ.55.4.8},
	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.},
	number = {4},
	journal = {Marine Technology Society Journal},
	author = {Miles, Travis and Murphy, Sarah and Kohut, Josh and Borsetti, Sarah and Munroe, Daphne},
	month = jul,
	year = {2021},
	keywords = {Mid-Atlantic Cold Pool, ocean interactions, offshore wind},
	pages = {72--87},
}

@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.},
	urldate = {2022-02-10},
	journal = {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},
	year = {2019},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/R8A2CZQJ/Gawarkiewicz et al. - 2019 - Characteristics of an Advective Marine Heatwave in.pdf:application/pdf},
}

@article{caesar_observed_2018,
	title = {Observed fingerprint of a weakening {Atlantic} {Ocean} overturning circulation},
	volume = {556},
	copyright = {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 CMIP5 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.},
	language = {en},
	number = {7700},
	urldate = {2022-02-10},
	journal = {Nature},
	author = {Caesar, L. and Rahmstorf, S. and Robinson, A. and Feulner, G. and Saba, V.},
	month = apr,
	year = {2018},
	note = {Number: 7700
Publisher: Nature Publishing Group},
	keywords = {Physical oceanography, Climate and Earth system modelling, Ocean sciences},
	pages = {191--196},
	file = {Accepted Version:/Users/sarah.gaichas/Zotero/storage/C89JH8MT/Caesar et al. - 2018 - Observed fingerprint of a weakening Atlantic Ocean.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/Z4T8QZRB/s41586-018-0006-5.html:text/html},
}

@article{caesar_current_2021,
	title = {Current {Atlantic} {Meridional} {Overturning} {Circulation} weakest in last millennium},
	volume = {14},
	copyright = {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.},
	language = {en},
	number = {3},
	urldate = {2022-02-10},
	journal = {Nature Geoscience},
	author = {Caesar, L. and McCarthy, G. D. and Thornalley, D. J. R. and Cahill, N. and Rahmstorf, S.},
	month = mar,
	year = {2021},
	note = {Number: 3
Publisher: Nature Publishing Group},
	keywords = {Climate change, Physical oceanography, Palaeoclimate},
	pages = {118--120},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/ZR5AD6YN/s41561-021-00699-z.html:text/html;Submitted Version:/Users/sarah.gaichas/Zotero/storage/W5YHDCL8/Caesar et al. - 2021 - Current Atlantic Meridional Overturning Circulatio.pdf:application/pdf},
}

@article{worm_predator_2003,
	title = {Predator diversity hotspots in the blue ocean},
	volume = {100},
	copyright = {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.},
	language = {en},
	number = {17},
	urldate = {2022-02-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Worm, Boris and Lotze, Heike K. and Myers, Ransom A.},
	month = aug,
	year = {2003},
	pmid = {12907699},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	pages = {9884--9888},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/I8KBR4UW/Worm et al. - 2003 - Predator diversity hotspots in the blue ocean.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/BXQXF25L/9884.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.},
	language = {en},
	number = {3},
	urldate = {2022-02-10},
	journal = {Marine Biology},
	author = {Potter, Inga F. and Galuardi, Benjamin and Howell, W. Huntting},
	month = mar,
	year = {2011},
	pages = {531--540},
	file = {Springer Full Text PDF:/Users/sarah.gaichas/Zotero/storage/WUH56KHX/Potter et al. - 2011 - Horizontal movement of ocean sunfish, Mola mola, i.pdf:application/pdf},
}

