FishDiet_EcoIndicators.bib

@article{tommasi_improved_2017,
	title = {Improved management of small pelagic fisheries through seasonal climate prediction},
	volume = {27},
	issn = {1939-5582},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/eap.1458},
	doi = {10.1002/eap.1458},
	abstract = {Populations of small pelagic fish are strongly influenced by climate. The inability of managers to anticipate environment-driven fluctuations in stock productivity or distribution can lead to overfishing and stock collapses, inflexible management regulations inducing shifts in the functional response to human predators, lost opportunities to harvest populations, bankruptcies in the fishing industry, and loss of resilience in the human food supply. Recent advances in dynamical global climate prediction systems allow for sea surface temperature (SST) anomaly predictions at a seasonal scale over many shelf ecosystems. Here we assess the utility of SST predictions at this “fishery relevant” scale to inform management, using Pacific sardine as a case study. The value of SST anomaly predictions to management was quantified under four harvest guidelines (HGs) differing in their level of integration of SST data and predictions. The HG that incorporated stock biomass forecasts informed by skillful SST predictions led to increases in stock biomass and yield, and reductions in the probability of yield and biomass falling below socioeconomic or ecologically acceptable levels. However, to mitigate the risk of collapse in the event of an erroneous forecast, it was important to combine such forecast-informed harvest controls with additional harvest restrictions at low biomass.},
	language = {en},
	number = {2},
	urldate = {2020-05-18},
	journal = {Ecological Applications},
	author = {Tommasi, Désirée and Stock, Charles A. and Pegion, Kathleen and Vecchi, Gabriel A. and Methot, Richard D. and Alexander, Michael A. and Checkley, David M.},
	year = {2017},
	note = {\_eprint: https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/eap.1458},
	keywords = {fisheries management, climate prediction, ecosystem-based management, forage fish, harvest guideline, Pacific sardine, seasonal forecast},
	pages = {378--388},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/AD8YAMF8/eap.html:text/html},
}

@article{essington_fishing_2015,
	title = {Fishing amplifies forage fish population collapses},
	volume = {112},
	copyright = {©  .           Freely available online through the PNAS open access option.},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/112/21/6648},
	doi = {10.1073/pnas.1422020112},
	abstract = {Forage fish support the largest fisheries in the world but also play key roles in marine food webs by transferring energy from plankton to upper trophic-level predators, such as large fish, seabirds, and marine mammals. Fishing can, thereby, have far reaching consequences on marine food webs unless safeguards are in place to avoid depleting forage fish to dangerously low levels, where dependent predators are most vulnerable. However, disentangling the contributions of fishing vs. natural processes on population dynamics has been difficult because of the sensitivity of these stocks to environmental conditions. Here, we overcome this difficulty by collating population time series for forage fish populations that account for nearly two-thirds of global catch of forage fish to identify the fingerprint of fisheries on their population dynamics. Forage fish population collapses shared a set of common and unique characteristics: high fishing pressure for several years before collapse, a sharp drop in natural population productivity, and a lagged response to reduce fishing pressure. Lagged response to natural productivity declines can sharply amplify the magnitude of naturally occurring population fluctuations. Finally, we show that the magnitude and frequency of collapses are greater than expected from natural productivity characteristics and therefore, likely attributed to fishing. The durations of collapses, however, were not different from those expected based on natural productivity shifts. A risk-based management scheme that reduces fishing when populations become scarce would protect forage fish and their predators from collapse with little effect on long-term average catches.},
	language = {en},
	number = {21},
	urldate = {2018-03-27},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Essington, Timothy E. and Moriarty, Pamela E. and Froehlich, Halley E. and Hodgson, Emma E. and Koehn, Laura E. and Oken, Kiva L. and Siple, Margaret C. and Stawitz, Christine C.},
	month = may,
	year = {2015},
	pmid = {25848018},
	keywords = {ecosystem-based management, Ecosystem-based management, Fisheries, fisheries, marine conservation, population collapse},
	pages = {6648--6652},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/S38BJQPF/Essington et al. - 2015 - Fishing amplifies forage fish population collapses.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/99A5RV7E/Essington et al. - 2015 - Fishing amplifies forage fish population collapses.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/D2N93NBC/Essington et al. - 2015 - Fishing amplifies forage fish population collapses.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/PYF7CV2B/6648.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/CH2Z5SHZ/6648.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{cury_small_2000,
	title = {Small pelagics in upwelling systems: patterns of interaction and structural changes in “wasp-waist” ecosystems},
	volume = {57},
	issn = {10543139},
	shorttitle = {Small pelagics in upwelling systems: patterns of interaction and structural changes in “wasp-waist” ecosystems},
	doi = {10.1006/jmsc.2000.0712},
	number = {3},
	journal = {ICES Journal of Marine Science},
	author = {Cury, P. and Bakun, A. and Crawford, R. J. M. and Jarre, A. and Quinones, R. A. and Shannon, L. J. and Verheye, H. M.},
	year = {2000},
	pages = {603--618},
}

@article{link_northeast_2008,
	title = {The {Northeast} {U}.{S}. continental shelf {Energy} {Modeling} and {Analysis} exercise ({EMAX}): {Ecological} network model development and basic ecosystem metrics},
	volume = {74},
	issn = {0924-7963},
	shorttitle = {The {Northeast} {U}.{S}. continental shelf {Energy} {Modeling} and {Analysis} exercise ({EMAX})},
	url = {http://www.sciencedirect.com/science/article/pii/S0924796308000560},
	doi = {10.1016/j.jmarsys.2008.03.007},
	abstract = {During the past half-century notable changes have occurred in the Northeast U.S. (NEUS) Continental Shelf Large Marine Ecosystem (LME). To understand how the system functions as a whole, to evaluate the potential responses of this ecosystem to numerous human-induced perturbations, and to elucidate the relative magnitude of key biota and processes, the Northeast Fisheries Science Center instituted the Energy Modeling and Analysis eXercise (EMAX). The primary goal of EMAX was to establish an ecological network model (i.e., a more nuanced energy budget) of the entire Northeast U.S. food web. The EMAX work focused on the interdisciplinary development of a network model which reflected contemporary conditions (1996–2000) in four major regions of the ecosystem:, Gulf of Maine, Georges Bank, Southern New England and Middle Atlantic Bight. The model had 36 network “nodes” or biomass state variables across a broad range of the biological hierarchy within each trophic level and incorporated a wide range of key rate processes. Because this ecosystem has been relatively well studied many of the biomass estimates were based on field measurements and biomass estimates from the scientific literature were required only for a relatively small number of nodes. The emphasis of EMAX was to explore the particular role of small pelagic fishes in the ecosystem. Our results show that small pelagic fishes are indeed keystone species in the ecosystem. We examined a suite of novel ecosystem metrics as we compared the four regions and provided a general, system-level description of the NEUS ecosystem. The general patterns of the network properties in the four regions were similar; however the network indices and metrics did reveal some noteworthy differences among regions reflecting their different oceanographic and faunal characteristics. The process of compiling and evaluating available data required by an ecosystem network model identified important gaps in our understanding which should be addressed during future ecosystem surveys. Moreover, exercises like EMAX will be a valuable starting point as we continue to progress towards ecosystem-based fisheries management (EBFM).},
	number = {1–2},
	urldate = {2016-01-13},
	journal = {Journal of Marine Systems},
	author = {Link, Jason and Overholtz, William and O'Reilly, John and Green, Jack and Dow, David and Palka, Debra and Legault, Chris and Vitaliano, Joseph and Guida, Vincent and Fogarty, Michael and Brodziak, Jon and Methratta, Lisa and Stockhausen, William and Col, Laurel and Griswold, Carolyn},
	month = nov,
	year = {2008},
	keywords = {Ecosystem-based fisheries management, Food web, Energy budget, Network analysis, Regional comparisons, Trophodynamics},
	pages = {453--474},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/W54DMZKV/S0924796308000560.html:text/html},
}

@article{link_response_2009,
	title = {Response of balanced network models to large-scale perturbation: {Implications} for evaluating the role of small pelagics in the {Gulf} of {Maine}},
	volume = {220},
	issn = {0304-3800},
	shorttitle = {Response of balanced network models to large-scale perturbation},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380008004973},
	doi = {10.1016/j.ecolmodel.2008.10.009},
	abstract = {Exploring the response of an ecosystem, and subsequent tradeoffs among its biological community, to human perturbations remains a key challenge for the implementation of an ecosystem approaches to fisheries (EAF). To address this and related issues, we developed two network (or energy budget) models, Ecopath and Econetwrk, for the Gulf of Maine ecosystem. These models included 31 network “nodes” or biomass state variables across a broad range of trophic levels, with the present emphasis to particularly elucidate the role of small pelagics. After initial network balancing, various perturbation scenarios were evaluated to explore how potential changes to different fish, fisheries and lower trophic levels can affect model outputs. Categorically across all scenarios and interpretations thereof, there was minimal change at the second trophic levels and most of the “rebalancing” after a perturbation occurred via alteration of the diet matrix. Yet the model results from perturbations to a balanced energy budget fall into one of three categories. First, some model results were intuitive and in obvious agreement with established ecological and fishing theory. Second, some model results were counter-intuitive upon initial observation, seemingly contradictory to known ecological and fishing theory; but upon further examination the results were explainable given the constraints of an equilibrium energy budget. Finally, some results were counter-intuitive and difficult to reconcile with theory or further examination of equilibrium constraints. A detailed accounting of biomass flows for example scenarios explores some of the non-intuitive results more rigorously. Collectively these results imply a need to carefully track biomass flows and results of any given perturbation and to critically evaluate the conditions under which a new equilibrium is obtained for these types of models, which has implications for dynamic simulations based off of them. Given these caveats, the role of small pelagics as a prominent component of this ecosystem remains a robust conclusion. We discuss how one might use this approach in the context of further developing an EAF, recognizing that a more holistic, integrated perspective will be required as we continue to evaluate tradeoffs among marine biological communities.},
	number = {3},
	urldate = {2016-01-13},
	journal = {Ecological Modelling},
	author = {Link, Jason and Col, Laurel and Guida, Vincent and Dow, David and O’Reilly, John and Green, Jack and Overholtz, William and Palka, Debra and Legault, Chris and Vitaliano, Joseph and Griswold, Carolyn and Fogarty, Michael and Friedland, Kevin},
	month = feb,
	year = {2009},
	keywords = {Food web, Energy budget, Network analysis, Trophodynamics, Ecosystem approaches to fisheries management, Tradeoffs},
	pages = {351--369},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/GNRU65HU/S0304380008004973.html:text/html},
}

@book{smith_trophic_2010,
	title = {The {Trophic} {Dynamics} of 50 {Finfish} and 2 {Squid} {Species} on the {Northeast} {US} {Continental} {Shelf}. {NOAA} {Technichal} {Memorandum} {NMFS}-{NE}-216},
	url = {http://www.nefsc.noaa.gov/publications/tm/tm216/},
	urldate = {2016-04-26},
	publisher = {National Marine Fisheries Service, 166 Water Street, Woods Hole, MA 02543-1026},
	author = {Smith, Brian E. and Link, Jason S.},
	year = {2010},
	file = {NOAA Tech Memo 216:/Users/sarah.gaichas/Zotero/storage/NFPWHQ6W/tm216.html:text/html},
}

@article{wilberg_incorporating_2009,
	title = {Incorporating {Time}-{Varying} {Catchability} into {Population} {Dynamic} {Stock} {Assessment} {Models}},
	volume = {18},
	issn = {1064-1262, 1547-6553},
	url = {http://www.tandfonline.com/doi/abs/10.1080/10641260903294647},
	doi = {10.1080/10641260903294647},
	language = {en},
	number = {1},
	urldate = {2016-02-12},
	journal = {Reviews in Fisheries Science},
	author = {Wilberg, Michael J. and Thorson, James T. and Linton, Brian C. and Berkson, Jim},
	month = dec,
	year = {2009},
	pages = {7--24},
	file = {Wilberg et al 2010 catchability.pdf - Wilberg et al 2010 catchability no cover.pdf:/Users/sarah.gaichas/Zotero/storage/5K24SWBG/Wilberg et al 2010 catchability no cover.pdf:application/pdf},
}

@article{smith_impacts_2011,
	title = {Impacts of fishing low-trophic level species on marine ecosystems},
	volume = {333},
	issn = {1095-9203 (Electronic) 0036-8075 (Linking)},
	shorttitle = {Impacts of fishing low-trophic level species on marine ecosystems},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21778363},
	doi = {10.1126/science.1209395},
	abstract = {Low-trophic level species account for more than 30\% of global fisheries production and contribute substantially to global food security. We used a range of ecosystem models to explore the effects of fishing low-trophic level species on marine ecosystems, including marine mammals and seabirds, and on other commercially important species. In five well-studied ecosystems, we found that fishing these species at conventional maximum sustainable yield (MSY) levels can have large impacts on other parts of the ecosystem, particularly when they constitute a high proportion of the biomass in the ecosystem or are highly connected in the food web. Halving exploitation rates would result in much lower impacts on marine ecosystems while still achieving 80\% of MSY.},
	language = {eng},
	number = {6046},
	journal = {Science},
	author = {Smith, A. D. and Brown, C. J. and Bulman, C. M. and Fulton, E. A. and Johnson, P. and Kaplan, I. C. and Lozano-Montes, H. and Mackinson, S. and Marzloff, M. and Shannon, L. J. and Shin, Y. J. and Tam, J.},
	month = aug,
	year = {2011},
	keywords = {Population Dynamics, Biodiversity, Biomass, *Food Chain, Animals, Models, Biological, *Ecosystem, *Fishes, *Aquatic Organisms, *Fisheries, Birds, Mammals, Oceans and Seas},
	pages = {1147--50},
	annote = {Smith, Anthony D MBrown, Christopher JBulman, Catherine MFulton, Elizabeth AJohnson, PennyKaplan, Isaac CLozano-Montes, HectorMackinson, StevenMarzloff, MartinShannon, Lynne JShin, Yunne-JaiTam, JorgeNew York, N.Y.Science. 2011 Aug 26;333(6046):1147-50. Epub 2011 Jul 21.},
}

@article{punt_exploring_2016,
	title = {Exploring the implications of the harvest control rule for {Pacific} sardine, accounting for predator dynamics: {A} {MICE} model},
	volume = {337},
	issn = {03043800},
	shorttitle = {Exploring the implications of the harvest control rule for {Pacific} sardine, accounting for predator dynamics},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0304380016302034},
	doi = {10.1016/j.ecolmodel.2016.06.004},
	abstract = {An ecosystem approach to forage fish management is required because forage fish support large fisheries, are prey for many valued species in marine food webs, and provide important social and cultural benefits to humans. Complex ecosystem models are often used to evaluate potential ecosystem consequences of forage fish fisheries, but there is seldom sufficient data to parameterize them, and full consideration of uncertainty is impossible. Models of Intermediate Complexity for Ecosystem assessment (MICE) provide a link between full ecosystem models and tactical (usually single-species) models typically used in fisheries management. MICE are ideal tools to form the basis for management strategy evaluations that compare the ability of candidate strategies to achieve goals related to target fisheries and broader ecosystem protection objectives. A MICE model is developed for the California Current Ecosystem (CCE) that focuses on the fishery for the northern subpopulation of Pacific sardine (Sardinops sajax) and the indirect impacts of the fishery on place-based predators, in particular brown pelicans (Pelecanus occidentalis) and California sea lions (Zalophus californianus), in the Southern California Bight. The model includes three forage species (sardine, northern anchovy Engraulis mordax, and ‘other forage’), an ‘other prey’ category, and two predator species (brown pelican and California sea lion) and evaluates the impacts of variable forage availability on adult predator reproductive success and survival. Parameterization of the model is based on available monitoring data and assessment outputs. The model is used to assess the ecosystem and fishery consequences of the current sardine management systems for Mexico, the USA, and Canada, with a focus on identifying which among a long list of sources of uncertainty in the system are most consequential for predictions of fishery impacts on predators. Key sources of uncertainty to consider in ecosystem assessments for the CCE are how prey abundance and availability impact predator demography and the extent to which the dynamics of prey populations are driven by environmental factors. Data are available for some of these sources of uncertainty for CCE sardine management, but much uncertainty remains, necessitating exploration of sensitivity to alternative model formulations and parameter values when providing advice on management strategies to decision makers.},
	language = {en},
	urldate = {2018-03-27},
	journal = {Ecological Modelling},
	author = {Punt, André E. and MacCall, Alec D. and Essington, Timothy E. and Francis, Tessa B. and Hurtado-Ferro, Felipe and Johnson, Kelli F. and Kaplan, Isaac C. and Koehn, Laura E. and Levin, Phillip S. and Sydeman, William J.},
	month = oct,
	year = {2016},
	pages = {79--95},
	file = {Punt et al. - 2016 - Exploring the implications of the harvest control .pdf:/Users/sarah.gaichas/Zotero/storage/ZZKNL8JQ/Punt et al. - 2016 - Exploring the implications of the harvest control .pdf:application/pdf},
}

@article{garrison_dietary_2000,
	title = {Dietary guild structure of the fish community in the {Northeast} {United} {States} continental shelf ecosystem},
	volume = {202},
	issn = {0171-8630, 1616-1599},
	url = {http://www.int-res.com/abstracts/meps/v202/p231-240/},
	doi = {10.3354/meps202231},
	abstract = {Trophic guild analysis identifies groups of species that use similar resources within a community. We evaluated the trophic guild structure in an assemblage of 40 fish species in the Northeast United States shelf ecosystem using a 25 yr database of food habits. We explicitly accounted for ontogenetic diet shifts by separating predator species into size classes. There were 14 significant trophic guilds. These distinguished predators based upon prey size and location in the water column (i.e., benthic to pelagic feeding). Ontogenetic diet shifts were important in guild structure, particularly within dominant piscivores. The mean dietary overlap both between and within guilds was notably lower than in other fish communities due to the broad spatial and temporal scale of the study, the diversity of prey types consumed, and the generalist nature of predators in this system. The guild concept is a useful framework to simplify highly connected, complex ecosystems like the Northeast US continental shelf and identify ecologically similar functional units.},
	language = {en},
	urldate = {2018-10-22},
	journal = {Marine Ecology Progress Series},
	author = {Garrison, Lp and Link, Js},
	year = {2000},
	pages = {231--240},
	file = {Garrison and Link - 2000 - Dietary guild structure of the fish community in t.pdf:/Users/sarah.gaichas/Zotero/storage/9N5PG6JF/Garrison and Link - 2000 - Dietary guild structure of the fish community in t.pdf:application/pdf},
}