@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},
	shorttitle = {Periodic swarms of the salp {Salpa} aspera in the {Slope} {Water} off the {NE} {United} {States}},
	url = {https://www.sciencedirect.com/science/article/pii/S0967063706000173},
	doi = {10.1016/j.dsr.2005.12.018},
	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.},
	language = {en},
	number = {5},
	urldate = {2022-02-10},
	journal = {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.},
	month = may,
	year = {2006},
	keywords = {Zooplankton, Atlantic Slope Water, Grazing, Salps, Vertical flux, Vertical migration},
	pages = {804--819},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/8MI4ES7W/S0967063706000173.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},
	language = {en},
	number = {12},
	urldate = {2022-02-10},
	journal = {Journal of Plankton Research},
	author = {Deibel, D. and Paffenhofer, G.-A.},
	month = dec,
	year = {2009},
	pages = {1571--1579},
	file = {Deibel and Paffenhofer - 2009 - Predictability of patches of neritic salps and dol.pdf:/Users/sarah.gaichas/Zotero/storage/NMP7TYMM/Deibel and Paffenhofer - 2009 - Predictability of patches of neritic salps and dol.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},
	shorttitle = {The {Savory} {Swimmer} {Swims} {North}},
	url = {https://doi.org/10.1163/1937240X-00002293},
	doi = {10.1163/1937240X-00002293},
	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.},
	number = {1},
	urldate = {2022-02-10},
	journal = {Journal of Crustacean Biology},
	author = {Johnson, David Samuel},
	month = jan,
	year = {2015},
	pages = {105--110},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/W7GI9Y3Y/Johnson - 2015 - The Savory Swimmer Swims North A Northern Range E.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/E72LINS9/2547817.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.},
	language = {en},
	urldate = {2022-02-10},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Pace, Sara M. and Powell, Eric N. and Mann, Roger},
	month = jun,
	year = {2018},
	keywords = {Climate change, Growth, Little Ice Age, Ocean quahog},
	pages = {8--22},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/Q3AYIQB6/S0022098117303568.html:text/html},
}

@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},
	shorttitle = {Ocean quahogs ({Arctica} islandica) and {Atlantic} surfclams ({Spisula} solidissima) on the {Mid}-{Atlantic} {Bight} continental shelf and {Georges} {Bank}},
	url = {https://www.sciencedirect.com/science/article/pii/S0031018218309118},
	doi = {10.1016/j.palaeo.2019.05.027},
	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.},
	language = {en},
	urldate = {2022-02-10},
	journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
	author = {Powell, Eric N. and Ewing, Anja M. and Kuykendall, Kelsey M.},
	month = jan,
	year = {2020},
	keywords = {Conservation paleobiology, Geographic distribution, Live-dead comparison, Range shift, Spatial time averaging, Species interaction},
	pages = {109205},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/4WR9VCIV/S0031018218309118.html:text/html},
}

@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.},
	language = {en},
	urldate = {2022-02-10},
	journal = {Marine Ecology Progress Series},
	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},
	month = jul,
	year = {2017},
	pages = {1--11},
	file = {Perretti et al. - 2017 - Regime shifts in fish recruitment on the Northeast.pdf:/Users/sarah.gaichas/Zotero/storage/7QCFZSR9/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:/Users/sarah.gaichas/Zotero/storage/XF3MPALT/Perretti et al. - 2017 - Regime shifts in fish recruitment on the Northeast.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},
	urldate = {2022-02-11},
	author = {BOEM},
	year = {2020},
	file = {Vineyard-Wind-1-Supplement-to-EIS.pdf:/Users/sarah.gaichas/Zotero/storage/QH37WLK6/Vineyard-Wind-1-Supplement-to-EIS.pdf:application/pdf},
}

@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.},
	language = {en},
	number = {12},
	urldate = {2022-03-02},
	journal = {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.},
	month = dec,
	year = {2021},
	note = {Publisher: Public Library of Science},
	keywords = {Climate change, Marine fish, Habitats, Anthropogenic climate change, Reefs, Surface water, Water columns, Wetlands},
	pages = {e0260654},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/NQ86SN57/Farr et al. - 2021 - An assessment of marine, estuarine, and riverine h.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/N6KWY7VL/article.html:text/html},
}

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

@article{du_pontavice_incorporating_nodate,
	title = {Incorporating environmental effects from ocean models improves a marine fish stock assessment},
	journal = {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{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},
	number = {9},
	urldate = {2022-03-09},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	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.},
	month = sep,
	year = {2009},
	note = {Publisher: NRC Research Press},
	pages = {1399--1403},
	file = {Submitted Version:/Users/sarah.gaichas/Zotero/storage/T4XCQXRH/Schick et al. - 2009 - Striking the right balance in right whale conserva.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.},
	language = {en},
	urldate = {2022-03-09},
	journal = {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.},
	month = jul,
	year = {2021},
	keywords = {Aerial surveys, Alternative energy, Migratory species},
	pages = {251--268},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/RRMM4GX9/Quintana-Rizzo et al. - 2021 - Residency, demographics, and movement patterns of .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/JULBB9SP/p251-268.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.},
	urldate = {2022-03-09},
	journal = {Frontiers in Marine Science},
	author = {Christiansen, Nils and Daewel, Ute and Djath, Bughsin and Schrum, Corinna},
	year = {2022},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/KM5GYFR5/Christiansen et al. - 2022 - Emergence of Large-Scale Hydrodynamic Structures D.pdf:application/pdf},
}

@article{depiper_learning_2021,
	title = {Learning by doing: collaborative conceptual modelling as a path forward in ecosystem-based management},
	volume = {78},
	issn = {1054-3139},
	shorttitle = {Learning by doing},
	url = {https://doi.org/10.1093/icesjms/fsab054},
	doi = {10.1093/icesjms/fsab054},
	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.},
	number = {4},
	urldate = {2022-08-08},
	journal = {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},
	month = aug,
	year = {2021},
	pages = {1217--1228},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/QNB5IWWH/DePiper et al. - 2021 - Learning by doing collaborative conceptual modell.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/32GVZRVC/6207633.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.},
	language = {en},
	number = {2},
	urldate = {2023-01-30},
	journal = {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.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/mcf2.10202},
	pages = {e10202},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/XQCD9PFS/Frick et al. - 2022 - Spatiotemporal Variation in Distribution, Size, an.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/MX9PWRI2/mcf2.html:text/html},
}

@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 CO2 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.},
	language = {en},
	number = {10},
	urldate = {2023-02-06},
	journal = {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.},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/2015GB005198},
	keywords = {aragonite saturation state, climatology, global oceans, ocean acidification, omega, pH},
	pages = {1656--1673},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/6SFBIUYM/Jiang et al. - 2015 - Climatological distribution of aragonite saturatio.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/2KN4NMRR/Jiang et al. - 2015 - Climatological distribution of aragonite saturatio.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/L46HKRQ7/2015GB005198.html:text/html},
}

@article{jacox_thermal_2020,
	title = {Thermal displacement by marine heatwaves},
	volume = {584},
	copyright = {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 MHWs1,4,12,13. 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.},
	language = {en},
	number = {7819},
	urldate = {2023-02-07},
	journal = {Nature},
	author = {Jacox, Michael G. and Alexander, Michael A. and Bograd, Steven J. and Scott, James D.},
	month = aug,
	year = {2020},
	note = {Number: 7819
Publisher: Nature Publishing Group},
	keywords = {Environmental health, Natural hazards, Physical oceanography},
	pages = {82--86},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/RQH97E2F/Jacox et al. - 2020 - Thermal displacement by marine heatwaves.pdf:application/pdf},
}

@article{jacox_global_2022,
	title = {Global seasonal forecasts of marine heatwaves},
	volume = {604},
	copyright = {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 MHWs11,12, 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.},
	language = {en},
	number = {7906},
	urldate = {2023-02-07},
	journal = {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},
	month = apr,
	year = {2022},
	note = {Number: 7906
Publisher: Nature Publishing Group},
	keywords = {Natural hazards, Physical oceanography},
	pages = {486--490},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/72I4J7C5/Jacox et al. - 2022 - Global seasonal forecasts of marine heatwaves.pdf:application/pdf},
}

@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 pCO2 was used to describe ocean acidification (OA) effects on Atlantic surfclam, Spisula solidissima, bioenergetics. Effects of elevated pCO2 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 pCO2 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.},
	language = {en},
	urldate = {2023-02-07},
	journal = {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.},
	month = may,
	year = {2022},
	keywords = {Atlantic surfclam, Climate change, Dynamic energy budget, Ocean acidification},
	pages = {105602},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/YL5CB4CJ/S0141113622000472.html:text/html},
}

@article{northeast_fisheries_science_center_us_noaa_2022,
	series = {{NOAA} technical memorandum {NMFS}-{NE} ; 292},
	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},
	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.)}},
	year = {2022},
	keywords = {Effect of wind power plants on, Fish surveys},
	annote = {SeriesInformation
NOAA technical memorandum NMFS-NE ; 292},
}

@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.},
	language = {en},
	urldate = {2023-02-09},
	journal = {Advances in Atmospheric Sciences},
	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},
	month = jan,
	year = {2023},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/35F3FL8P/Cheng et al. - 2023 - Another Year of Record Heat for the Oceans.pdf:application/pdf},
}