@article{levin_thirty-two_2016,
	title = {Thirty-two essential questions for understanding the social–ecological system of forage fish: the case of pacific herring},
	volume = {2},
	issn = {2096-4129},
	shorttitle = {Thirty-two essential questions for understanding the social–ecological system of forage fish},
	url = {https://doi.org/10.1002/ehs2.1213},
	doi = {10.1002/ehs2.1213},
	abstract = {Forage fishes are ecologically and economically important low trophic level species, and in recent years interest in their biology and management has intensified. Pacific Herring are emblematic of the management issues facing forage species—they are central components of the Northeast Pacific pelagic food web and support important commercial fisheries. In addition, the importance of Herring to indigenous peoples have made them cultural keystone species. We employed a participatory process to promote collaborative priority-setting for this critical forage species. Working with managers, the fisheries industry, indigenous peoples, and scientists, we co-constructed a conceptual model of the Pacific Herring social–ecological system in the Northeast Pacific. We then identified a set of questions, that, if answered, would significantly increase our ability to sustainably manage the Herring . Our objective was to generate a road map for scientists who wish to conduct useful forage fish research, for resource managers who wish to develop new research efforts that could fill critical gaps, and for public agencies and private foundations seeking to prioritize funding on forage fish issues in the Pacific. With this socio-cultural centrality comes complexity for fisheries management. Our participatory process highlighted the value of conceptualizing the full SES, overcame disciplinary differences in scientific approaches, research philosophy, and language, and charted a path forward for future research and management for forage species.},
	number = {4},
	urldate = {2020-06-22},
	journal = {Ecosystem Health and Sustainability},
	author = {Levin, Phillip S. and Francis, Tessa B. and Taylor, Nathan G.},
	month = apr,
	year = {2016},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1002/ehs2.1213},
	keywords = {forage fish, fisheries, Pacific Ocean, interdisciplinary science, Pacific Herring, social–ecological system},
	pages = {e01213},
	file = {Full Text:/Users/sarah.gaichas/Zotero/storage/33UANILC/Levin et al. - 2016 - Thirty-two essential questions for understanding t.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/VRQJ8BIX/Levin et al. - 2016 - Thirty-two essential questions for understanding t.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/FV8TEW8I/ehs2.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/PPBV6WC9/ehs2.html:text/html},
}

@book{collette_bigelow_2002,
	address = {Washington, DC},
	edition = {3rd ed. edition},
	title = {Bigelow and {Schroeder}'s {Fishes} of the {Gulf} of {Maine}, {Third} {Edition}},
	isbn = {978-1-56098-951-6},
	abstract = {Fifteen years in the making, this updated edition raises the high standard of Bigelow and Schroeder's 1953 reference by drawing from a much larger base of information. Thirty-eight experts in fisheries biology and ichthyology clearly distill the enormous amount of knowledge gained during the past fifty years, including distribution figures from thirty years of annual trawl surveys; food habit accounts from surveys of the stomach contents of more than 30,000 fishes; and egg distribution data from a survey exceeding 10,000 samples. The contributors update Bigelow and Schroeder's 1953 material while presenting a wealth of new information, including thirty-three additional species accounts. By adding fifty percent more material and focusing the volume on data, the editors address the needs of today's biologists, the commercial fishing industry, and marine enthusiasts, and ensure that Bigelow and Schroeder's Fishes of the Gulf of Maine, Third Edition, will become the standard work in the field for the next fifty years.},
	language = {English},
	publisher = {Smithsonian Books},
	author = {Collette, Bruce B. and Klein-Macphee, Grace},
	month = jun,
	year = {2002},
	keywords = {Nature / Animals / Fish, Science / Life Sciences / Zoology / Ichthyology \& Herpetology},
}

@article{deroba_dream_2018,
	title = {The dream and the reality: meeting decision-making time frames while incorporating ecosystem and economic models into management strategy evaluation},
	copyright = {All rights reserved},
	issn = {0706-652X},
	shorttitle = {The dream and the reality},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfas-2018-0128},
	doi = {10.1139/cjfas-2018-0128},
	abstract = {Atlantic herring in the Northwest Atlantic have been managed with  interim harvest control rules (HCRs). A stakeholder driven management  strategy evaluation (MSE) was conducted that incorporated a broad range  of objectives. The MSE process was completed within one year. Constant  catch, conditional constant catch, and a biomass-based (BB) HCR with a  15\% restriction on the interannual change in the quota could achieve  more stable yields than BB HCRs without such restrictions, but could not  attain as high of yields and resulted in more negative outcomes for  terns (a herring predator). A similar range of performance could be  achieved by applying a BB HCR annually, every three years, or every five  years. Predators (i.e., dogfish, tuna, and terns) were generally  insensitive to the range of HCRs. While median net revenues were  sensitive to some HCRs, most HCRs produced a stable equilibrium of net revenue. In order to meet  management needs, some aspects of the simulations were less than might  be considered scientifically ideal, but using models of intermediate  complexity formed a foundation for future improvements.},
	urldate = {2018-07-20},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Deroba, Jonathan J. and Gaichas, Sarah K. and Lee, Min-Yang and Feeney, Rachel G. and Boelke, Deirdre V. and Irwin, Brian J},
	month = jul,
	year = {2018},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/TVTK7H33/cjfas-2018-0128.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/BK7NK9IE/cjfas-2018-0128.html:text/html},
}

@article{stock_woods_2021,
	title = {The {Woods} {Hole} {Assessment} {Model} ({WHAM}): {A} general state-space assessment framework that incorporates time- and age-varying processes via random effects and links to environmental covariates},
	volume = {240},
	issn = {0165-7836},
	shorttitle = {The {Woods} {Hole} {Assessment} {Model} ({WHAM})},
	url = {https://www.sciencedirect.com/science/article/pii/S0165783621000953},
	doi = {10.1016/j.fishres.2021.105967},
	abstract = {The rapid changes observed in many marine ecosystems that support fisheries pose a challenge to stock assessment and management predicated on time-invariant productivity and considering species in isolation. In single-species assessments, two main approaches have been used to account for productivity changes: allowing biological parameters to vary stochastically over time (empirical), or explicitly linking population processes such as recruitment (R) or natural mortality (M) to environmental covariates (mechanistic). Here, we describe the Woods Hole Assessment Model (WHAM) framework and software package, which combines these two approaches. WHAM can estimate time- and age-varying random effects on annual transitions in numbers at age (NAA), M, and selectivity, as well as fit environmental time-series with process and observation errors, missing data, and nonlinear links to R and M. WHAM can also be configured as a traditional statistical catch-at-age (SCAA) model in order to easily bridge from status quo models and test them against models with state-space and environmental effects, all within a single framework. We fit models with and without (independent or autocorrelated) random effects on NAA, M, and selectivity to data from five stocks with a broad range of life history, fishing pressure, number of ages, and time-series length. Models that included random effects performed well across stocks and processes, especially random effects models with a two dimensional (2D) first-order autoregressive, AR(1), covariance structure over age and year. We conducted simulation tests and found negligible or no bias in estimation of important assessment outputs (SSB, F, stock status, and catch) when the operating and estimation models matched. However, bias in SSB and F was often non-trivial when the estimation model was less complex than the operating model, especially when models without random effects were fit to data simulated from models with random effects. Bias of the variance and correlation parameters controlling random effects was also negligible or slightly negative as expected. Our results suggest that WHAM can be a useful tool for stock assessment when environmental effects on R or M, or stochastic variation in NAA transitions, M, or selectivity are of interest. In the U.S. Northeast, where the productivity of several groundfish stocks has declined, conducting assessments in WHAM with time-varying processes via random effects or environment-productivity links may account for these trends and potentially reduce retrospective bias.},
	language = {en},
	urldate = {2021-05-26},
	journal = {Fisheries Research},
	author = {Stock, Brian C. and Miller, Timothy J.},
	month = aug,
	year = {2021},
	keywords = {Stock assessment, Recruitment, Environmental effects, Natural mortality, Random effects, State-space, Template Model Builder (TMB), Time-varying},
	pages = {105967},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/UQJRN3K3/Stock and Miller - 2021 - The Woods Hole Assessment Model (WHAM) A general .pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/3FFX3ISS/S0165783621000953.html:text/html;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/SGFEARBH/S0165783621000953.html:text/html},
}

@article{dwyer_greenland_2010,
	series = {Proceedings of the {Seventh} {International} {Symposium} on {Flatfish} {Ecology}, {Part} {II}},
	title = {Greenland halibut diet in the {Northwest} {Atlantic} from 1978 to 2003 as an indicator of ecosystem change},
	volume = {64},
	issn = {1385-1101},
	url = {https://www.sciencedirect.com/science/article/pii/S1385110110000572},
	doi = {10.1016/j.seares.2010.04.006},
	abstract = {The Northwest Atlantic marine community underwent dramatic changes during the last 30years, including the collapse of many groundfish stocks and an increase in shrimp populations. Greenland halibut Reinhardtius hippoglossoides is an important commercial species and one of the top fish predators in this system. It is a large, wide-ranging flatfish that is found at depths up to 2200m and it has an opportunistic diet which makes it a potential candidate for an ecosystem indicator. Analysis of stomach contents of Greenland halibut between 1978 and 2003 indicates that diet composition reflects the major changes in community structure. Over the entire period there was a clear increase in the importance of invertebrates, particularly after 1992. This change was associated with a higher importance of Pandalus shrimp and Gonatus squid and a protracted reliance on zooplankton by predators under 25cm length. Capelin Mallotus villosus was the dominant prey between 1978 and 1992 for predators in the 12–63cm range, but its importance dropped off drastically in the mid 1990s. Levels of main prey in the diet of Greenland halibut correlated well with fishery-independent surveys. Greenland halibut sample capelin well, compared to bottom trawl surveys and acoustic surveys. Greenland halibut consumed small shrimp which are not routinely caught by surveys and may be important in deriving information on year classes and growth of shrimp. Our results suggest that Greenland halibut's diet is a useful tracker of ecosystem change.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Journal of Sea Research},
	author = {Dwyer, K. S. and Buren, A. and Koen-Alonso, M.},
	month = nov,
	year = {2010},
	keywords = {Ecosystem, Community Changes, Fish Predator, Indicator},
	pages = {436--445},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/8YTYNCMK/S1385110110000572.html:text/html},
}

@article{heim_marine_2021,
	title = {Marine ecosystem indicators are sensitive to ecosystem boundaries and spatial scale},
	volume = {125},
	issn = {1470-160X},
	url = {https://www.sciencedirect.com/science/article/pii/S1470160X21001874},
	doi = {10.1016/j.ecolind.2021.107522},
	abstract = {Time series indicators are widely used in ecosystem-based management. A suite of indicators is typically calculated for a static region or multiple subregions and presented in an ecosystem assessment (EA). These are used to guide management decisions or determine environmental status. Yet, few studies have examined how the spatial scale of an EA influences indicator behavior. We explore this question using the Northwest Atlantic continental shelf ecosystem (USA). We systematically divided the ecosystem at six spatial scales (31 unique units), covering spatial extents from 250,000 km2 to 20,000 km2. The same 22 indicators were calculated for each unit, assessed for trends, and evaluated as 31 independent EAs. We found that the detected signals of indicator trends depended on the spatial scale at which the ecosystem was defined. A single EA for the whole region differed by 23\% (in terms of the 22 indicator trend tests) relative to ones for spatially nested 120,000 km2 subunits, and by up to 36\% for EAs at smaller scales. Indicator trend disagreement occurred because (most common) a localized trend was perceived as widespread, (common) a local trend was obscured by aggregating data over a large region, or (least common) a local trend switched direction when examined at a broader scale. Yet, there was variation among indicators in their scale sensitivity related to trophic level. Indicators of temperature, chlorophyll-a, and zooplankton were spatially coherent: trends portrayed were similar regardless of scale. Mid-trophic level indicators (fish and invertebrates) showed more spatial variation in trends. We also compared trend magnitude and indicator values to spatial extent and found relationships consistent with scaling theory. Indicators at broad scales produced subdued trends and values relative to indicators developed at smaller spatial scales, which often portrayed ‘hotspots’ of local abundance or strong trend. Our results imply that subsequent uses of indicators (e.g., determining environmental status, risk assessments, management decisions) are also sensitive to ecosystem delineation and scale. We suggest that indicators and EAs should be done at multiple spatial scales and complimented with spatially explicit analysis to reflect the hierarchical structure of ecosystems. One scale is not best, but rather we gain a new level of understanding at each scale examined that can contribute to management decisions in a multiscale governance framework characterized by goals and objectives with relevance at different scales.},
	language = {en},
	urldate = {2021-06-10},
	journal = {Ecological Indicators},
	author = {Heim, Kurt C. and Thorne, Lesley H. and Warren, Joseph D. and Link, Jason S. and Nye, Janet A.},
	month = jun,
	year = {2021},
	keywords = {Ecosystem based management, Marine ecosystems, Ecosystem indicators, Dynamic Ocean management, Problem of scale, Spatial scale},
	pages = {107522},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/EIRL8PJH/Heim et al. - 2021 - Marine ecosystem indicators are sensitive to ecosy.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/AV9B3B2Q/S1470160X21001874.html:text/html},
}

@article{iverson_seabirds_2007,
	title = {Seabirds as indicators of food web structure and ecosystem variability: qualitative and quantitative diet analyses using fatty acids},
	volume = {352},
	issn = {0171-8630, 1616-1599},
	shorttitle = {Seabirds as indicators of food web structure and ecosystem variability},
	url = {https://www.int-res.com/abstracts/meps/v352/p235-244/},
	doi = {10.3354/meps07073},
	abstract = {The dynamics of predator–prey relationships, the structure of food webs, and the foraging behavior of individuals are critical to understanding animal ecology, interactions of predators with their prey, and effects of environmental variability on ecosystems. Like many other predators, seabirds are effective samplers of prey populations, and their diets can provide information about lower trophic levels over a range of spatial and temporal scales. Recognizing limitations of traditional methods of diet analysis, we validated the use of fatty acid (FA) signatures of subcutaneous adipose tissue biopsies for estimating diets of free-ranging seabirds. Calibration coefficients (CCs) for individual FAs were determined from captive common murres (n = 13) fed a long-term, single-species diet. Quantitative FA signature analysis (QFASA), using these CCs, was then validated in murres (n = 26) and red-legged kittiwakes (n = 13) fed controlled mixed-species diets. FAs were analyzed from 426 free-ranging red-legged Rissa brevirostris and black-legged kittiwakes R. tridactyla, and common Uria aalge and thick-billed murres U. lomvia from the Bering Sea, 284 of which were also sampled for stomach contents analysis. Qualitatively, FA signatures revealed distinct separation of diets among all 4 species, and further separation by location and year. QFASA diet estimates were similar to those based on stomach contents, with diets of kittiwakes dominated by myctophids, while those of murres comprised a mixture of other forage species. QFASA estimates were indicative of regional habitat differences, and were consistent with other aspects of seabird ecology at our study sites. We conclude that seabird FAs provide important information about ecosystems, but this will likely depend on each species’ foraging behavior and the complexities of the ecosystem it occupies.},
	language = {en},
	urldate = {2021-06-10},
	journal = {Marine Ecology Progress Series},
	author = {Iverson, Sara J. and Springer, Alan M. and Kitaysky, Alexander S.},
	month = dec,
	year = {2007},
	keywords = {Seabirds, Food webs, Diet, Black-legged kittiwakes Rissa tridactyla, Common murres Uria aalge, Fatty acids, Red-legged kittiwakes Rissa brevirostris, Thick-billed murres Uria lomvia},
	pages = {235--244},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/G3MKVFAU/Iverson et al. - 2007 - Seabirds as indicators of food web structure and e.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/9L3L2IWX/p235-244.html:text/html},
}

@article{reid_antarctic_2005,
	title = {Antarctic ecosystem monitoring: quantifying the response of ecosystem indicators to variability in {Antarctic} krill},
	volume = {62},
	issn = {1054-3139},
	shorttitle = {Antarctic ecosystem monitoring},
	url = {https://doi.org/10.1016/j.icesjms.2004.11.003},
	doi = {10.1016/j.icesjms.2004.11.003},
	abstract = {The utility of upper-trophic-level species as ecosystem indicators is determined by our ability to relate changes in indices of their performance to changes at lower trophic levels. Such relationships were assessed using indices of predator performance (response vectors) for four predator species, together with independent ship-based acoustic estimates of abundance of their main prey, Antarctic krill (Euphausia superba), from South Georgia in the South Atlantic Ocean. Out of 32 response vectors investigated, 13 showed a significant non-linear relationship, based on a Holling Type II response, to krill abundance, and just five showed a significant linear relationship. Predator responses reflecting the processes during summer, when prey surveys were undertaken, showed the closest relationship with prey abundance. Distinct relationships existed between the variability of indices and the biological processes they measured. Body mass variables had the lowest variability (CVs \<10\%), whereas those measuring breeding success showed the greatest variability (CVs \>50\%). Multivariate indices, produced by combining response vectors from all four predator species into a single combined index, provided a better fit with krill data than any of the individual vectors. Whereas population size parameters for individual species showed no relationship with annual estimates of krill abundance, a combined, multispecies population size index did show a significant response. Understanding the form of the relationship between concurrent indicators of prey abundance and key ecosystem metrics/reference points, such as population size, is crucial to the application of monitoring data to management action.},
	number = {3},
	urldate = {2021-06-10},
	journal = {ICES Journal of Marine Science},
	author = {Reid, Keith and Croxall, John P. and Briggs, Dirk R. and Murphy, Eugene J.},
	month = jan,
	year = {2005},
	pages = {366--373},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/REE8PCNI/Reid et al. - 2005 - Antarctic ecosystem monitoring quantifying the re.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/7IARQEAP/660016.html:text/html},
}

@article{carroll_review_2019,
	title = {A review of methods for quantifying spatial predator–prey overlap},
	volume = {28},
	issn = {1466-8238},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.12984},
	doi = {10.1111/geb.12984},
	abstract = {Background Studies that attempt to measure shifts in species distributions often consider a single species in isolation. However, understanding changes in spatial overlap between predators and their prey might provide deeper insight into how species redistribution affects food web dynamics. Predator–prey overlap metrics Here, we review a suite of 10 metrics [range overlap, area overlap, the local index of collocation (Pianka's O), Hurlbert's index, biomass-weighted overlap, asymmetrical alpha, Schoener's D, Bhattacharyya's coefficient, the global index of collocation and the AB ratio] that describe how two species overlap in space, using concepts such as binary co-occurrence, encounter rates, spatial niche similarity, spatial independence, geographical similarity and trophic transfer. We describe the specific ecological insights that can be gained using each overlap metric, in order to determine which is most appropriate for describing spatial predator–prey interactions for different applications. Simulation and case study We use simulated predator and prey distributions to demonstrate how the 10 metrics respond to variation in three types of predator–prey interactions: changing spatial overlap between predator and prey, changing predator population size and changing patterns of predator aggregation in response to prey density. We also apply these overlap metrics to a case study of a predatory fish (arrowtooth flounder, Atheresthes stomias) and its prey (juvenile walleye pollock, Gadus chalcogrammus) in the Eastern Bering Sea, AK, USA. We show how the metrics can be applied to understand spatial and temporal variation in the overlap of species distributions in this rapidly changing Arctic ecosystem. Conclusions Using both simulated and empirical data, we provide a roadmap for ecologists and other practitioners to select overlap metrics to describe particular aspects of spatial predator–prey interactions. We outline a range of research and management applications for which each metric may be suited.},
	language = {en},
	number = {11},
	urldate = {2021-09-01},
	journal = {Global Ecology and Biogeography},
	author = {Carroll, Gemma and Holsman, Kirstin K. and Brodie, Stephanie and Thorson, James T. and Hazen, Elliott L. and Bograd, Steven J. and Haltuch, Melissa A. and Kotwicki, Stan and Samhouri, Jameal and Spencer, Paul and Willis-Norton, Ellen and Selden, Rebecca L.},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/geb.12984},
	keywords = {climate change, ecosystem models, cold pool, species interactions, species distribution models, arrowtooth flounder, Eastern Bering Sea, predator–prey overlap, spatial overlap, walleye pollock},
	pages = {1561--1577},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/EBDT6LSU/geb.html:text/html;Snapshot:/Users/sarah.gaichas/Zotero/storage/5EHTETPH/geb.html:text/html},
}

@article{ng_predator_2021,
	title = {Predator stomach contents can provide accurate indices of prey biomass},
	volume = {78},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsab026},
	doi = {10.1093/icesjms/fsab026},
	abstract = {Diet-based annual biomass indices can potentially use predator stomach contents to provide information about prey biomass and may be particularly useful for species that are otherwise poorly sampled, including ecologically important forage fishes. However, diet-based biomass indices may be sensitive to underlying ecological dynamics between predators and prey, such as predator functional responses and changes in overlap in space and time. To evaluate these factors, we fit spatio-temporal models to stomach contents of five Atlantic herring (Clupea harengus) predators and survey catch data for predators and Atlantic herring. We identified drivers of variation in stomach contents, evaluated spatial patterns in stomach content data, and produced predator-specific indices of seasonal Atlantic herring biomass. After controlling for spatio-temporal processes and predator length, diet-based indices of biomass shared similar decadal trends but varied substantially between predators and seasons on shorter time scales. Diet-based indices reflected prey biomass more than prey availability, but weak correlations indicated that not all biological processes were controlled for. Results provide potential guidance for developing diet-based biomass indices and contribute to a body of evidence demonstrating the utility of predator diet data to provide information about relative prey biomass.},
	number = {3},
	urldate = {2021-09-01},
	journal = {ICES Journal of Marine Science},
	author = {Ng, Elizabeth L and Deroba, Jonathan J and Essington, Timothy E and Grüss, Arnaud and Smith, Brian E and Thorson, James T},
	month = jul,
	year = {2021},
	pages = {1146--1159},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/69FKJSA6/Ng et al. - 2021 - Predator stomach contents can provide accurate ind.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/2X7SANRP/6145864.html:text/html},
}

@article{gruss_spatio-temporal_2020,
	title = {Spatio-temporal analyses of marine predator diets from data-rich and data-limited systems},
	volume = {21},
	issn = {1467-2979},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12457},
	doi = {10.1111/faf.12457},
	abstract = {Accounting for variation in prey mortality and predator metabolic potential arising from spatial variation in consumption is an important task in ecology and resource management. However, there is no statistical method for processing stomach content data that accounts for fine-scale spatio-temporal structure while expanding individual stomach samples to population-level estimates of predation. Therefore, we developed an approach that fits a spatio-temporal model to both prey-biomass-per-predator-biomass data (i.e. the ratio of prey biomass in stomachs to predator weight) and predator biomass survey data, to predict “predator-expanded-stomach-contents” (PESCs). PESC estimates can be used to visualize either the annual landscape of PESCs (spatio-temporal variation), or can be aggregated across space to calculate annual variation in diet proportions (variation among prey items and among years). We demonstrated our approach in two contrasting scenarios: a data-rich situation involving eastern Bering Sea (EBS) large-size walleye pollock (Gadus chalcogrammus, Gadidae) for 1992–2015; and a data-limited situation involving West Florida Shelf red grouper (Epinephelus morio, Epinephelidae) for 2011–2015. Large walleye pollock PESC was predicted to be higher in very warm years on the Middle Shelf of the EBS, where food is abundant. Red grouper PESC was variable in north-western Florida waters, presumably due to spatio-temporal variation in harmful algal bloom severity. Our approach can be employed to parameterize or validate diverse ecosystem models, and can serve to address many fundamental ecological questions, such as providing an improved understanding of how climate-driven changes in spatial overlap between predator and prey distributions might influence predation pressure.},
	language = {en},
	number = {4},
	urldate = {2021-11-03},
	journal = {Fish and Fisheries},
	author = {Grüss, Arnaud and Thorson, James T. and Carroll, Gemma and Ng, Elizabeth L. and Holsman, Kirstin K. and Aydin, Kerim and Kotwicki, Stan and Morzaria-Luna, Hem N. and Ainsworth, Cameron H. and Thompson, Kevin A.},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12457},
	keywords = {diet proportions, Poisson-link delta model, predation pressure, predator-expanded-stomach-contents, spatio-temporal model, stomach content data},
	pages = {718--739},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/ETSV75XQ/faf.html:text/html},
}

@article{thorson_comparing_2017,
	title = {Comparing estimates of abundance trends and distribution shifts using single- and multispecies models of fishes and biogenic habitat},
	volume = {74},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsw193},
	doi = {10.1093/icesjms/fsw193},
	abstract = {Several approaches have been developed over the last decade to simultaneously estimate distribution or density for multiple species (e.g. “joint species distribution” or “multispecies occupancy” models). However, there has been little research comparing estimates of abundance trends or distribution shifts from these multispecies models with similar single-species estimates. We seek to determine whether a model including correlations among species (and particularly species that may affect habitat quality, termed “biogenic habitat”) improves predictive performance or decreases standard errors for estimates of total biomass and distribution shift relative to similar single-species models. To accomplish this objective, we apply a vector-autoregressive spatio-temporal (VAST) model that simultaneously estimates spatio-temporal variation in density for multiple species, and present an application of this model using data for eight US Pacific Coast rockfishes (Sebastes spp.), thornyheads (Sebastolobus spp.), and structure-forming invertebrates (SFIs). We identified three fish groups having similar spatial distribution (northern Sebastes, coastwide Sebastes, and Sebastolobus species), and estimated differences among groups in their association with SFI. The multispecies model was more parsimonious and had better predictive performance than fitting a single-species model to each taxon individually, and estimated fine-scale variation in density even for species with relatively few encounters (which the single-species model was unable to do). However, the single-species models showed similar abundance trends and distribution shifts to those of the multispecies model, with slightly smaller standard errors. Therefore, we conclude that spatial variation in density (and annual variation in these patterns) is correlated among fishes and SFI, with congeneric fishes more correlated than species from different genera. However, explicitly modelling correlations among fishes and biogenic habitat does not seem to improve precision for estimates of abundance trends or distribution shifts for these fishes.},
	number = {5},
	urldate = {2021-11-04},
	journal = {ICES Journal of Marine Science},
	author = {Thorson, James T. and Barnett, Lewis A. K.},
	month = may,
	year = {2017},
	pages = {1311--1321},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/BDBIBD5D/Thorson and Barnett - 2017 - Comparing estimates of abundance trends and distri.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/F62SPRTP/2907795.html:text/html},
}

@article{thorson_spatio-temporal_2019,
	title = {Spatio-temporal models of intermediate complexity for ecosystem assessments: {A} new tool for spatial fisheries management},
	volume = {20},
	issn = {1467-2979},
	shorttitle = {Spatio-temporal models of intermediate complexity for ecosystem assessments},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12398},
	doi = {10.1111/faf.12398},
	abstract = {Multispecies models are widely used to evaluate management trade-offs arising from species interactions. However, identifying climate impacts and sensitive habitats requires integrating spatial heterogeneity and environmental impacts into multispecies models at fine spatial scales. We therefore develop a spatio-temporal model of intermediate complexity for ecosystem assessments (a “MICE-in-space”), which is fitted to survey sampling data and time series of fishing mortality using maximum-likelihood techniques. The model is implemented in the VAST R package, and it can be configured to range from purely descriptive to including ratio-dependent interactions among species. We demonstrate this model using data for four groundfishes in the Gulf of Alaska using data from 1982 to 2015. Model selection for this case-study shows that models with species interactions are parsimonious, although a model specifying separate density dependence without interactions also has substantial support. The AIC-selected model estimates a significant, negative impact of Alaska pollock (Gadus chalcogrammus, Gadidae) on productivity of other species and suggests that recent fishing mortality for Pacific cod (G. microcephalus, Gadidae) is above the biological reference point (BRP) resulting in 40\% of unfished biomass; other models show similar trends but different scales due to different BRP estimates. A simulation experiment shows that fitting a model with fewer species at a coarse spatial resolution degrades estimation performance, but that interactions and biological reference points can still be estimated accurately. We conclude that MICE-in-space models can simultaneously estimate fishing impacts, species trade-offs, biological reference points and habitat quality. They are therefore suitable to forecast short-term climate impacts, optimize survey designs and designate protected habitats.},
	language = {en},
	number = {6},
	urldate = {2021-11-04},
	journal = {Fish and Fisheries},
	author = {Thorson, James T. and Adams, Grant and Holsman, Kirstin},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12398},
	keywords = {VAST, ecosystem model, spatio-temporal model, essential fish habitat, models of intermediate complexity for ecosystem assessments},
	pages = {1083--1099},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/YJHSUG3P/Thorson et al. - 2019 - Spatio-temporal models of intermediate complexity .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/ENJIGEPF/faf.html:text/html},
}

@article{suca_environmental_2021,
	title = {Environmental drivers and trends in forage fish occupancy of the {Northeast} {US} shelf},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsab214},
	doi = {10.1093/icesjms/fsab214},
	abstract = {The Northeast US shelf ecosystem is undergoing unprecedented changes due to long-term warming trends and shifts in regional hydrography leading to changes in community composition. However, it remains uncertain how shelf occupancy by the region's dominant, offshore small pelagic fishes, also known as forage fishes, has changed throughout the late 20th and early 21st centuries. Here, we use species distribution models to estimate the change in shelf occupancy, mean weighted latitude, and mean weighted depth of six forage fishes on the Northeast US shelf, and whether those trends were linked to coincident hydrographic conditions. Our results suggest that observed shelf occupancy is increasing or unchanging for most species in both spring and fall, linked both to gear shifts and increasing bottom temperature and salinity. Exceptions include decreases to observed shelf occupancy by sand lance and decreases to Atlantic herring's inferred habitat suitability in the fall. Our work shows that changes in shelf occupancy and inferred habitat suitability have varying coherence, indicating complex mechanisms behind observed shelf occupancy for many species. Future work and management can use these results to better isolate the aspects of forage fish life histories that are important for determining their occupancy of the Northeast US shelf.},
	number = {fsab214},
	urldate = {2021-11-10},
	journal = {ICES Journal of Marine Science},
	author = {Suca, Justin J and Deroba, Jonathan J and Richardson, David E and Ji, Rubao and Llopiz, Joel K},
	month = nov,
	year = {2021},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/EC8FG2KS/Suca et al. - 2021 - Environmental drivers and trends in forage fish oc.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/RQAFI9JI/6419780.html:text/html},
}

@article{perretti_spatio-temporal_2019,
	title = {Spatio-temporal dynamics of summer flounder ({Paralichthys} dentatus) on the {Northeast} {US} shelf},
	volume = {215},
	issn = {0165-7836},
	url = {https://www.sciencedirect.com/science/article/pii/S0165783619300712},
	doi = {10.1016/j.fishres.2019.03.006},
	abstract = {Summer flounder (Paralichthys dentatus) are an economically and ecologically important fish on the Northeast U.S. shelf. There is evidence that their spatial distribution has shifted over time. However, there are conflicting reports on the importance of various potential drivers of the shift. Here, we investigate whether the stock has shifted and the extent to which this can be attributed to changes in abundance, size-structure, environmental variables, and fishing. We do so using a vector-autoregressive spatio-temporal model that incorporates data from two seasonal bottom trawl surveys that together span the nearshore and offshore Northeast US shelf over the past 41 years. We find that the summer flounder distribution has shifted north and east in both the spring and fall. The shift is observed in both recruits and spawners, with recruits shifting northward faster than spawners, suggesting that increased spawner abundance may not be driving the shift in recruits. We find that only a small portion of the variability in distribution can be attributed to changes in abundance, fishing, or environmental covariates. Instead, the shift is most strongly attributed to unidentified factors.},
	language = {en},
	urldate = {2022-01-04},
	journal = {Fisheries Research},
	author = {Perretti, Charles T. and Thorson, James T.},
	month = jul,
	year = {2019},
	keywords = {Distribution shift, Spatiotemporal model, Summer flounder},
	pages = {62--68},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/2NVTWNIF/Perretti and Thorson - 2019 - Spatio-temporal dynamics of summer flounder (Paral.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/YX8UUKBN/S0165783619300712.html:text/html},
}

@article{fredston_range_2021,
	title = {Range edges of {North} {American} marine species are tracking temperature over decades},
	volume = {27},
	issn = {1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.15614},
	doi = {10.1111/gcb.15614},
	abstract = {Understanding the dynamics of species range edges in the modern era is key to addressing fundamental biogeographic questions about abiotic and biotic drivers of species distributions. Range edges are where colonization and extirpation processes unfold, and so these dynamics are also important to understand for effective natural resource management and conservation. However, few studies to date have analyzed time series of range edge positions in the context of climate change, in part because range edges are difficult to detect. We first quantified positions for 165 range edges of marine fishes and invertebrates from three U.S. continental shelf regions using up to five decades of survey data and a spatiotemporal model to account for sampling and measurement variability. We then analyzed whether those range edges maintained their edge thermal niche—the temperatures found at the range edge position—over time. A large majority of range edges (88\%) maintained either summer or winter temperature extremes at the range edge over the study period, and most maintained both (76\%), although not all of those range edges shifted in space. However, we also found numerous range edges—particularly poleward edges and edges in the region that experienced the most warming—that did not shift at all, shifted further than predicted by temperature alone, or shifted opposite the direction expected, underscoring the multiplicity of factors that drive changes in range edge positions. This study suggests that range edges of temperate marine species have largely maintained the same edge thermal niche during periods of rapid change and provides a blueprint for testing whether and to what degree species range edges track temperature in general.},
	language = {en},
	number = {13},
	urldate = {2022-02-14},
	journal = {Global Change Biology},
	author = {Fredston, Alexa and Pinsky, Malin and Selden, Rebecca L. and Szuwalski, Cody and Thorson, James T. and Gaines, Steven D. and Halpern, Benjamin S.},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15614},
	keywords = {climate change, biogeography, global warming, range limit, range margin, thermal niche, thermal tolerance},
	pages = {3145--3156},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/BZZASJD9/gcb.html:text/html},
}

@article{schoener_nonsynchronous_1970,
	title = {Nonsynchronous {Spatial} {Overlap} of {Lizards} in {Patchy} {Habitats}},
	volume = {51},
	issn = {1939-9170},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.2307/1935376},
	doi = {10.2307/1935376},
	abstract = {Sympatric native Anolis species with similar structural habitats but contrasting climatic habitats are closer in head and body size on species—rich than on depauperate islands. In two localities, sympatric Anolis species with differential occurrences in sun or shade sought lower, more shaded perches during midday, resulting in partly nonsynchronous utilization of the vegetation by the two species. The second observation may be related to the first in the following way: nonsynchronous spatial overlap could dictate relatively great resource overlap for species coinhabiting patchy or edge areas, requiring great differences between the species in prey size in addition to those in climatic habitat. The extent of such overlap on small depauperate islands could be greater if these contained a greater proportion of patchy or edge habitats (with respect to insolation), or if climatic preferences were broader and more overlapping than on large, species—rich islands. In each locality, the relatively more shade—inhabiting species occurred more often on larger perches and on lower perches than did the other species. In both species of the Bermudan pair, adult males occupied higher and larger perches, and in grahami, shadier perches, than did female—sized individuals. The statistical significance of these and other differences was evaluated using several unweighted g2 procedures, Cochran's weighted g2 test and a partitioning technique for analyzing interactions among variables in complex contingency tables. The last method is described in detail in the papaer by Fienberg, immediately following this one.},
	language = {en},
	number = {3},
	urldate = {2022-02-14},
	journal = {Ecology},
	author = {Schoener, Thomas W.},
	year = {1970},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2307/1935376},
	pages = {408--418},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/IA7MI8HG/1935376.html:text/html},
}

@article{thompson_feeding_2020,
	title = {A feeding guild indicator to assess environmental change impacts on marine ecosystem structure and functioning},
	volume = {57},
	issn = {1365-2664},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2664.13662},
	doi = {10.1111/1365-2664.13662},
	abstract = {Integrating food web indicators into ecological status assessments is central to developing effective management measures that can improve degraded ecosystems. This is because they can reveal how ecosystems respond to environmental change that cannot be inferred from studying habitat, species or assemblages alone. However, the substantial investment required to monitor food webs (e.g. via stomach contents analysis) and the lack of internationally agreed approaches to assessing them has hampered their development. Inventories of trophic interactions have been collated world-wide and across biomes, and can be applied to infer food web structure and energy flow. Here, we compile a new marine dataset containing 8,092 unique predator–prey interactions from 415,294 fish stomachs. We demonstrate how feeding guilds (i.e. groupings based on diet and life stage) could be defined systematically and in a way that is conducive to their application internationally across ecosystems; and apply them to the North Sea fish assemblage to demonstrate their responsiveness to anthropogenic pressures. We found evidence for seven distinct feeding guilds. Differences between guilds were related to predator size, which positively correlated with piscivory, phylogeny, with multiple size classes of a species often in the same guild, and habitat, as pelagic, benthic and shallow-coastal foraging was apparent. Guild biomasses were largely consistent through time at the North Sea-level and spatially aggregated at the regional level with change relating to changes in resource availability, temperature, fishing and the biomass of other guilds. This suggests that fish biomass was partitioned across broad feeding and environmental niches, and changes over time were governed partly by guild carrying capacities, but also by a combination of covariates with contrasting patterns of change. Management of the North Sea ecosystem could therefore be adaptive and focused towards specific guilds and pressures in a given area. Synthesis and applications. We propose a food web indicator which has been explicitly called for to inform policy via food web status assessment as part of the European Union's Marine Strategy Framework Directive and the indicator toolkit supporting The Convention for the Protection of the Marine Environment of the North-East Atlantic (the ‘OSPAR Convention’).},
	language = {en},
	number = {9},
	urldate = {2022-02-15},
	journal = {Journal of Applied Ecology},
	author = {Thompson, Murray S. A. and Pontalier, Hugo and Spence, Michael A. and Pinnegar, John K. and Greenstreet, Simon P. R. and Moriarty, Meadhbh and Hélaouët, Pierre and Lynam, Christopher P.},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2664.13662},
	keywords = {marine ecosystem, ecological status assessment, ecosystem structure and function, environmental change, feeding guilds, fishing impacts, food web indicator, good environmental status},
	pages = {1769--1781},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/EHAM2RJD/Thompson et al. - 2020 - A feeding guild indicator to assess environmental .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/ZXUV6JBM/1365-2664.html:text/html},
}