@incollection{intergovernmental_panel_on_climate_change_ipcc_technical_2022,
	address = {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},
	urldate = {2023-02-09},
	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)}},
	year = {2022},
	doi = {10.1017/9781009157964.002},
	pages = {39--70},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/YTYETR2P/Intergovernmental Panel on Climate Change (IPCC) - 2022 - Technical Summary.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/LI7W69HX/3428BF3C6ADE0C52755DBC3AA5CFE48B.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},
	shorttitle = {Impacts of ocean acidification on marine organisms},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.12179},
	doi = {10.1111/gcb.12179},
	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.},
	language = {en},
	number = {6},
	urldate = {2023-02-09},
	journal = {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},
	year = {2013},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.12179},
	keywords = {calcification, carbonate chemistry, climate change, cumulative effects, pH},
	pages = {1884--1896},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/2BGEGWQI/Kroeker et al. - 2013 - Impacts of ocean acidification on marine organisms.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/MXQBVCPU/gcb.html:text/html},
}

@article{cameron_effects_2022,
	title = {Effects of elevated {pCO2} 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 CO2-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 pCO2 and temperature (pCO2 = 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 pCO2, and mortality occurred when elevated pCO2 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 pCO2. Concentrations of dissolved inorganic carbon (DIC) and total alkalinity in the EPF increased above seawater concentrations in response to elevated pCO2. 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 [CO32−] under elevated pCO2 treatments. The combination of low respiration rates, high EPF [CO32−], and low calcification rates under elevated pCO2 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 pCO2 on scallop performance.},
	language = {en},
	number = {8},
	urldate = {2023-02-09},
	journal = {Limnology and Oceanography},
	author = {Cameron, Louise P. and Grabowski, Jonathan H. and Ries, Justin B.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/lno.12153},
	pages = {1670--1686},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/VYIDAN72/Cameron et al. - 2022 - Effects of elevated pCO2 and temperature on the ca.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/WZRTIW97/lno.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.},
	urldate = {2023-02-09},
	journal = {Frontiers in Physiology},
	author = {Zakroff, Casey J. and Mooney, T. Aran},
	year = {2020},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/78WTLYZM/Zakroff and Mooney - 2020 - Antagonistic Interactions and Clutch-Dependent Sen.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 pCO2 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 CO2. However, patterns of physiological response and energy management, based on comparisons of yolk consumption and growth, varied among trials. Interactions between pCO2 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.},
	language = {en},
	number = {5},
	urldate = {2023-02-09},
	journal = {Marine Biology},
	author = {Zakroff, Casey and Mooney, T. Aran and Berumen, Michael L.},
	month = apr,
	year = {2019},
	pages = {62},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/X66KNCAA/Zakroff et al. - 2019 - Dose-dependence and small-scale variability in res.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},
	shorttitle = {Detection of {Habitat} {Shifts} of {Cetacean} {Species}},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.877580},
	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.},
	urldate = {2023-02-09},
	journal = {Frontiers in Marine Science},
	author = {Chavez-Rosales, Samuel and Josephson, Elizabeth and Palka, Debra and Garrison, Lance},
	year = {2022},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/LUB7B7QK/Chavez-Rosales et al. - 2022 - Detection of Habitat Shifts of Cetacean Species A.pdf:application/pdf},
}

@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 CO2, 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.},
	language = {en},
	urldate = {2023-02-10},
	journal = {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},
	month = sep,
	year = {2019},
	pages = {106188},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/VE844TMQ/Saba et al. - 2019 - Recommended priorities for research on ecological .pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/7W96H8S8/S0272771418308710.html:text/html},
}

@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.},
	language = {en},
	number = {5},
	urldate = {2023-02-10},
	journal = {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.},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2021JC017187},
	keywords = {bottom temperature, Northeast U.S. shelf, seasonal prediction},
	pages = {e2021JC017187},
	annote = {e2021JC017187 2021JC017187},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/3L7WWQB4/Chen et al. - 2021 - Seasonal Prediction of Bottom Temperature on the N.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/N63FT62N/2021JC017187.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.},
	language = {en},
	number = {6},
	urldate = {2023-02-10},
	journal = {Fisheries Oceanography},
	author = {Schonfeld, Adena J. and Gartland, James and Latour, Robert J.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/fog.12611},
	keywords = {Chesapeake Bay, climate change, dynamic factor analysis, ecosystem exchange, quantitative fisheries ecology},
	pages = {615--628},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/CMPT9N65/Schonfeld et al. - 2022 - Spatial differences in estuarine utilization by se.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/9TR5LIA9/fog.html:text/html},
}

@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.},
	language = {en},
	urldate = {2023-02-10},
	journal = {Marine Ecology Progress Series},
	author = {Flanders, Kelly R. and Olson, Zachary H. and Ono, Kathryn A.},
	month = nov,
	year = {2020},
	keywords = {Diet, Foraging ecology, Grey seal, Halichoerus grypus, Molecular scatology, Next-generation sequencing, Prey DNA},
	pages = {227--240},
}

@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.},
	number = {11},
	urldate = {2023-02-10},
	journal = {Canadian Journal of Zoology},
	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.},
	month = nov,
	year = {2019},
	note = {Publisher: NRC Research Press},
	pages = {1071--1077},
}

@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.},
	language = {en},
	number = {4},
	urldate = {2023-02-10},
	journal = {Conservation Genetics Resources},
	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.},
	month = dec,
	year = {2019},
	pages = {481--485},
}

@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.},
	number = {4},
	urldate = {2023-02-10},
	journal = {Northeastern Naturalist},
	author = {McCosker, Christina and Flanders, Kelly and Ono, Kathryn and Dufault, Michelle and Mellone, Dominique and Olson, Zachary},
	month = nov,
	year = {2020},
	note = {Publisher: Eagle Hill Institute},
	pages = {681--700},
}

@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},
	journal = {Reports},
	author = {Fabrizio, Mary and Tuckey, Troy and Smith, Shannon and Ross, Paige and Snyder, Richard and Wang, Harry and Bever, Aaron},
	month = jan,
	year = {2022},
	file = {"Characterization of Nursery Habitats used by Black Sea Bass and Summer" by Mary C. Fabrizio, Troy D. Tuckey et al.:/Users/sarah.gaichas/Zotero/storage/ZX26PBBZ/2837.html:text/html},
}

@article{white_ducks_2020,
  author = {White, Timothy P. and Veit, Richard R.},
  title = {Spatial ecology of long-tailed ducks and white-winged scoters wintering on Nantucket Shoals},
  journal = {Ecosphere},
  volume = {11},
  number = {1},
  pages = {e03002},
  keywords = {aerial surveys, Atlantic Ocean, ecotone, feeding ecology, local enhancement, long-tailed duck, Nantucket Shoals, sea duck, spatial anchor, spatial synchrony, white-winged scoter},
  doi = {https://doi.org/10.1002/ecs2.3002},
  url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.3002},
  eprint = {https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3002},
  abstract = {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.},
  year = {2020}
}

@article{sorochan_narw_forage_2021,
    author = {Sorochan, K A and Plourde, S and Baumgartner, M F and Johnson, C L},
    title = "{Availability, supply, and aggregation of prey (Calanus spp.) in foraging areas of the North Atlantic right whale (Eubalaena glacialis)}",
    journal = {ICES Journal of Marine Science},
    volume = {78},
    number = {10},
    pages = {3498-3520},
    year = {2021},
    month = {10},
    abstract = "{The North Atlantic right whale (NARW), Eubalaena glacialis, resides primarily on western North Atlantic continental shelves where this endangered species is susceptible to vessel strike and entanglement in fishing gear. Mitigation of these threats is dependent on the ability to predict variations in NARW occurrence. North of the Mid-Atlantic Bight, the distribution of NARWs is influenced by their prey, mainly copepods of the genus Calanus. We review factors that promote suitable foraging habitat from areas where NARWs have been observed feeding. We then synthesize our findings within a conceptual framework in which availability (i.e. shallow prey depth), supply, and aggregation of prey occur together to facilitate suitable foraging habitat. By definition, the depth of prey on the shelf is constrained to ≤200 m and other mechanisms may occur locally that further enhance prey availability. Enhanced production of prey occurs in coastal currents, which transport the copepods to NARW foraging areas. Prey concentrating mechanisms are not well-characterized. Information gaps that impede rapid and dynamic prediction of suitable foraging habitat include limited data on the spatial and temporal variation of prey and environmental conditions at local scales (i.e. 0.1–1 km), motility of prey, and diving behaviour of NARWs.}",
    issn = {1054-3139},
    doi = {10.1093/icesjms/fsab200},
    url = {https://doi.org/10.1093/icesjms/fsab200},
    eprint = {https://academic.oup.com/icesjms/article-pdf/78/10/3498/41772910/fsab200.pdf},
}