@article{malek_trophic_2016,
	title = {Trophic structure of a coastal fish community determined with diet and stable isotope analyses},
	volume = {89},
	issn = {1095-8649},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jfb.13059},
	doi = {10.1111/jfb.13059},
	abstract = {A combination of dietary guild analysis and nitrogen (δ15N) and carbon (δ13C) stable-isotope analysis was used to assess the trophic structure of the fish community in Rhode Island and Block Island Sounds, an area off southern New England identified for offshore wind energy development. In the autumn of 2009, 2010 and 2011, stomach and tissue samples were taken from 20 fish and invertebrate species for analysis of diet composition and δ15N and δ13C signatures. The food chain in Rhode Island and Block Island Sounds comprises approximately four trophic levels within which the fish community is divided into distinct dietary guilds, including planktivores, benthivores, crustacivores and piscivores. Within these guilds, inter-species isotopic and dietary overlap is high, suggesting that resource partitioning or competitive interactions play a major role in structuring the fish community. Carbon isotopes indicate that most fishes are supported by pelagic phytoplankton, although there is evidence that benthic production also plays a role, particularly for obligate benthivores such as skates Leucoraja spp. This type of analysis is useful for developing an ecosystem-based approach to management, as it identifies species that act as direct links to basal resources as well as species groups that share trophic roles.},
	language = {en},
	number = {3},
	urldate = {2022-02-15},
	journal = {Journal of Fish Biology},
	author = {Malek, A. J. and Collie, J. S. and Taylor, D. L.},
	year = {2016},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jfb.13059},
	keywords = {trophic ecology, fish diet, food webs, north-west Atlantic, δ13C, δ15N},
	pages = {1513--1536},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/9GGIG8BW/Malek et al. - 2016 - Trophic structure of a coastal fish community dete.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/MPNQ5R67/jfb.html:text/html},
}

@article{chagaris_ecological_2020,
	title = {Ecological {Reference} {Points} for {Atlantic} {Menhaden} {Established} {Using} an {Ecosystem} {Model} of {Intermediate} {Complexity}},
	volume = {7},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2020.606417},
	abstract = {Atlantic menhaden (Brevoortia tyrannus) are an important forage fish for many predators, and they also support the largest commercial fishery by weight on the U.S. East Coast. Menhaden management has been working toward ecological reference points (ERPs) that account for menhaden’s role in the ecosystem. The goal of this work was to develop menhaden ERPs using ecosystem models. An existing Ecopath with Ecosim model of the Northwest Atlantic Continental Shelf (NWACS) was reduced in complexity from 61 to 17 species/functional groups. The new NWACS model of intermediate complexity for ecosystems (NWACS-MICE) serves to link the dynamics of menhaden with key managed predators. Striped bass (Morone saxatilis) were determined to be most sensitive to menhaden harvest and therefore served as an indicator of ecosystem impacts. ERPs were based on the tradeoff relationship between the equilibrium biomass of striped bass and menhaden fishing mortality (F). The ERPs were defined as the menhaden F rates that maintain striped bass at their biomass target and threshold when striped bass are fished at their Ftarget, and all other modeled species were fished at status quo levels. These correspond to an ERP Ftarget of 0.19 and an ERP Fthreshold of 0.57, which are lower than the single species reference points by 30–40\%, but higher than current (2017) menhaden F. The ERPs were then fed back into the age-structured stock assessment model projections to provide information on total allowable catch. The ERPs developed in this study were adopted by the Atlantic menhaden Management Board, marking a shift toward ecosystem-based fishery management for this economically and ecologically important species.},
	urldate = {2022-06-10},
	journal = {Frontiers in Marine Science},
	author = {Chagaris, David and Drew, Katie and Schueller, Amy and Cieri, Matt and Brito, Joana and Buchheister, Andre},
	year = {2020},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/278EYDLM/Chagaris et al. - 2020 - Ecological Reference Points for Atlantic Menhaden .pdf:application/pdf},
}

@article{drew_balancing_2021,
	title = {Balancing {Model} {Complexity}, {Data} {Requirements}, and {Management} {Objectives} in {Developing} {Ecological} {Reference} {Points} for {Atlantic} {Menhaden}},
	volume = {8},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2021.608059},
	abstract = {Atlantic menhaden is an important forage fish and the target of the largest fishery along the US East Coast by volume. Since 1999, managers at the Atlantic States Marine Fisheries Commission, stakeholders, and scientists have been interested in developing ecological reference points (ERPs) that account for menhaden’s role as a forage species. To accomplish this, we developed a suite of modeling approaches that incorporated predation on menhaden and changes in productivity over time and allowed for evaluation of trade-offs between menhaden harvest and ecosystem management objectives. These approaches ranged in complexity, from models with minimal data requirements and few assumptions to approaches with extensive data needs and detailed assumptions. This included a surplus production model with a time-varying intrinsic growth rate, a Steele-Henderson surplus production model, a multispecies statistical catch-at-age model, an Ecopath with Ecosim (EwE) model with a limited predator and prey field, and a full EwE model. We evaluated how each model could address managers’ objectives and compared outputs across the approaches, highlighting their strengths, weaknesses, and management utility. All models produced estimates of age-1 + biomass and exploitation rate that were similar in trend and magnitude to the single-species statistical catch-at-age model, especially in recent years. While the less complex models were relativity easy to implement and update, they lacked key elements needed to manage multiple species simultaneously. More complex models required a wider array of data and were more difficult to update within the current management time-frames, but produced a more useful framework for managers. Ultimately, an EwE model of intermediate complexity coupled with the existing single-species assessment model was recommended for use in management.},
	urldate = {2022-06-10},
	journal = {Frontiers in Marine Science},
	author = {Drew, Katie and Cieri, Matthew and Schueller, Amy M. and Buchheister, Andre and Chagaris, David and Nesslage, Geneviève and McNamee, Jason E. and Uphoff, James H.},
	year = {2021},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/WAWN52DS/Drew et al. - 2021 - Balancing Model Complexity, Data Requirements, and.pdf:application/pdf},
}

@article{thorson_implementing_2016,
	title = {Implementing a generic method for bias correction in statistical models using random effects, with spatial and population dynamics examples},
	volume = {175},
	issn = {0165-7836},
	url = {https://www.sciencedirect.com/science/article/pii/S0165783615301399},
	doi = {10.1016/j.fishres.2015.11.016},
	abstract = {Statistical models play an important role in fisheries science when reconciling ecological theory with available data for wild populations or experimental studies. Ecological models increasingly include both fixed and random effects, and are often estimated using maximum likelihood techniques. Quantities of biological or management interest (“derived quantities”) are then often calculated as nonlinear functions of fixed and random effect estimates. However, the conventional “plug-in” estimator for a derived quantity in a maximum likelihood mixed-effects model will be biased whenever the estimator is calculated as a nonlinear function of random effects. We therefore describe and evaluate a new “epsilon” estimator as a generic bias-correction estimator for derived quantities. We use simulated data to compare the epsilon-method with an existing bias-correction algorithm for estimating recruitment in four configurations of an age-structured population dynamics model. This simulation experiment shows that the epsilon-method and the existing bias-correction method perform equally well in data-rich contexts, but the epsilon-method is slightly less biased in data-poor contexts. We then apply the epsilon-method to a spatial regression model when estimating an index of population abundance, and compare results with an alternative bias-correction algorithm that involves Markov-chain Monte Carlo sampling. This example shows that the epsilon-method leads to a biologically significant difference in estimates of average abundance relative to the conventional plug-in estimator, and also gives essentially identical estimates to a sample-based bias-correction estimator. The epsilon-method has been implemented by us as a generic option in the open-source Template Model Builder software, and could be adapted within other mixed-effects modeling tools such as Automatic Differentiation Model Builder for random effects. It therefore has potential to improve estimation performance for mixed-effects models throughout fisheries science.},
	language = {en},
	urldate = {2022-07-29},
	journal = {Fisheries Research},
	author = {Thorson, James T. and Kristensen, Kasper},
	month = mar,
	year = {2016},
	keywords = {Stock assessment, Random effects, Template Model Builder (TMB), Bias correction, Epsilon estimator, Mixed-effects model},
	pages = {66--74},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/EULWM2HW/S0165783615301399.html:text/html;Thorson and Kristensen - 2016 - Implementing a generic method for bias correction .pdf:/Users/sarah.gaichas/Zotero/storage/AZC44RWT/Thorson and Kristensen - 2016 - Implementing a generic method for bias correction .pdf:application/pdf},
}

@article{reynolds_daily_2007,
	title = {Daily {High}-{Resolution}-{Blended} {Analyses} for {Sea} {Surface} {Temperature}},
	volume = {20},
	issn = {0894-8755, 1520-0442},
	url = {https://journals.ametsoc.org/view/journals/clim/20/22/2007jcli1824.1.xml},
	doi = {10.1175/2007JCLI1824.1},
	abstract = {Abstract Two new high-resolution sea surface temperature (SST) analysis products have been developed using optimum interpolation (OI). The analyses have a spatial grid resolution of 0.25° and a temporal resolution of 1 day. One product uses the Advanced Very High Resolution Radiometer (AVHRR) infrared satellite SST data. The other uses AVHRR and Advanced Microwave Scanning Radiometer (AMSR) on the NASA Earth Observing System satellite SST data. Both products also use in situ data from ships and buoys and include a large-scale adjustment of satellite biases with respect to the in situ data. Because of AMSR’s near-all-weather coverage, there is an increase in OI signal variance when AMSR is added to AVHRR. Thus, two products are needed to avoid an analysis variance jump when AMSR became available in June 2002. For both products, the results show improved spatial and temporal resolution compared to previous weekly 1° OI analyses. The AVHRR-only product uses Pathfinder AVHRR data (currently available from January 1985 to December 2005) and operational AVHRR data for 2006 onward. Pathfinder AVHRR was chosen over operational AVHRR, when available, because Pathfinder agrees better with the in situ data. The AMSR–AVHRR product begins with the start of AMSR data in June 2002. In this product, the primary AVHRR contribution is in regions near land where AMSR is not available. However, in cloud-free regions, use of both infrared and microwave instruments can reduce systematic biases because their error characteristics are independent.},
	language = {EN},
	number = {22},
	urldate = {2022-08-01},
	journal = {Journal of Climate},
	author = {Reynolds, Richard W. and Smith, Thomas M. and Liu, Chunying and Chelton, Dudley B. and Casey, Kenneth S. and Schlax, Michael G.},
	month = nov,
	year = {2007},
	note = {Publisher: American Meteorological Society
Section: Journal of Climate},
	pages = {5473--5496},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/UZNKFHJT/Reynolds et al. - 2007 - Daily High-Resolution-Blended Analyses for Sea Sur.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/BNA66FUA/journals\$002fclim\$002f20\$002f22\$002f2007jcli1824.1.html:text/html},
}

@misc{saha_avhrr_2018,
	title = {{AVHRR} {Pathfinder} version 5.3 level 3 collated ({L3C}) global 4km sea surface temperature for 1981-{Present}. [1985-2021]. {NOAA} {National} {Centers} for {Environmental} {Information}. {Dataset}.},
	url = {https://doi.org/10.7289/v52j68xx},
	abstract = {This product is a long-term Climate Data Record (1981–present) that builds on the historic aspect of Pathfinder Sea Surface Temperature (SST) (Saha et. al 2018). It contains global, twice-daily (Day and Night) 4km SST derived from measurements captured by Advanced Very High Resolution Radiometer (AVHRR) instruments aboard NOAA polar-orbiting satellites.},
	language = {en},
	urldate = {2022-08-01},
	author = {Saha, Korak, Saha and Zhao, Xuepeng and Zhang, Huai-min and Casey, Kenneth S. and Zhang, Dexin and Baker-Yeboah, Sheelela and Kilpatrick, Katherine A. and Evans, Robert H. and Ryan, Thomas and Relph, John M.},
	year = {2018},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/25ZKASG4/avhrr-pathfinder-sst.html:text/html},
}

@misc{r_core_team_r_2022,
	address = {Vienna, Austria},
	title = {R: {A} {Language} and {Environment} for {Statistical} {Computing}},
	url = {https://www.R-project.org},
	publisher = {R Foundation for Statistical Computing},
	author = {R Core Team},
	year = {2022},
}

@article{thorson_surprising_2021,
	title = {The surprising sensitivity of index scale to delta-model assumptions: {Recommendations} for model-based index standardization},
	volume = {233},
	issn = {01657836},
	shorttitle = {The surprising sensitivity of index scale to delta-model assumptions},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0165783620302629},
	doi = {10.1016/j.fishres.2020.105745},
	abstract = {Delta-models (a.k.a. hurdle models) are widely used to fit biomass samples that include zeros and a skewed response for positive catches, and spatio-temporal extensions of these models are increasingly used to quantify trends in abundance (i.e., estimate abundance indices). Previous research has shown estimated indices are proportional to changes in abundance. However, little research has tested the performance of delta-models for estimating “scale”; that is, whether abundance indices are not just proportional to population changes but also have the correct absolute value. We use data for twenty species in the eastern Bering Sea and Gulf of Alaska as well as a factorial experiment conditioned on data for Gulf of Alaska Pacific cod to support five conclusions related to scale in spatio-temporal delta-models. First, we show that conventional (nonspatial) delta-models are surprisingly sensitive to the a priori choice of probability distribution for positive catches, where gamma and Tweedie models give similar scale estimates but other distributions generally differ. Second, these same distri­ butions also estimate widely different scales when using spatio-temporal delta-models, and the delta-gamma and Tweedie models provide similar scale to design-based indices. Third, model selection using marginal AIC often identifies the lognormal distribution as most parsimonious, despite it resulting in systematically higher abun­ dance than design-based indices for many species. Fourth, scale is sensitive to the spatial resolution (i.e., number of knots) used in fitting the spatio-temporal model when using a naïve “empirical Bayes” estimator, but less sensitive when applying an epsilon bias-correction estimator. Fifth, the factorial simulation experiment suggests that the Tweedie and delta-gamma distributions perform well even when applied to data simulated from an inverse-Gaussian or lognormal distribution, whereas the opposite is not true. We conclude that index scale is sensitive to delta-model specification, and we make five recommendations when using spatio-temporal deltamodels for index standardization: (1) apply the epsilon or other bias-correction methods to reduce sensitivity of index scale on spatio-temporal model resolution; either (2) compare the scale of delta-model indices with that of design-based indices when design-based indices are available or (3) use the delta-gamma or Tweedie distribution by default when design-based indices are not available; (4) do not assume that AIC will identify the model specification that results in the most appropriate scale; and (5) consider apparent mismatches in index scale depending upon whether an assessment model specifies or estimates the associated catchability coefficient and whether the design-based index is believed to measure total abundance for a fully-selected age or length-class.},
	language = {en},
	urldate = {2022-08-04},
	journal = {Fisheries Research},
	author = {Thorson, James T. and Cunningham, Curry J. and Jorgensen, Elaina and Havron, Andrea and Hulson, Peter-John F. and Monnahan, Cole C. and von Szalay, Paul},
	month = jan,
	year = {2021},
	keywords = {Stock assessment, VAST, Abundance index, Catchability coefficient, Delta model, Tweedie distribution, Vector autoregressive spatio-temporal model},
	pages = {105745},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/SND4TRFL/S0165783620302629.html:text/html;Thorson et al. - 2021 - The surprising sensitivity of index scale to delta.pdf:/Users/sarah.gaichas/Zotero/storage/N9EVY2WT/Thorson et al. - 2021 - The surprising sensitivity of index scale to delta.pdf:application/pdf},
}

@article{gruss_developing_2019,
	title = {Developing spatio-temporal models using multiple data types for evaluating population trends and habitat usage},
	volume = {76},
	issn = {1054-3139, 1095-9289},
	url = {https://academic.oup.com/icesjms/article/76/6/1748/5479986},
	doi = {10.1093/icesjms/fsz075},
	abstract = {Abstract
            Spatio-temporal models have become key tools for evaluating population trends and habitat usage. We developed a spatio-temporal modelling framework employing a combination of encounter/non-encounter, count, and biomass data collected by different monitoring programs (“combined data”). The three data types are predicted using a computationally efficient approximation to a compound Poisson-gamma process. We fitted spatio-temporal models to combined data for Gulf of Mexico (GOM) red snapper (Lutjanus campechanus) for 2006–2014. These spatio-temporal models provided insights into GOM red snapper spatial distribution patterns, which we corroborated by comparing to past predictions generated using only encounter/non-encounter data. However, relying on biomass and count data in addition to encounter/non-encounter data also allowed us to reconstruct biomass trends for GOM red snapper and to examine patterns of distribution shifts and range expansion/contraction for this population for the first time. Moreover, combining multiple data types improved the precision of reconstructed population trends and some variables quantifying habitat usage. Finally, scenarios and simulation experiments conditioned upon red snapper data showed that the improvement in fitting to combined data is greater when biomass data for the study population are lacking for an entire subregion and, to a lesser extent, for an entire time period (e.g. in early years).},
	language = {en},
	number = {6},
	urldate = {2022-08-04},
	journal = {ICES Journal of Marine Science},
	author = {Grüss, Arnaud and Thorson, James T},
	editor = {Jardim, Ernesto},
	month = dec,
	year = {2019},
	pages = {1748--1761},
	file = {Grüss and Thorson - 2019 - Developing spatio-temporal models using multiple d.pdf:/Users/sarah.gaichas/Zotero/storage/UKZVZDGQ/Grüss and Thorson - 2019 - Developing spatio-temporal models using multiple d.pdf:application/pdf},
}

@article{caracappa_northeast_2022,
	title = {A northeast {United} {States} {Atlantis} marine ecosystem model with ocean reanalysis and ocean color forcing},
	volume = {471},
	issn = {0304-3800},
	url = {https://www.sciencedirect.com/science/article/pii/S030438002200148X},
	doi = {10.1016/j.ecolmodel.2022.110038},
	abstract = {The northeast United States Atlantis model (NEUSv2) is an end-to-end ecosystem model that can simulate biogeochemical, ecological, fishery, management, and socio-economic processes within marine ecosystems. As a major update to the original model, NEUSv2 includes changes to the model's functional group definitions and forcing data. NEUSv2 is the first Atlantis model to use a satellite-ocean-color-derived phytoplankton size class model that was tuned specifically for the region to force marine primary production. Additionally, physical ocean variables (currents, temperature, and salinity) were updated using a high-resolution global ocean reanalysis. Despite its coarse resolution, NEUSv2 was capable of reproducing the broad spatial patterns seen in the physical and biological forcing sources, with the exception of some circulation features. NEUSv2 produced plausible zooplankton and planktivore biomass, a stable lower trophic food web, and recent trends in zooplankton biomass. NEUSv2 meets calibration criteria for the persistence and long-term stability of functional group biomass. Given the success of this new Atlantis forcing approach, we detail the observations and challenges regarding spatial scale-related processes, data assimilation, and biological calibration. We also discuss possible tradeoffs with model scope, calibration, and the availability of feedback mechanisms. This NEUSv2 hindcast is well suited for exploring ecosystem-level sensitivity to lower trophic processes and for testing alternative biogeochemical forcing. Further developments will improve model performance for higher trophic levels.},
	language = {en},
	urldate = {2022-08-08},
	journal = {Ecological Modelling},
	author = {Caracappa, Joseph C. and Beet, Andrew and Gaichas, Sarah and Gamble, Robert J. and Hyde, Kimberly J. W. and Large, Scott I. and Morse, Ryan E. and Stock, Charles A. and Saba, Vincent S.},
	month = sep,
	year = {2022},
	keywords = {Atlantis, biogeochemical forcing, end-to-end models, global reanalysis, lower trophic levels, marine ecosystem models, ocean color, primary production},
	pages = {110038},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/NKQNC7BM/Caracappa et al. - 2022 - A northeast United States Atlantis marine ecosyste.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/HV3YDQ5H/S030438002200148X.html:text/html},
}

@article{plaganyi_when_2014,
	title = {When the {SURFs} up, forage fish are key},
	volume = {159},
	issn = {0165-7836},
	url = {https://www.sciencedirect.com/science/article/pii/S0165783614001647},
	doi = {10.1016/j.fishres.2014.05.011},
	abstract = {A novel method for identifying “key” prey species such as forage fish, upon which upper trophic level predators depend, is proposed. Forage fish fisheries collectively constitute 30\% of global fishery landings and are important prey for other fished species as well as marine mammals and seabirds. The SURF index (SUpportive Role to Fishery ecosystems) for each prey species weights food web connectance by the importance of trophic connections, so that higher scores indicate a greater potential for indirect food web effects of forage fish fisheries. We show that the SURF index is less sensitive to choices on degree of taxonomic aggregation of analysis than typical connectance measures. Moreover, we show that SURF provides more robust predictions of which species have greatest effects on other food web components. This rapid and empirically based method has utility in ensuring that management plans for these species take into account the broader ecosystem impacts of different harvest levels.},
	language = {en},
	urldate = {2022-08-16},
	journal = {Fisheries Research},
	author = {Plagányi, Éva E. and Essington, Timothy E.},
	month = nov,
	year = {2014},
	keywords = {Food web, Forage fish, Connectance, Diet matrix, Ecological metric},
	pages = {68--74},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/4BDD39M6/S0165783614001647.html:text/html},
}

@article{buchheister_evaluating_2017,
	title = {Evaluating {Ecosystem}-{Based} {Reference} {Points} for {Atlantic} {Menhaden}},
	volume = {9},
	issn = {null},
	url = {https://doi.org/10.1080/19425120.2017.1360420},
	doi = {10.1080/19425120.2017.1360420},
	abstract = {Implementation of an ecosystem approach to fisheries management (EAFM) for forage fish requires methods to evaluate tradeoffs associated with competing management objectives that focus on supporting fishery yields or providing food for predators. We developed an Ecopath with Ecosim ecosystem model of the U.S. Northwest Atlantic continental shelf (NWACS) for the period 1982–2013 to inform an EAFM for Atlantic Menhaden Brevoortia tyrannus. The model (with 61 trophic groups and 8 fishing fleets) was parameterized and fitted to time series using data from stock assessments, surveys, and literature. Fifty-year simulations evaluated how Atlantic Menhaden fishing mortality rates (F) influenced different ecosystem indicators, including population biomasses, fishery yields, prey-to-predator ratios, and the proportion of trophic groups that were positively or negatively affected. We quantified tradeoffs associated with a range of alternative ecosystem-based reference points for Atlantic Menhaden F and biomass (B), including F for maximum sustainable yield (FMSY), 0.5FMSY, proxies for current single-species F reference points, 75\% of virgin unfished biomass (B0), and 40\%B0. Striped Bass Morone saxatilis were most sensitive to increases in Atlantic Menhaden fishing, largely due to their strong dietary reliance on this prey species, but other higher-trophic-level groups (birds, highly migratory species, sharks, and marine mammals) were also negatively impacted. Other commercially important predators of Atlantic Menhaden (e.g., Bluefish Pomatomus saltatrix and Weakfish Cynoscion regalis) had moderate to negligible responses at the highest levels of Atlantic Menhaden F. The alternative reference points considered resulted in (1) variable Atlantic Menhaden biomasses (40–75\% of B0) and yields (54–100\% of MSY), (2) up to a 60\% decline in Striped Bass B and yield, (3) negative impacts on the B of ≤13\% of modeled groups, and (4) positive impacts on the B of ≤6\% of modeled groups. Simulations demonstrated the varied responses, potential winners and losers, and tradeoffs resulting from alternative management strategies for Atlantic Menhaden. These results and the NWACS model can help to advance an EAFM for Atlantic Menhaden and other fishes.Received April 4, 2017; accepted July 19, 2017},
	number = {1},
	urldate = {2022-10-17},
	journal = {Marine and Coastal Fisheries},
	author = {Buchheister, Andre and Miller, Thomas J. and Houde, Edward D.},
	month = jan,
	year = {2017},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/19425120.2017.1360420},
	pages = {457--478},
}

@article{northeast_area_monitoring__assessment_program_neamap_monitoring_2021,
	title = {Monitoring {Living} {Marine} {Resources} in the {Mid}‐{Atlantic} {Bight}:},
	url = {https://scholarworks.wm.edu/reports/2552},
	doi = {10.25773/K5BV-PP81},
	language = {en},
	urldate = {2022-10-21},
	journal = {Virginia Institute of Marine Science, William \& Mary},
	author = {Northeast Area Monitoring \& Assessment Program (NEAMAP), and Virginia Shark Monitoring \& Assessment Program (VASMAP) and Latour, Robert J. and Gartland, James and Bonzek, Christopher F.},
	year = {2021},
	note = {Publisher: Virginia Institute of Marine Science, William \& Mary},
	file = {Northeast Area Monitoring & Assessment Program (NEAMAP) and Virginia Shark Monitoring & Assessment Program (VASMAP) - 2021 - Monitoring Living Marine Resources in the Mid‐Atla.pdf:/Users/sarah.gaichas/Zotero/storage/TXHDWDCY/Northeast Area Monitoring & Assessment Program (NEAMAP) and Virginia Shark Monitoring & Assessment Program (VASMAP) - 2021 - Monitoring Living Marine Resources in the Mid‐Atla.pdf:application/pdf},
}

@book{zuur_mixed_2009,
	address = {New York, NY},
	series = {Statistics for {Biology} and {Health}},
	title = {Mixed effects models and extensions in ecology with {R}},
	isbn = {978-0-387-87457-9 978-0-387-87458-6},
	url = {http://link.springer.com/10.1007/978-0-387-87458-6},
	language = {en},
	urldate = {2022-10-24},
	publisher = {Springer},
	author = {Zuur, Alain F. and Ieno, Elena N. and Walker, Neil and Saveliev, Anatoly A. and Smith, Graham M.},
	year = {2009},
	doi = {10.1007/978-0-387-87458-6},
	keywords = {environment, phytoplankton, ecology, ecological analysis, ecological statistics, GLM, mixed effects modeling, plankton, R and ecology},
	file = {Full Text:/Users/sarah.gaichas/Zotero/storage/3VB54DIR/Zuur et al. - 2009 - Mixed effects models and extensions in ecology wit.pdf:application/pdf},
}

@article{soudijn_harvesting_2021,
	title = {Harvesting forage fish can prevent fishing-induced population collapses of large piscivorous fish},
	volume = {118},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.1917079118},
	doi = {10.1073/pnas.1917079118},
	abstract = {Fisheries have reduced the abundances of large piscivores—such as gadids (cod, pollock, etc.) and tunas—in ecosystems around the world. Fisheries also target smaller species—such as herring, capelin, and sprat—that are important parts of the piscivores’ diets. It has been suggested that harvesting of these so-called forage fish will harm piscivores. Multispecies models used for fisheries assessments typically ignore important facets of fish community dynamics, such as individual-level bioenergetics and/or size structure. We test the effects of fishing for both forage fish and piscivores using a dynamic, multitrophic, size-structured, bioenergetics model of the Baltic Sea. In addition, we analyze historical patterns in piscivore-biomass declines and fishing mortalities of piscivores and forage fish using global fish-stock assessment data. Our community-dynamics model shows that piscivores benefit from harvesting of their forage fish when piscivore fishing mortality is high. With substantial harvesting of forage fish, the piscivores can withstand higher fishing mortality. On the other hand, when piscivore fishing mortality is low, piscivore biomass decreases with more fishing of the forage fish. In accordance with these predictions, our statistical analysis of global fisheries data shows a positive interaction between the fishing mortalities of forage-fish stocks and piscivore stocks on the strength of piscivore-biomass declines. While overfishing of forage fish must be prevented, our study shows that reducing fishing pressures on forage fish may have unwanted negative side effects on piscivores. In some cases, decreasing forage-fish exploitation could cause declines, or even collapses, of piscivore stocks.},
	number = {6},
	urldate = {2022-10-26},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Soudijn, Floor H. and Daniël van Denderen, P. and Heino, Mikko and Dieckmann, Ulf and de Roos, André M.},
	month = feb,
	year = {2021},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e1917079118},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/KP59YJMF/Soudijn et al. - 2021 - Harvesting forage fish can prevent fishing-induced.pdf:application/pdf},
}

@article{nefsc_64th_2018,
	title = {64th {Northeast} {Regional} {Stock} {Assessment} {Workshop} (64th {SAW}) {Assessment} {Report}},
	url = {https://repository.library.noaa.gov/view/noaa/23690},
	doi = {10.25923/SWK4-1E81},
	urldate = {2022-10-27},
	journal = {Northeast Fisheries Science Center (U.S.) reference document},
	author = {NEFSC},
	year = {2018},
	note = {Publisher: Northeast Fisheries Science Center (U.S.)},
	annote = {SeriesInformation
Northeast Fisheries Science Center reference document ; 18-06},
}

@article{wiedenmann_something_2022,
	title = {Something strange in the neighborhood: {Diverging} signals in stock assessment data for {Northeast} {U}.{S}. fish stocks},
	volume = {29},
	issn = {1365-2400},
	shorttitle = {Something strange in the neighborhood},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fme.12532},
	doi = {10.1111/fme.12532},
	abstract = {In the Northeast U.S., many stock assessments have a history of problematic model diagnostics, with multiple age-based assessments recently being rejected in the peer review process, and are not suitable for management advice. The role in which diverging signals in the coastwide bottom trawl survey may be contributing to assessment problems was explored here for 18 stocks in the region. Specifically, trends in total mortality (Z) estimated from catch curve analysis and a relative measure of the harvest rate (total catch/survey index; called relative F) were evaluated. Across stocks, relative F has declined over time, on average, since the mid-1990s, yet Z has not for many stocks. Weak positive or even negative correlations between relative F and Z resulted for 13 stocks. This diverging signal appears to be contributing to assessment model performance, as larger retrospective patterns (a measure of assessment uncertainty) occurred for stocks with negative correlations between relative F and Z. While a variety of mechanisms could be involved in these diverging signals, the available evidence suggests that unreported catch and/or increasing natural mortality likely play a role to varying degrees for each stock.},
	language = {en},
	number = {3},
	urldate = {2022-10-27},
	journal = {Fisheries Management and Ecology},
	author = {Wiedenmann, John and Legault, Christopher M.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/fme.12532},
	keywords = {stock assessment, climate change, predation, groundfish, misreported catch, retrospective pattern},
	pages = {269--285},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/4XPAJRXK/fme.html:text/html},
}

@article{link_using_2004,
	title = {Using fish stomachs as samplers of the benthos: integrating long-term and broad scales},
	volume = {269},
	issn = {0171-8630, 1616-1599},
	shorttitle = {Using fish stomachs as samplers of the benthos},
	url = {https://www.int-res.com/abstracts/meps/v269/p265-275/},
	doi = {10.3354/meps269265},
	abstract = {Sampling benthic organisms in a synoptic manner is difficult, particularly at the scale of large marine ecosystems. Several known omnivorous and benthivorous fishes were evaluated as possible samplers of the benthic community on the scale of the
US northeast continental shelf ecosystem, collected from the early 1970s to 2001. Frequency of occurrence of organisms in the diet across time was examined as an index of relative abundance. Other prey and sampling caveats were accounted for by
considering only those predators that met criteria such as adequate sample size, appropriate diet compositions, asymptotic stomach-prey curves, and relative constancy of all major prey groups comprising the diet. The geographic distribution of a suite of
benthic organisms found in the stomachs of predators was also examined. The benthic organisms focused on were ophiuroids, echinoids, holothuroideans, asteroids, octopods, stomatopods, cumaceans, pagurids, aphroditids, anthozoans, hydrozoans and
caprellids. Of these 12 prey groups, only 3 showed a decline over time based on evidence from multiple predator stomachs. Most benthic organisms exhibited non-negative trends in an index of relative abundance, and 2 showed an increase over the
time-series. Additionally, many of the organisms were widely distributed, with some concentrated more on Georges Bank and others more in the Gulf of Maine. Only 1 of 9 organisms showed a shift in distribution compared to studies from 50 yr earlier. I
conclude that at broad spatial and temporal scales, the routine and systematic sampling of fish stomachs can be a useful indirect method for inferring information about benthic communities on continental shelves.},
	language = {en},
	urldate = {2022-10-27},
	journal = {Marine Ecology Progress Series},
	author = {Link, Jason S.},
	month = mar,
	year = {2004},
	keywords = {Georges Bank, Gulf of Maine, Spatial distribution, Abundance index, Benthic communities, Benthic ecology, Continental shelves, Disturbance, Fish feeding},
	pages = {265--275},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/QBPAZMMV/Link - 2004 - Using fish stomachs as samplers of the benthos in.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/CDUEEF9S/p265-275.html:text/html},
}

@article{cook_use_2012,
	title = {Use of fishes as sampling tools for understanding biodiversity and ecosystem functioning in the ocean},
	volume = {454},
	issn = {0171-8630, 1616-1599},
	url = {https://www.int-res.com/abstracts/meps/v454/p1-18/},
	doi = {10.3354/meps09773},
	abstract = {Across the globe, regulatory bodies are moving towards an ecosystem-based approach to management (EAM) of oceans. As part of this directive, criteria have been outlined for defining ecologically and biologically significant areas and marine protected areas. One of the first steps in identifying either is the development of an inventory of species’ spatial distributions and the identification of habitats used by different life history stages of these species. Many of these data have been gleaned from research vessel trawl surveys that only sample a slice of the ecosystem. Here, for the first time, food habits data collected from a trawl survey were integrated with the original trawl data to improve estimates of species richness, distribution, and habitat associations with the objective of providing additional information for an EAM. The inclusion of stomach content data increased the number and size range of species observed: its greatest value was in describing invertebrate and small finfish species richness. We found differences in the spatial patterns and the influence of environmental factors on species richness between stomach and trawl samples. We conclude that the addition of stomach data can en rich the de finition process for spatial management tools, adding dimensions that would otherwise be missed. This has important implications for EAM since we may not be using all of the resources at our disposal.},
	language = {en},
	urldate = {2022-10-27},
	journal = {Marine Ecology Progress Series},
	author = {Cook, A. M. and Bundy, A.},
	month = may,
	year = {2012},
	keywords = {Biodiversity, Ecosystem, Marine, Environmental factors, Species richness, Survey},
	pages = {1--18},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/6TE3BD9P/Cook and Bundy - 2012 - Use of fishes as sampling tools for understanding .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/YTU4LZP4/p1-18.html:text/html},
}

@article{lasley-rasher_it_2015,
	title = {It takes guts to locate elusive crustacean prey},
	volume = {538},
	issn = {0171-8630, 1616-1599},
	url = {https://www.int-res.com/abstracts/meps/v538/p1-12/},
	doi = {10.3354/meps11481},
	abstract = {Mobile crustacean prey, i.e. crangonid, euphausiid, mysid, and pandalid shrimp, are vital links in marine food webs. Their intermediate sizes and characteristic caridoid escape responses lead to chronic underestimation when sampling at large spatial scales with either plankton nets or large trawl nets. Here, as discrete sampling units, we utilized individual fish diets (i.e. fish biosamplers) collected by the US National Marine Fisheries Service and Northeast Fisheries Science Center to examine abundance and location of these prey families over large spatial and temporal scales in the northeastern US shelf large ecosystem. We found these prey families to be important to a wide variety of both juvenile and adult demersal fishes from Cape Hatteras to the Scotian Shelf. Fish biosamplers further revealed significant spatial shifts in prey in early spring. Distributions of mysids and crangonids in fish diets shoaled significantly from February to March. Distributions of euphausiids and pandalids in fish diets shifted northward during March. Of multiple hypotheses for these shifts, prey migration is most strongly supported. Rather than only the classic ontogenetic shift from feeding on shrimp to piscivory, of the 25 identified diet shifts in fish predators, 12 shifts were toward increased shrimp feeding frequency with increasing body length.},
	language = {en},
	urldate = {2022-10-27},
	journal = {Marine Ecology Progress Series},
	author = {Lasley-Rasher, R. S. and Brady, D. C. and Smith, B. E. and Jumars, P. A.},
	month = oct,
	year = {2015},
	keywords = {Northwest Atlantic, Pandalidae, Fish feeding, Crangonidae, Euphausiidae, Migration, Mysidae},
	pages = {1--12},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/LGWQYA6Q/Lasley-Rasher et al. - 2015 - It takes guts to locate elusive crustacean prey.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/I6JVF4JM/p1-12.html:text/html},
}

@article{robertson_accounting_2022,
	title = {Accounting for a nonlinear functional response when estimating prey dynamics using predator diet data},
	volume = {13},
	issn = {2041-210X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13795},
	doi = {10.1111/2041-210X.13795},
	abstract = {Forage fish species are key in the transfer of energy from lower to upper trophic levels in marine ecosystems. Therefore, understanding their population dynamics, including population levels, is crucial for understanding productivity and the regulation of marine food webs. However, many forage fishes are poorly sampled by bottom trawl surveys, leading to poor estimates of their abundance. These estimates can be improved by using predator stomachs contents as an additional sampling strategy; however, nonlinear relationships between prey abundance and predator consumption (i.e. the functional response) may bias stomachs data as well. Using predator stomachs contents and bottom trawl survey data, this study aimed to minimize this bias by developing a model to estimate prey dynamics and account for the predator functional response. This model was tested using a series of simulations and applied to a case study of northern sand lance Ammodytes dubius on the Grand Bank, Newfoundland, Canada. The simulations revealed that when predators consumed prey following a nonlinear functional response, our model outperformed a classical model (the model adopted by most studies) that assumed a linear functional response. In the case study, we estimated the relative abundance of sand lance from 1995 to 2018, which exhibited oscillatory dynamics with a period of approximately 7 years. Our results demonstrate that our model is capable of more accurately estimating the abundance of data-limited prey populations, which contributes to a better understanding of food web dynamics.},
	language = {en},
	number = {4},
	urldate = {2022-10-27},
	journal = {Methods in Ecology and Evolution},
	author = {Robertson, Matthew D. and Koen-Alonso, Mariano and Regular, Paul M. and Cadigan, Noel and Zhang, Fan},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.13795},
	keywords = {food web, forage fish, population dynamics, Grand Bank, integrated model, sand lance},
	pages = {880--893},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/X2DJUFCE/2041-210X.html:text/html},
}

@article{sydeman_integrating_2022,
	title = {Integrating seabird dietary and groundfish stock assessment data: {Can} puffins predict pollock spawning stock biomass in the {North} {Pacific}?},
	volume = {23},
	issn = {1467-2979},
	shorttitle = {Integrating seabird dietary and groundfish stock assessment data},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12611},
	doi = {10.1111/faf.12611},
	abstract = {Information on the annual variability in abundance and growth of juvenile groundfish can be useful for predicting fisheries stocks, but is often poorly known owing to difficulties in sampling fish in their first year of life. In the Western Gulf of Alaska (WGoA) and Eastern Bering Sea (EBS) ecosystems, three species of puffin (tufted and horned puffin, Fratercula cirrhata, Fratercula corniculata, and rhinoceros auklet, Cerorhinca monocerata, Alcidae), regularly prey upon (i.e., “sample”) age-0 groundfish, including walleye pollock (Gadus chalcogramma, Gadidae) and Pacific cod (Gadus microcephalus, Gadidae). Here, we test the hypothesis that integrating puffin dietary data with walleye pollock stock assessment data provides information useful for fisheries management, including indices of interannual variation in age-0 abundance and growth. To test this hypothesis, we conducted cross-correlation and regression analyses of puffin-based indices and spawning stock biomass (SSB) for the WGoA and EBS walleye pollock stocks. For the WGoA, SSB leads the abundance of age-0 fish in the puffin diet, indicating that puffins sample the downstream production of the WGoA spawning stock. By contrast, the abundance and growth of age-0 fish sampled by puffins lead SSB for the EBS stock by 1–3 years, indicating that the puffin diet proxies incoming year class strength for this stock. Our study indicates connectivity between the WGoA and EBS walleye pollock stocks. Integration of non-traditional data sources, such as seabird diet data, with stock assessment data appears useful to inform information gaps important for managing US fisheries in the North Pacific.},
	language = {en},
	number = {1},
	urldate = {2022-10-27},
	journal = {Fish and Fisheries},
	author = {Sydeman, William J. and Thompson, Sarah Ann and Piatt, John F. and Zador, Stephani G. and Dorn, Martin W.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12611},
	keywords = {spawning stock biomass, leading indicators, marine bird food habits, Northeast Pacific, puffins, verification},
	pages = {213--226},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/6IQWY7ZH/Sydeman et al. - 2022 - Integrating seabird dietary and groundfish stock a.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/M9Y7T5C9/faf.html:text/html},
}

@article{smith_multispecies_2020,
	title = {Multispecies functional responses reveal reduced predation at high prey densities and varied responses among and within trophic groups},
	volume = {21},
	issn = {1467-2979},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12468},
	doi = {10.1111/faf.12468},
	abstract = {Understanding predator–prey interactions is critical for marine fisheries and ecosystem management as they shape community structure, regulate prey populations and present energy demands critical for community sustainability. We examined multispecies functional responses of 17 fishes (48 predator-size combinations) spanning piscivores, planktivores and benthivores for the northeast US continental shelf. Similar to previous work, linear relationships between predation and prey density (Holling type I response) were not supported, since model estimates of handling time were greater than zero for the prey considered. Instead, a clear majority of the predators sampled were Holling type III feeders (sigmoidal; prey switching or learning). For piscivores, nearly all responses were Holling type III with the exception of one being Holling type II (hyperbolic; satiation). Planktivores and benthivores exhibited a combination of type IV (feeding confusion at high prey density) and Holling type III responses. The relationships were predator- and prey-dependent, which is counter to assumptions that are often made of trophic groups. Decreased predation at high prey densities (type IV response) present among planktivores and benthivores suggests an overestimation of predation can occur if ignored. This contrasts with fish and squid prey which primarily invoked a Holling type III response. Functional responses are key to modelling trophic interactions for multispecies and ecosystem models. By refining these inputs in a multispecies context with empirical data, we can advance our understanding of whole-shelf ecology and improve decision-making tools for resource management.},
	language = {en},
	number = {5},
	urldate = {2022-10-27},
	journal = {Fish and Fisheries},
	author = {Smith, Brian E. and Smith, Laurel A.},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12468},
	keywords = {Northwest Atlantic, trophic interactions, continental shelf, Bayesian inference, feeding guilds, functional feeding response},
	pages = {891--905},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/2BBGVKHA/faf.html:text/html},
}

@article{mills_diets_2007,
	title = {Diets of top predators indicate pelagic juvenile rockfish ({Sebastes} spp.) abundance in the {California} {Current} {System}},
	volume = {16},
	issn = {1365-2419},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2419.2007.00429.x},
	doi = {10.1111/j.1365-2419.2007.00429.x},
	abstract = {Diets of top predators may be useful indicators to the availability of forage fish in marine ecosystems. Juvenile rockfish (young-of-the-year Sebastes spp.) compose a significant part of the diet for many predators in the central California Current, including chinook salmon (Oncorhynchus tshawytscha), and several species of marine birds and mammals. Herein, we develop annual indices of juvenile rockfish relative abundance by collating time series data sets on: (i) the proportion of rockfish in the diet of three species of seabirds breeding on Southeast Farallon Island (1975–2002); (ii) the number of rockfish in chinook salmon stomachs (1980–99); and (iii) the abundance of rockfish captured in scientific mid-water trawl net surveys (1983–2002). We used Principal Component Analysis (PCA) to combine indices, and refer to these as ‘Multivariate Rockfish Indices’ (MRI). Combining time series verifies the patterns shown by each alone and provides a synoptic perspective on juvenile rockfish relative abundance. The diets of predators with the largest foraging ranges (Common Murre, Uria aalge) and chinook salmon co-varied strongly with the net samples, and appear to be the best indicators. The salmon also sampled species of Sebastes not caught in the nets. The MRI reveals interannual variability in juvenile rockfish abundance, a substantial decline in abundance in the 1990s, and a partial recovery in the early 2000s. Predator-based sampling is a cost-effective enhancement of scientific net sampling.},
	language = {en},
	number = {3},
	urldate = {2022-10-27},
	journal = {Fisheries Oceanography},
	author = {Mills, K. L. and Laidig, T. and Ralston, S. and Sydeman, W. J.},
	year = {2007},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2419.2007.00429.x},
	keywords = {diet, Principal Component Analysis, ecosystem approach, seabirds, indicators, climate variability, California Current System, Cepphus columba, Cerorhinca monocerata, chinook salmon, Oncorhynchus tshawytscha, rockfish, Sebastes, Uria aalge},
	pages = {273--283},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/96QS5FGQ/j.1365-2419.2007.00429.html:text/html},
}

@article{rohan_spatial_2017,
	title = {Spatial and ontogenetic patterns of {Pacific} cod ({Gadus} macrocephalus {Tilesius}) predation on octopus in the eastern {Bering} {Sea}},
	volume = {100},
	issn = {1573-5133},
	url = {https://doi.org/10.1007/s10641-016-0561-2},
	doi = {10.1007/s10641-016-0561-2},
	abstract = {In 2012, the North Pacific Fishery Management Council adopted a consumption-based stock assessment method to determine catch limits for the non-target, multi-species octopus complex in the Bering Sea-Aleutian Islands (BSAI) fishery management area. The method uses Pacific cod (Gadus macrocephalus) diet data as a basis for estimating octopus complex natural mortality and minimum biomass. To enhance understanding of the predator-prey interaction between Pacific cod and octopus, we examined patterns of octopus consumption by Pacific cod using long-term stomach contents data from the eastern Bering Sea continental shelf, a large, ecologically unique subarea of the BSAI. Generalized additive modeling of octopus presence/absence in Pacific cod diets revealed distinct spatial, ontogenetic and seasonal consumption patterns. Prey octopus frequency of occurrence (FO) generally increased with bottom depth, latitude and Pacific cod fork length, and FO in the southern BSAI was lower during winter and spring than during summer. Prey octopus FO patterns may reflect overall consumption patterns and likely indicate long-term distribution patterns of small-sized ({\textless}1 kg) octopus on the EBS shelf, although we could not visually distinguish between octopus species using prey remains. Multi-species beak length-to-body mass regressions developed from three octopus species allowed reasonable estimation of prey octopus mass, and we found Pacific cod fork length was positively correlated with prey octopus mass, suggesting predator-prey interactions are sensitive to predator and prey size composition. Pacific cod consumed octopus with estimated masses ranging from 0.000017 kg to 4.62 kg, while octopus taken during concurrent bottom trawl surveys range from 0.05 kg to greater than 25 kg. Based on our findings, we expect the consumption-based stock assessment underestimates BSAI octopus complex biomass because it cannot account for larger octopus, such as the 10–20 kg Enteroctopus dofleini which dominate incidental take in BSAI Pacific cod pot fishery.},
	language = {en},
	number = {4},
	urldate = {2022-10-27},
	journal = {Environmental Biology of Fishes},
	author = {Rohan, Sean K. and Buckley, Troy W.},
	month = apr,
	year = {2017},
	keywords = {Bering Sea, Pacific cod, Beak measurement, Giant octopus, Predator-prey interaction},
	pages = {361--373},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/LR9YZLM7/Rohan and Buckley - 2017 - Spatial and ontogenetic patterns of Pacific cod (G.pdf:application/pdf},
}

@article{fahrig_predator_1993,
	title = {Predator {Stomachs} as {Sampling} {Tools} for {Prey} {Distribution}: {Atlantic} {Cod} ( \textit{{Gadus} morhua} ) and {Capelin} ( \textit{{Mallotus} villosus} )},
	volume = {50},
	issn = {0706-652X, 1205-7533},
	shorttitle = {Predator {Stomachs} as {Sampling} {Tools} for {Prey} {Distribution}},
	url = {http://www.nrcresearchpress.com/doi/10.1139/f93-175},
	doi = {10.1139/f93-175},
	abstract = {We demonstrate a direct relationship between the amount of prey (capelin, Mallotus villosus) in its predators' stomachs (Atlantic cod, Gadus morhua) and the biomass of the prey in the same localities. The relationship at a local scale implies that predator stomach contents can be used to estimate prey distribution. There is no evidence for either (1) a negative effect of local predator abundance on stomach contents (expected if local prey depletion and/or feeding interference occurs when predator density is high) or (2) a negative effect of the amount of other food in cod stomachs on the amount of capelin in the stomachs (expected if prey switching occurs). There is a negative effect of bottom depth on amount of capelin in cod stomachs as expected, since capelin are pelagic and cod are primarily bottom-dwelling, resulting in less vertical overlap between the species in deep water. This type of analysis may be useful in other predator–prey systems. Simultaneous stomach samples and independent biomass estimates of the prey are required, but once the model is built, it permits estimation of prey distribution in places and times when no direct survey of the prey can be done.},
	language = {en},
	number = {7},
	urldate = {2022-10-27},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Fahrig, Lenore and Lilly, George R. and Miller, Daniel S.},
	month = jul,
	year = {1993},
	pages = {1541--1547},
	file = {Fahrig_et_al_1993-Predator-stomachs-as-sampling-tools.pdf:/Users/sarah.gaichas/Zotero/storage/HQWGXTLA/Fahrig_et_al_1993-Predator-stomachs-as-sampling-tools.pdf:application/pdf},
}

@article{nefsc_2022_2022,
	title = {2022 {State} of the {Ecosystem} {Mid}-{Atlantic}},
	url = {https://apps-nefsc.fisheries.noaa.gov/rcb/publications/soe/SOE-MAFMC_2022_Final.pdf},
	language = {en},
	journal = {Northeast Fisheries Science Center (U.S.)},
	author = {NEFSC},
	year = {2022},
	pages = {48},
	file = {2022 State of the Ecosystem Mid-Atlantic.pdf:/Users/sarah.gaichas/Zotero/storage/EJFBT9LJ/2022 State of the Ecosystem Mid-Atlantic.pdf:application/pdf},
}

@article{staudinger_role_2020,
	title = {The role of sand lances ({Ammodytes} sp.) in the {Northwest} {Atlantic} {Ecosystem}: {A} synthesis of current knowledge with implications for conservation and management},
	volume = {21},
	issn = {1467-2979},
	shorttitle = {The role of sand lances ({Ammodytes} sp.) in the {Northwest} {Atlantic} {Ecosystem}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12445},
	doi = {10.1111/faf.12445},
	abstract = {The American sand lance (Ammodytes americanus, Ammodytidae) and the Northern sand lance (A. dubius, Ammodytidae) are small forage fishes that play an important functional role in the Northwest Atlantic Ocean (NWA). The NWA is a highly dynamic ecosystem currently facing increased risks from climate change, fishing and energy development. We need a better understanding of the biology, population dynamics and ecosystem role of Ammodytes to inform relevant management, climate adaptation and conservation efforts. To meet this need, we synthesized available data on the (a) life history, behaviour and distribution; (b) trophic ecology; (c) threats and vulnerabilities; and (d) ecosystem services role of Ammodytes in the NWA. Overall, 72 regional predators including 45 species of fishes, two squids, 16 seabirds and nine marine mammals were found to consume Ammodytes. Priority research needs identified during this effort include basic information on the patterns and drivers in abundance and distribution of Ammodytes, improved assessments of reproductive biology schedules and investigations of regional sensitivity and resilience to climate change, fishing and habitat disturbance. Food web studies are also needed to evaluate trophic linkages and to assess the consequences of inconsistent zooplankton prey and predator fields on energy flow within the NWA ecosystem. Synthesis results represent the first comprehensive assessment of Ammodytes in the NWA and are intended to inform new research and support regional ecosystem-based management approaches.},
	language = {en},
	number = {3},
	urldate = {2022-11-01},
	journal = {Fish and Fisheries},
	author = {Staudinger, Michelle D. and Goyert, Holly and Suca, Justin J. and Coleman, Kaycee and Welch, Linda and Llopiz, Joel K. and Wiley, David and Altman, Irit and Applegate, Andew and Auster, Peter and Baumann, Hannes and Beaty, Julia and Boelke, Deirdre and Kaufman, Les and Loring, Pam and Moxley, Jerry and Paton, Suzanne and Powers, Kevin and Richardson, David and Robbins, Jooke and Runge, Jeffrey and Smith, Brian and Spiegel, Caleb and Steinmetz, Halley},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12445},
	keywords = {ecosystem-based management, forage fish, life history, trophic ecology, sand lance, Ammodytes},
	pages = {522--556},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/B34NPC4B/Staudinger et al. - 2020 - The role of sand lances (Ammodytes sp.) in the Nor.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/WDCYR2JA/faf.html:text/html},
}

@article{link_does_2002,
	title = {Does food web theory work for marine ecosystems?},
	volume = {230},
	issn = {0171-8630, 1616-1599},
	url = {https://www.int-res.com/abstracts/meps/v230/p1-9/},
	doi = {10.3354/meps230001},
	abstract = {More recent and extensive food web studies have questioned some of the prevailing paradigms of food web theory. Yet with few exceptions, most food webs and associated metrics are reported for freshwater or terrestrial systems. I analyzed the
food web of the Northeast US Shelf ecosystem across a large spatial and temporal extent. This speciose food web exhibits a predator:prey ratio (0.95) and percentage of intermediate species (89\%) similar to most other food webs. Other statistics, such as
the percentage of omnivory (62\%), percentage of cannibalistic species (31\%), number of cycles (5\%), and the total number of links (L; 1562) and species (S; 81) are similar to more recent and extensively studied food webs. Finally, this food
web exhibits a linkage density (L/S; 19.3), connectivity (C; 48.2\%), and Lyapunov stability proxy (S x C; 39.1) that are an order of magnitude higher than other webs or are disproportionate to
the number of species observed in this system. Although the exact S and C relationship is contentious, the connectivity of food webs with more than 40 species is approximately 10\%, which is very different from the near 50\% observed for this
ecosystem. The openness of marine ecosystems, lack of specialists, long lifespans, and large size changes across the life histories of many marine species can collectively make marine food webs more highly connected than their terrestrial and freshwater
counterparts, contrary to food web theory. Changes in connectivity also have ramifications for ecosystem functioning and Lyapunov stability. The high connectivity of this food web and the mathematical determinants for stability are consistent with the
weak nature of species interactions that have been observed and that are required for system persistence. Yet the historically high exploitation rates of marine organisms obfuscate our understanding of marine food web stability. It is possible that marine
food webs are inherently very different from their terrestrial or freshwater counterparts, implying the need for modified paradigms of food web theory.},
	language = {en},
	urldate = {2022-11-04},
	journal = {Marine Ecology Progress Series},
	author = {Link, Jason},
	month = apr,
	year = {2002},
	keywords = {Species interactions, Connectivity, Continental shelf, Food web dynamics, Predator, Prey, Stability},
	pages = {1--9},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/MCNNKWV7/Link - 2002 - Does food web theory work for marine ecosystems.pdf:application/pdf;Marine Ecology Progress Series 230\:1 - m230p001.pdf:/Users/sarah.gaichas/Zotero/storage/MEKMZXCH/m230p001.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/2YUJF6D2/p1-9.html:text/html},
}

@article{jones_learning_2022,
	title = {Learning {From} the {Study} {Fleet}: {Maintenance} of a {Large}-{Scale} {Reference} {Fleet} for {Northeast} {U}.{S}. {Fisheries}},
	volume = {9},
	issn = {2296-7745},
	shorttitle = {Learning {From} the {Study} {Fleet}},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.869560},
	abstract = {Logbook data from commercial fisheries are a vital component in the machinery of management, including tracking the volume of catches and allocating catch spatially. At the same time, logbooks can provide a unique window into the ecological and sociological conditions in marine fisheries, where fishermen interact with marine species and environments frequently and broadly. Traditional logbooks, however, often are not sufficiently standardized (when personal logs), or lack the detail (when regulatory documents) required to adequately understand fisheries ecosystems. The Study Fleet program, operated by the Northeast Fisheries Science Center’s Cooperative Research Branch, was developed to address these shortfalls by engaging members of the fishing industry in collecting high-resolution catch, effort, and environmental data using electronic logbooks. Since its inception, the Study Fleet has expanded from a small project focused on collecting detailed catch information from the New England multispecies groundfish fishery to a program with a wider scope encompassing a variety of fisheries, gears, and environmental parameters from North Carolina to Maine U.S. Over the years, a number of lessons have been learned about recruiting and supporting industry partners, managing the data, evolving technical specifications, and the challenges associated with analyzing and applying self-reported fisheries data. Here we describe the current state of the program and provide summaries of the Study Fleet program operations and outcomes from 2007-2020, with an eye towards successes, challenges, and applicability of the approach in other regions. We suggest other reference fleet programs, as well as other developing fishery dependent data collections (e.g., electronic monitoring programs), develop detailed roadmaps for each data collection to keep participants engaged as collaborators, target specific fisheries to keep resources from being stretched too thin, and partner with data users early. Additionally, we suggest programs invest in the long-term participation of individual fishermen, carefully weigh the pros and cons of involvement in regulatory reporting, and plan data products and applications well in advance to ensure that the sampling scheme and granularity of the data meet the needs of stock assessment, ecosystem, and oceanographic scientists.},
	urldate = {2022-11-15},
	journal = {Frontiers in Marine Science},
	author = {Jones, Andrew W. and Burchard, Katie A. and Mercer, Anna M. and Hoey, John J. and Morin, Michael D. and Gianesin, Giovanni L. and Wilson, Jacob A. and Alexander, Calvin R. and Lowman, Brooke A. and Duarte, Debra G. and Goethel, David and Ford, James and Ruhle, James and Sykes, Rodman and Sawyer, Troy},
	year = {2022},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/6EJQGXUH/Jones et al. - 2022 - Learning From the Study Fleet Maintenance of a La.pdf:application/pdf},
}

@article{checkley_climate_2017,
	title = {Climate, {Anchovy}, and {Sardine}},
	volume = {9},
	url = {https://doi.org/10.1146/annurev-marine-122414-033819},
	doi = {10.1146/annurev-marine-122414-033819},
	abstract = {Anchovy and sardine populated productive ocean regions over hundreds of thousands of years under a naturally varying climate, and are now subject to climate change of equal or greater magnitude occurring over decades to centuries. We hypothesize that anchovy and sardine populations are limited in size by the supply of nitrogen from outside their habitats originating from upwelling, mixing, and rivers. Projections of the responses of anchovy and sardine to climate change rely on a range of model types and consideration of the effects of climate on lower trophic levels, the effects of fishing on higher trophic levels, and the traits of these two types of fish. Distribution, phenology, nutrient supply, plankton composition and production, habitat compression, fishing, and acclimation and adaptation may be affected by ocean warming, acidification, deoxygenation, and altered hydrology. Observations of populations and evaluation of model skill are essential to resolve the effects of climate change on these fish.},
	number = {1},
	urldate = {2023-01-26},
	journal = {Annual Review of Marine Science},
	author = {Checkley, David M. and Asch, Rebecca G. and Rykaczewski, Ryan R.},
	year = {2017},
	pmid = {28045355},
	note = {\_eprint: https://doi.org/10.1146/annurev-marine-122414-033819},
	keywords = {fish, variability, change, mixing, nitrate, river, upwelling},
	pages = {469--493},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/JBBBCQZY/Checkley et al. - 2017 - Climate, Anchovy, and Sardine.pdf:application/pdf},
}

@article{thompson_indicators_2019,
	title = {Indicators of pelagic forage community shifts in the {California} {Current} {Large} {Marine} {Ecosystem}, 1998–2016},
	volume = {105},
	issn = {1470-160X},
	url = {https://www.sciencedirect.com/science/article/pii/S1470160X19304029},
	doi = {10.1016/j.ecolind.2019.05.057},
	abstract = {Forage fishes are ecologically and economically important in marine ecosystems worldwide and thus are a focal topic for ecosystem-based fisheries management. In the California Current Large Marine Ecosystem (CCLME), the community dynamics of forage populations have been studied at regional spatial scales, but not across regions. To evaluate indicators of the forage community at the ecosystem-wide scale, we examine temporal variability of forage assemblages in Northern (Oregon/Washington), Central (California; Point Reyes to Monterey Bay) and Southern (southern California) regions of the CCLME from 1998 through 2016 which include years with unprecedented climate variability. Forage communities fluctuated greatly between years within each region owing to regionally low abundances of common taxa in at least some years (e.g., rockfishes Sebastes spp. in each region). Comparison of species assemblages among regions indicate that that temporal shifts in assemblage structure were largely synchronous throughout the CCLME. However, dynamics of most individual taxa were out of phase between regions, indicating that different taxa drove the variability in each region. Within regions, taxa with similar adult ecological niches tended to co-vary, suggesting synchronous responses to environmental forcing. Major changes in forage assemblage structure are descriptively linked to large oceanographic perturbations such as the transition from El Niño to La Niña conditions in 1998, anomalous upwelling in 2005, and the onset of a large marine heatwave in fall-winter 2013–2014. Changes in forage assemblage structure are reflected in prey switching in the diet of California sea lions, Zalophus californianus, in the Southern region. The multivariate forage indices that we develop can serve as effective indicators of regional forage community composition shifts in the CCLME and provide managers with context on spatio-temporal changes in the structure of forage fish communities important to top predators in this system.},
	language = {en},
	urldate = {2023-01-26},
	journal = {Ecological Indicators},
	author = {Thompson, Andrew R. and Harvey, Chris J. and Sydeman, William J. and Barceló, Caren and Bograd, Steven J. and Brodeur, Richard D. and Fiechter, Jerome and Field, John C. and Garfield, Newell and Good, Thomas P. and Hazen, Elliott L. and Hunsicker, Mary E. and Jacobson, Kym and Jacox, Michael G. and Leising, Andrew and Lindsay, Joshua and Melin, Sharon R. and Santora, Jarrod A. and Schroeder, Isaac D. and Thayer, Julie A. and Wells, Brian K. and Williams, Gregory D.},
	month = oct,
	year = {2019},
	keywords = {Ecosystem-based management, Indicators, Food web ecology, California Current Large Marine Ecosystem, Forage, Predators, Spatial heterogeneity, Trophic dynamics},
	pages = {215--228},
	file = {Accepted Version:/Users/sarah.gaichas/Zotero/storage/SY5E8I77/Thompson et al. - 2019 - Indicators of pelagic forage community shifts in t.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/ES6E5HSK/S1470160X19304029.html:text/html},
}

@article{rice_management_2014,
	title = {Management of fisheries on forage species: the test-bed for ecosystem approaches to fisheries},
	volume = {71},
	issn = {1095-9289, 1054-3139},
	shorttitle = {Management of fisheries on forage species},
	url = {https://academic.oup.com/icesjms/article/71/1/143/645606},
	doi = {10.1093/icesjms/fst151},
	abstract = {In the 1970s and 1980s, core ideas about management of fisheries on forage species emerged from work on the dynamics of foodweb models and multispecies assessments, leading to proposals for management that took some account of the role of forage species in marine ecosystems. Key developments in those years are summarized in the first part of this paper. From the 1980s to the 2000s, studies of the response of forage species to environmental variation brought into question the robustness of management strategies for forage species. As a result, additional management strategies were proposed to accommodate environmental drivers as well as dependent predators. The paper reviews these developments. This paper brings these separate lines together in a systematic framework for evaluating the performance of six different management strategies for forage species, relative to four different ecosystem considerations, as well as relative to the contribution of forage fisheries to economic prosperity and food security. The tabulated outcomes synthesize primary and secondary literature and meeting deliberations as the application of an ecosystem approach to management has evolved. No strategy is optional for all forage fisheries. As experience accumulates, the guidance in the tables comprising the framework will improve.},
	language = {en},
	number = {1},
	urldate = {2023-01-26},
	journal = {ICES Journal of Marine Science},
	author = {Rice, Jake and Duplisea, Daniel},
	month = jan,
	year = {2014},
	pages = {143--152},
	file = {Rice and Duplisea - 2014 - Management of fisheries on forage species the tes.pdf:/Users/sarah.gaichas/Zotero/storage/IKVUQAS5/Rice and Duplisea - 2014 - Management of fisheries on forage species the tes.pdf:application/pdf},
}

@article{mcgowan_variability_2019,
	series = {Understanding {Ecosystem} {Processes} in the {Gulf} of {Alaska}: {Volume} 2},
	title = {Variability in species composition and distribution of forage fish in the {Gulf} of {Alaska}},
	volume = {165},
	issn = {0967-0645},
	url = {https://www.sciencedirect.com/science/article/pii/S0967064516303824},
	doi = {10.1016/j.dsr2.2016.11.019},
	abstract = {In the Gulf of Alaska (GOA), forage fish species, such as age-0 walleye pollock (Gadus chalcogrammus), capelin (Mallotus villosus), Pacific herring (Clupea pallasii), and mesopelagic fishes (e.g. Myctophidae), are ecologically important as both consumers of zooplankton, and as prey for fish, seabirds, and marine mammals. As part of the Gulf of Alaska Integrated Ecosystem Research Program, an acoustic-trawl survey was conducted in the summer and fall of 2011 and 2013 to quantify variability in species composition, density, and distributions of forage fish over the continental shelf and slope in the central and eastern regions of the GOA. The forage fish community in 2011 was characterized by the absence of age-0 pollock and lower densities of capelin, herring, and mesopelagics compared to observations in 2013. Age-0 pollock were abundant across both regions in summer 2013, but were rarely observed in fall. In contrast, summer observations of herring were rare, while aggregations of herring were observed over the eastern GOA shelf in fall of both years. Seasonal changes in community composition are attributed to the transport of age-0 pollock from offshore waters in summer to nearshore waters in fall, and to immigration of herring to the eastern GOA shelf in fall. Forage fish spatial patterns varied within and between regions due to intra- and interspecific differences in horizontal and vertical distributions that were correlated with bottom depth. Observed spatial and temporal variability in community composition and distributions of forage fish species may potentially impact predator foraging in the GOA, as well as the effectiveness of monitoring to detect changes in forage fish biomass.},
	language = {en},
	urldate = {2023-01-27},
	journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
	author = {McGowan, David W. and Horne, John K. and Parker-Stetter, Sandra L.},
	month = jul,
	year = {2019},
	keywords = {Gulf of Alaska, forage fish, distribution, walleye pollock, Capelin, mesopelagic, Pacific herring, wavelets},
	pages = {221--237},
	file = {Accepted Version:/Users/sarah.gaichas/Zotero/storage/DMW92QYV/McGowan et al. - 2019 - Variability in species composition and distributio.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/WSZAWGSH/S0967064516303824.html:text/html},
}

@article{engelhard_forage_2014,
	title = {Forage fish, their fisheries, and their predators: who drives whom?},
	volume = {71},
	issn = {1054-3139},
	shorttitle = {Forage fish, their fisheries, and their predators},
	url = {https://doi.org/10.1093/icesjms/fst087},
	doi = {10.1093/icesjms/fst087},
	abstract = {Engelhard, G. H., Peck, M. A., Rindorf, A., Smout, S. C., van Deurs, M., Raab, K., Andersen, K. H., Garthe, S., Lauerburg, R. A. M., Scott, F., Brunel, T., Aarts, G., van Kooten, T., and Dickey-Collas, M. Forage fish, their fisheries, and their predators: who drives whom? – ICES Journal of Marine Science, 71: .The North Sea has a diverse forage fish assemblage, including herring, targeted for human consumption; sandeel, sprat, and Norway pout, exploited by industrial fisheries; and some sardine and anchovy, supporting small-scale fisheries. All show large abundance fluctuations, impacting on fisheries and predators. We review field, laboratory, and modelling studies to investigate the drivers of this complex system of forage fish. Climate clearly influences forage fish productivity; however, any single-species considerations of the influence of climate might fail if strong interactions between forage fish exist, as in the North Sea. Sandeel appears to be the most important prey forage fish. Seabirds are most dependent on forage fish, due to specialized diet and distributional constraints (breeding colonies). Other than fisheries, key predators of forage fish are a few piscivorous fish species including saithe, whiting, mackerel, and horse-mackerel, exploited in turn by fisheries; seabirds and seals have a more modest impact. Size-based foodweb modelling suggests that reducing fishing mortality may not necessarily lead to larger stocks of piscivorous fish, especially if their early life stages compete with forage fish for zooplankton resources. In complex systems, changes in the impact of fisheries on forage fish may have potentially complex (and perhaps unanticipated) consequences on other commercially and/or ecologically important species.},
	number = {1},
	urldate = {2023-01-27},
	journal = {ICES Journal of Marine Science},
	author = {Engelhard, Georg H. and Peck, Myron A. and Rindorf, Anna and C. Smout, Sophie and van Deurs, Mikael and Raab, Kristina and Andersen, Ken H. and Garthe, Stefan and Lauerburg, Rebecca A.M. and Scott, Finlay and Brunel, Thomas and Aarts, Geert and van Kooten, Tobias and Dickey-Collas, Mark},
	month = jan,
	year = {2014},
	pages = {90--104},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/S9W3GHLV/Engelhard et al. - 2014 - Forage fish, their fisheries, and their predators.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/FYLBVSK8/643678.html:text/html},
}

@article{hilborn_recent_2022,
	title = {Recent trends in abundance and fishing pressure of agency-assessed small pelagic fish stocks},
	volume = {23},
	issn = {1467-2979},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12690},
	doi = {10.1111/faf.12690},
	abstract = {Small pelagic fishes are used for human consumption, fishmeal and fish oil. They constitute 25\% of global fish catch and have been of considerable conservation concern because of their intermediate position in aquatic food webs, often being a dominant dietary component of marine predators. This paper provides an overview of trends in abundance and fishing pressure on small pelagic fish stocks from single-species scientific assessments that constitute 60\% of global small pelagic catch. While most individual stocks have exhibited wide variability in abundance (typical of small pelagics compared with other fish taxa), across stocks there has been remarkable stability in average fishing pressure and biomass since 1970. On average, since 1970, the biomass of assessed small pelagic stocks is estimated to have been slightly above the biomass that would produce maximum sustainable yield, but estimation of this quantity for highly fluctuating stocks is quite uncertain. There were significant differences among assessed regions, with the Mediterranean and Black Sea of greatest concern for high and growing fishing pressure. The 40\% of global small pelagic fish catch not covered by single-species quantitative stock assessments since 1970 comes largely from Asia, where catches have continued to increase. At regional levels, the average abundance of assessed small pelagic fish is largely unrelated to average fishing pressure, which we argue results both from the portfolio effect, where numerous stocks fluctuate with little correlation in abundance, and from the short life span of small pelagics coupled with recruitment largely independent of spawning abundance.},
	language = {en},
	number = {6},
	urldate = {2023-03-16},
	journal = {Fish and Fisheries},
	author = {Hilborn, Ray and Buratti, Claudio C. and Díaz Acuña, Erich and Hively, Daniel and Kolding, Jeppe and Kurota, Hiroyuki and Baker, Nicole and Mace, Pamela M. and de Moor, Carryn L. and Muko, Soyoka and Osio, Giacomo Chato and Parma, Ana M. and Quiroz, Juan-Carlos and Melnychuk, Michael C.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12690},
	keywords = {fisheries management, overfishing, small pelagic fish, small pelagic fishes, sustainable fishing},
	pages = {1313--1331},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/LN5V7B7V/Hilborn et al. - 2022 - Recent trends in abundance and fishing pressure of.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/X9NSKJPK/faf.html:text/html},
}

@article{isaacs_humble_2016,
	title = {The humble sardine (small pelagics): fish as food or fodder},
	volume = {5},
	issn = {2048-7010},
	shorttitle = {The humble sardine (small pelagics)},
	url = {https://doi.org/10.1186/s40066-016-0073-5},
	doi = {10.1186/s40066-016-0073-5},
	abstract = {The group of small pelagic fish is the largest species group landed globally. A significant proportion of this nutrient-rich food is processed and lost to livestock feed, fish feed, fish oil, pet food and omega-rich vitamins. The nutritional importance of small pelagics as an easily digestible protein source, rich in essential lipids with fatty acids (EPA/DHA), essential amino acids, minerals and vitamins, is well known and documented. Small pelagics contain all the elements of a healthy and nutritionally optimal food source for humans and are an important contributor to the food and nutritional security of many poor, low-income households in developing countries.},
	number = {1},
	urldate = {2023-03-16},
	journal = {Agriculture \& Food Security},
	author = {Isaacs, Moenieba},
	month = nov,
	year = {2016},
	keywords = {Food security, Small pelagics, Consumption, Large-scale, Nutrition, Small-scale, South Africa, Tanzania},
	pages = {27},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/4Q75ALAD/Isaacs - 2016 - The humble sardine (small pelagics) fish as food .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/B4RDQY7R/s40066-016-0073-5.html:text/html},
}

@article{peck_small_2021,
	title = {Small pelagic fish in the new millennium: {A} bottom-up view of global research effort},
	volume = {191},
	issn = {0079-6611},
	shorttitle = {Small pelagic fish in the new millennium},
	url = {https://www.sciencedirect.com/science/article/pii/S0079661120302299},
	doi = {10.1016/j.pocean.2020.102494},
	abstract = {Small pelagic fish (SPF) play extremely important ecological roles in marine ecosystems, form some of the most economically valuable fisheries resources, and play a vital role in global food security. Due to their short generation times and tight coupling to lower trophic levels, populations of SPF display large boom-and-bust dynamics that are closely linked to climate variability. To reveal emerging global research trends on SPF as opposed to more recently published, ecosystem-specific reviews of SPF, we reviewed the literature published in two, 6-year periods in the new millennium (2001–2006, and 2011–2016) straddling the publication of a large, global review of the dynamics of SPF in 2009. We explored intrinsic and extrinsic (bottom-up) factors influencing the dynamics of SPF such as anchovies, sardines, herrings and sprats within the sub-order Clupeidae. Published research efforts within 16 different biogeographic ocean regions were compiled (more than 900 studies) and compared to identify i) new milestones and advances in our understanding, ii) emerging research trends and iii) remaining gaps in knowledge. Studies were separated into 5 categories (field, laboratory, mesocosms, long-term statistical analyses and spatially-explicit modelling) and discussed in relation to 10 bottom-up categories including 5 abiotic factors (temperature, salinity, pH, dissolved oxygen, density), 3 physical processes (advection, turbulence, turbidity) and 2 biotic factors (prey quantity and quality). The peer-reviewed literature reflects changes in the number of studies between the two time periods including increases (Mediterranean Sea, Humboldt Current) and decreases (Australia, Benguela Current). Our review highlights i) gaps in ecological knowledge on young juveniles and, in general, on the impacts of hypoxia and heatwaves on SPF, ii) the utility of paleo studies in exploring population drivers, iii) the continued need to develop spatially-explicit, full life-cycle models, iv) the importance of exploring how density-dependent processes impact vital rates (growth, survival, reproduction), and v) the benefits of international collaboration for knowledge transfer and building unifying hypotheses on the role of bottom-up factors and processes that regulate SPF populations.},
	language = {en},
	urldate = {2023-03-16},
	journal = {Progress in Oceanography},
	author = {Peck, Myron A. and Alheit, Jürgen and Bertrand, Arnaud and Catalán, Ignacio A. and Garrido, Susana and Moyano, Marta and Rykaczewski, Ryan R. and Takasuka, Akinori and van der Lingen, Carl D.},
	month = feb,
	year = {2021},
	pages = {102494},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/X9SIYR2W/Peck et al. - 2021 - Small pelagic fish in the new millennium A bottom.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/MUNKLITX/S0079661120302299.html:text/html},
}

@article{mcclatchie_forage_2018,
	title = {Forage fish, small pelagic fisheries and recovering predators: managing expectations},
	volume = {21},
	issn = {1469-1795},
	shorttitle = {Forage fish, small pelagic fisheries and recovering predators},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/acv.12421},
	doi = {10.1111/acv.12421},
	language = {en},
	number = {6},
	urldate = {2023-03-16},
	journal = {Animal Conservation},
	author = {McClatchie, S. and Vetter, R. D. and Hendy, I. L.},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/acv.12421},
	pages = {445--447},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/5L8GKUTL/McClatchie et al. - 2018 - Forage fish, small pelagic fisheries and recoverin.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/KIUJLGBQ/acv.html:text/html},
}

@article{sanchirico_direct_2021,
	title = {Direct and ancillary benefits of ecosystem-based fisheries management in forage fish fisheries},
	volume = {31},
	issn = {1939-5582},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/eap.2421},
	doi = {10.1002/eap.2421},
	abstract = {Natural resource management is evolving toward holistic, ecosystem-based approaches to decision making. The ecosystem science underpinning these approaches needs to account for the complexity of multiple interacting components within and across coupled natural–human systems. In this research, we investigate the potential economic and ecological gains from adopting ecosystem-based approaches for the sardine and anchovy fisheries off of the coast of California, USA. Research has shown that while predators in this system are likely substituting one forage species for another, the assemblage of sardine and anchovy can be a significant driver of predator populations. Currently, the harvest control rules for sardine and anchovy fisheries align more with traditional single species framework. We ask what are the economic and ecological gains when jointly determining the harvest control rules for both forage fish stocks and their predators relative to the status quo? What are the implications of synchronous and anti-synchronous environmental recruitment variation between the anchovy and sardine stocks on optimal food-web management? To investigate these questions, we develop an economic-ecological model for sardine, anchovy, a harvested predator (halibut), and an endangered predator (Brown Pelican) that includes recruitment variability over time driven by changing environmental conditions. Utilizing large-scale numerical optimal control methods, we investigate how the multiple variants of integrated management of sardine, anchovy, and halibut impact the overall economic condition of the fisheries and Brown Pelican populations over time. We find significant gains in moving to integrated catch control rules both in terms of the economic gains of the fished stocks, and in terms of the impacts on the Brown Pelican populations. We also compare the relative performance of current stylized catch control rules to optimal single species and optimal ecosystem-based fisheries management (EBFM) across ecological and economic dimensions, where the former trade-off considerable economic value for ecological goals. More generally, we demonstrate how EBFM approaches introduce and integrate additional management levers for policymakers to achieve non-fishery objectives at lowest costs to the fishing sectors.},
	language = {en},
	number = {7},
	urldate = {2023-03-16},
	journal = {Ecological Applications},
	author = {Sanchirico, James N. and Essington, Timothy E.},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/eap.2421},
	keywords = {natural resource management, bioeconomics, optimal control, pseudo-spectral numerical techniques},
	pages = {e02421},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/XN7IRJLQ/Sanchirico and Essington - 2021 - Direct and ancillary benefits of ecosystem-based f.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/DR5JWFLB/eap.html:text/html},
}

@article{siple_forage_2019,
	title = {Forage fish fisheries management requires a tailored approach to balance trade-offs},
	volume = {20},
	issn = {1467-2979},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12326},
	doi = {10.1111/faf.12326},
	abstract = {Ecosystem-based fishery management requires considering the effects of actions on social, natural and economic systems. These considerations are important for forage fish fisheries, because these species provide ecosystem services as a key prey in food webs and support valuable commercial fisheries. Forage fish stocks fluctuate naturally, and fishing may make these fluctuations more pronounced, yet harvest strategies intended to ameliorate these effects might adversely affect fisheries and communities. Here, we evaluate trade-offs among a diverse suite of management objectives by simulating outcomes from several harvest strategies on forage fish species. We demonstrate that some trade-offs (like those between catches and minimizing collapse length) were universal among forage species and could not be eliminated by the use of different control rules. We also demonstrate that trade-offs vary among forage fish species, with strong trade-offs between stable, high catches and high-biomass periods (“bonanzas”) for menhaden- and anchovy-like fish, and counterintuitive trade-offs for sardine-like fish between shorter collapses and longer bonanzas. We find that harvest strategies designed to maintain stability in catches will result in more severe collapses. Finally, we show that the ability of assessments to detect rapid changes in population status greatly affects control rule performance and the degree and type of trade-offs, increasing the risk and severity of collapses and reducing catches. Together, these results demonstrate that while default harvest strategies are useful in data-poor situations, management strategy evaluations that are tailored to specific forage fish may better balance trade-offs.},
	language = {en},
	number = {1},
	urldate = {2023-03-16},
	journal = {Fish and Fisheries},
	author = {Siple, Margaret C. and Essington, Timothy E. and E. Plagányi, Éva},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12326},
	keywords = {management strategy evaluation, ecosystem-based fisheries management, population dynamics, small pelagics},
	pages = {110--124},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/3WLY3GJ5/Siple et al. - 2019 - Forage fish fisheries management requires a tailor.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/XL7W96SC/faf.html:text/html},
}

@article{koehn_structured_2021,
	title = {A structured seabird population model reveals how alternative forage fish control rules benefit seabirds and fisheries},
	volume = {31},
	issn = {1939-5582},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/eap.2401},
	doi = {10.1002/eap.2401},
	abstract = {Fisheries for forage fish may affect the survival and reproduction of piscivorous predators, especially seabirds. However, seabirds have evolved life history strategies to cope with natural fluctuations in prey and it is difficult to separate effects of fishing on seabirds from impacts of natural variability. To date, potential impacts of forage fisheries on seabirds have mainly been explored using ecosystem models that simplify seabird–forage-fish dynamics. We sought to explore how different forage fish harvest policies affect seabirds, accounting for structured population dynamics, life history specifics, and variation in forage fish dependencies across life stages; and how impacts vary across seabird and forage fish life histories. To explore these impacts, we developed an age-stage structured seabird model that incorporates seabird diet specialization, foraging behavior, and reproductive strategy, as well as different functional responses between prey availability and adult survival, juvenile survival, reproductive success, and breeder propensity. We parameterized this model for two contrasting seabird life histories: (1) a low fecundity, limited foraging range, diet specialist (“restricted”); and (2) a high fecundity, wide ranging, diet generalist (“flexible”). Each was paired with two different forage fish prey archetypes that were fished under various control rules. The restricted seabird population was expectedly less robust to constant fishing pressure than the flexible seabird, and this sensitivity was mainly due to functional response parameterization, rather than other life history parameters. Particularly, the restricted seabird was highly sensitive to the relationship between prey availability and adult survival but was not sensitive to the relationship between prey and reproductive success. An adaptive biomass-limit harvest rule for forage fish resulted in substantially higher seabird abundance compared to constant fishing across all scenarios, with minimal trade-offs to the fishery (depending on fishery management objectives). However, mechanisms governing the impact of the forage fish fishery on the seabird varied by forage fish type. Therefore, tailoring forage fish management strategies to forage fish life history can lead to mutually acceptable outcomes for fisheries and seabirds. If data or time are limited, an adaptive control rule is likely a safe bet for meeting seabird conservation objectives with limited impacts to fisheries.},
	language = {en},
	number = {7},
	urldate = {2023-03-16},
	journal = {Ecological Applications},
	author = {Koehn, Laura E. and Siple, Margaret C. and Essington, Timothy E.},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/eap.2401},
	keywords = {fisheries management, forage fish, seabirds, model simulations},
	pages = {e02401},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/MNHZ27EU/Koehn et al. - 2021 - A structured seabird population model reveals how .pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/GASRK5JK/eap.html:text/html},
}

@article{alder_forage_2008,
	title = {Forage {Fish}: {From} {Ecosystems} to {Markets}},
	volume = {33},
	shorttitle = {Forage {Fish}},
	url = {https://doi.org/10.1146/annurev.environ.33.020807.143204},
	doi = {10.1146/annurev.environ.33.020807.143204},
	abstract = {Fisheries targeting small-to-medium pelagic, so-called forage fish, impact on human food security and marine ecosystems. Because their operations are shrouded by the myth that forage fish are unsuitable for human consumption, the role of these fisheries in intensive food production is not well understood or appreciated. Thus, although they account for over 30\% of global landings of marine fish annually, our knowledge of how these levels of removal impact on marine ecosystems is limited. Nevertheless, there is considerable scope for policy makers to change the current management of these fisheries and to enhance their contribution to food security and economic development. Industry and consumers also have an important role in finding the balance between these fisheries contributing to human food security and poverty alleviation on the one hand, and sustaining intensive animal food production systems, especially aquaculture, on the other.},
	number = {1},
	urldate = {2023-03-16},
	journal = {Annual Review of Environment and Resources},
	author = {Alder, Jacqueline and Campbell, Brooke and Karpouzi, Vasiliki and Kaschner, Kristin and Pauly, Daniel},
	year = {2008},
	note = {\_eprint: https://doi.org/10.1146/annurev.environ.33.020807.143204},
	keywords = {small pelagics, aquaculture, fishmeal},
	pages = {153--166},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/UYUSEGAS/Alder et al. - 2008 - Forage Fish From Ecosystems to Markets.pdf:application/pdf},
}

@article{bertrand_interactions_2004,
	title = {Interactions between fish and fisher's spatial distribution and behaviour: an empirical study of the anchovy ({Engraulis} ringens) fishery of {Peru}},
	volume = {61},
	issn = {1054-3139},
	shorttitle = {Interactions between fish and fisher's spatial distribution and behaviour},
	url = {https://doi.org/10.1016/j.icesjms.2004.07.016},
	doi = {10.1016/j.icesjms.2004.07.016},
	abstract = {Fishing data provide, with wide spatio-temporal coverage, inexpensive information about exploited species, but a precondition for their interpretation is a good comprehension of fish and fisher spatial dynamics and interactions. In Peru, anchovy (Engraulis ringens) is exploited by an industrial fleet of about 800 purse-seiners operating all along the coast. Using simultaneous acoustic survey and commercial fishing data for the 1998–2001 time period, we present a preliminary, exploratory, and empirical approach to identify the nature of potential interactions between Peruvian anchovy and fisher behaviour. We show that (i) Peruvian anchovy exhibited a composite spatial strategy for the study period, i.e. a change in biomass was associated with both change in geographical extension and density; (ii) fishing behaviour significantly varied within and among vessels in terms of travel duration, searching duration, and number of fishing sets; and (iii) interactions between fish and fisher behaviours differed according to the spatial scale. At a fish stock scale (the scale of fishing ground selection for fishers), fishing was more efficient with low biomass and high spatial concentration (low stock range and high biomass); at a local fish spatial scale (the scale of searching for a school inside the fishing ground), fishing performance was favoured by high mean local abundances and low spatial concentration (the way fish is distributed inside its stock range); finally, at the school scale (the scale of the fishing set), both high abundance and high spatial concentration were favourable to fishing success.},
	number = {7},
	urldate = {2023-03-16},
	journal = {ICES Journal of Marine Science},
	author = {Bertrand, Sophie and Díaz, Erich and Ñiquen, Miguel},
	month = jan,
	year = {2004},
	pages = {1127--1136},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/73JBBZ57/Bertrand et al. - 2004 - Interactions between fish and fisher's spatial dis.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/CEMNGCSS/879273.html:text/html},
}

@article{chavez_northern_2008,
	series = {The {Northern} {Humboldt} {Current} {System}: {Ocean} {Dynamics}, {Ecosystem} {Processes}, and {Fisheries}},
	title = {The northern {Humboldt} {Current} {System}: {Brief} history, present status and a view towards the future},
	volume = {79},
	issn = {0079-6611},
	shorttitle = {The northern {Humboldt} {Current} {System}},
	url = {https://www.sciencedirect.com/science/article/pii/S0079661108001651},
	doi = {10.1016/j.pocean.2008.10.012},
	language = {en},
	number = {2},
	urldate = {2023-03-16},
	journal = {Progress in Oceanography},
	author = {Chavez, Francisco P. and Bertrand, Arnaud and Guevara-Carrasco, Renato and Soler, Pierre and Csirke, Jorge},
	month = oct,
	year = {2008},
	pages = {95--105},
	file = {ScienceDirect Full Text PDF:/Users/sarah.gaichas/Zotero/storage/YVNUB325/Chavez et al. - 2008 - The northern Humboldt Current System Brief histor.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/YV2R4WU2/S0079661108001651.html:text/html},
}

@article{oleary_adapting_2020,
	title = {Adapting to climate-driven distribution shifts using model-based indices and age composition from multiple surveys in the walleye pollock ({Gadus} chalcogrammus) stock assessment},
	volume = {29},
	issn = {1365-2419},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/fog.12494},
	doi = {10.1111/fog.12494},
	abstract = {The northern Bering Sea is transitioning from an Arctic to subarctic fish community as climate warms. Scientists and managers aim to understand how these changing conditions are influencing fish biomass and spatial distribution in this region, as both are used to inform stock assessments and fisheries management advice. Here, we use a spatio-temporal model for walleye pollock (Gadus chalcogrammus) to provide two inputs to its stock assessment model: (a) an alternative model-based biomass index and (b) alternative model-based age compositions. Both inputs were derived from multiple fishery-independent data that span different regions of space and time. We developed an assessment model that utilizes both the standard and model-based inputs from multiple surveys despite inconsistencies in spatial and temporal coverage, and we found that using these data provide an improved spatial and temporal scope of total pollock biomass. Age composition information indicated that pollock density is increasing and moving farther north, particularly for older pollock. We found that including an index of cold pool extent could be used to extrapolate pollock densities in the northern Bering Sea in unsampled years. Stock assessment parameter estimates were similar for standard and model-based input. This study demonstrates that spatio-temporal model-based estimates of a biomass index and age composition can facilitate rapid changes in stock assessment structure in response to climate-driven shifts in spatial distribution. We conclude that assimilating data from regions neighboring standard survey areas, such as the Chukchi Sea and western Bering Sea, would improve understanding and management efforts as fish distributions change under a warming climate.},
	language = {en},
	number = {6},
	urldate = {2023-03-16},
	journal = {Fisheries Oceanography},
	author = {O’Leary, Cecilia A. and Thorson, James T. and Ianelli, James N. and Kotwicki, Stan},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/fog.12494},
	keywords = {Bering Sea, VAST, walleye pollock, climate adaption, cold pool extent, index standardization, vector autoregressive spatio-temporal model},
	pages = {541--557},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/JP57KZ2Z/O’Leary et al. - 2020 - Adapting to climate-driven distribution shifts usi.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/YKYK8X99/fog.html:text/html},
}

@article{jacobson_surplus_2001,
	title = {Surplus production, variability, and climate change in the great sardine and anchovy fisheries},
	volume = {58},
	issn = {0706-652X, 1205-7533},
	url = {http://www.nrcresearchpress.com/doi/10.1139/f01-110},
	doi = {10.1139/f01-110},
	abstract = {We used fishery and survey data to calculate annual surplus production (ASP) and instantaneous surplus production rates (ISPR) for eight anchovy and nine sardine stocks. In addition, we calculated ASP per unit spawning area for six anchovy and six sardine stocks. Median ASP was highest for stocks with highest median biomass (mostly anchovies), and ASP was typically about 16\% of stock biomass. ASP was often negative, more frequently for anchovies (36\% of years) than for sardines (17\% of years). ISPR was less variable for sardines and autocorrelated for longer-lived stocks (mostly sardines). Strong biomass increases tended to be preceded by short, abrupt increases in ISPR, and declines were pronounced when catches exceeded ASP for 5 years or more. The longest "runs" of positive and negative production were 21 and 4 years for sardine off Japan, 10 and 3 years for sardine off California, 8 and 2 years for anchovy off Peru, and 4 and 3 years for anchovy off California. ISPR is more sensitive to environmental changes than catch, biomass, or ASP and appear to be better for identifying environmentally induced regime shifts. Long time series show evidence of density-dependent effects on ASP in anchovies and sardines, but environmentally induced variation appears to dominate.},
	language = {en},
	number = {9},
	urldate = {2023-03-16},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Jacobson, Larry D and De Oliveira, Jose A.A and Barange, Manuel and Cisneros-Mata, Miguel A and Félix-Uraga, Roberto and Hunter, John R and Kim, Jin Yeong and Matsuura, Yasunobu and Ñiquen, Miguel and Porteiro, Carmela and Rothschild, Brian and Sanchez, Ramiro P and Serra, Rodolfo and Uriarte, Andres and Wada, Tokio},
	month = sep,
	year = {2001},
	pages = {1891--1903},
}

@article{boerema_stock_1973,
	title = {Stock {Assessment} of the {Peruvian} {Anchovy} ( \textit{{Engraulis} ringens} ) and {Management} of the {Fishery}},
	volume = {30},
	issn = {0015-296X},
	url = {http://www.nrcresearchpress.com/doi/10.1139/f73-351},
	doi = {10.1139/f73-351},
	abstract = {The upwelling of cool nutrient-rich water makes the area off Peru one of the most productivein the world. The first major use of this resource was the production of guano. In 1957 the fishery for anchoveta (Engraulis ringens) for reduction to meal and oil began on a significant scale. Catches rocketed to 8 million tons by 1964 making Peru the country with the biggest catch of fish. Most of the production (averaging some 2 millions tons of meal) is exported, and fish meal is (with copper) one of the two biggest earners of foreign exchange in the Peruvian economy.Scientific studies of the resource, including collection of detailed statistical data of the fishery have been carried out from an early stage. Research has been facilitated by the setting up of the Instituto del Mar del Peru, with the assistance of UNDP and FAO. Studies of the population dynamics of anchoveta have shown that by 1965 the stock was being heavily exploited, and that under average conditions the sustainable yield was around 8–10 million tons, being higher when the bird population is low.Regulations to manage and conserve the stock include a closed season in the middle of the year when catches are low, and at the beginning of the year when small fish are abundant, and a limit to the total catch during a fishing season (September–August). However, regulations have not prevented development of great excess capacity in vessels and processing plants.During 1972 there was a severe crisis in the fishery, when there were unusual oceanographic conditions and an almost complete recruitment failure. Catches in the second half of the year had to be cut to nearly nothing. Hopefully the stock is now rebuilding, but these events emphasize the need to reduce the excess capacity, so as to improve the economic status of the industry and stability of the stock.},
	language = {en},
	number = {12},
	urldate = {2023-03-16},
	journal = {Journal of the Fisheries Research Board of Canada},
	author = {Boerema, L. K. and Gulland, J. A.},
	month = dec,
	year = {1973},
	pages = {2226--2235},
}

@article{sydeman_sixty-five_2020,
	title = {Sixty-five years of northern anchovy population studies in the southern {California} {Current}: a review and suggestion for sensible management},
	volume = {77},
	issn = {1054-3139},
	shorttitle = {Sixty-five years of northern anchovy population studies in the southern {California} {Current}},
	url = {https://doi.org/10.1093/icesjms/fsaa004},
	doi = {10.1093/icesjms/fsaa004},
	abstract = {The central stock of northern anchovy (CSNA; Engraulis mordax), the most abundant small pelagic fish in the southern California Current, is key to ecosystem functions. We review drivers of its population dynamics in relation to management. Springtime upwelling intensity lagged by 2 years co-varied positively with CSNA biomass, as did the abundance of Pacific sardine (Sardinops sagax; weakly negative). CSNA population dynamics indicate the need for a multi-species stock assessment, but given serious challenges with modelling population collapse and recovery dynamics, and its moderate fisheries, we suggest that sensible management could be a simple 2-tier harvest control rule designed to emphasize the key trophic role of CSNA in the ecosystem while maintaining moderate socio-economic services. We recommend a monitoring fishery of no more than 5 KMT year−1 split between central and southern California when the stock falls below the long-term median abundance estimate of 380 KMT across the California portion of its range, and a catch limit of 25 KMT year−1 when the stock is above this reference point. This rule would be precautionary, serving to maintain the most important small pelagic forage in the ecosystem, various fisheries interests, and information streams when the population is in a collapsed state.},
	number = {2},
	urldate = {2023-03-16},
	journal = {ICES Journal of Marine Science},
	author = {Sydeman, William J and Dedman, Simon and García-Reyes, Marisol and Thompson, Sarah Ann and Thayer, Julie A and Bakun, Andrew and MacCall, Alec D},
	month = mar,
	year = {2020},
	pages = {486--499},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/SFCJEPN7/Sydeman et al. - 2020 - Sixty-five years of northern anchovy population st.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/MDYSKN9D/5734670.html:text/html},
}

@article{kuriyama_assessment_2022,
	title = {Assessment of the {Northern} anchovy ({Engraulis} mordax) central subpopulation in 2021 for {U}.{S}. management},
	url = {https://repository.library.noaa.gov/view/noaa/45013},
	doi = {10.25923/JV24-1539},
	urldate = {2023-03-16},
	author = {Kuriyama, Peter T.},
	year = {2022},
	note = {Publisher: Southwest Fisheries Science Center (U.S.)},
	annote = {SeriesInformation
NOAA technical memorandum NMFS-SWFSC ; 665},
}

@article{koehn_developing_2016,
	title = {Developing a high taxonomic resolution food web model to assess the functional role of forage fish in the {California} {Current} ecosystem},
	volume = {335},
	issn = {0304-3800},
	url = {https://www.sciencedirect.com/science/article/pii/S0304380016301909},
	doi = {10.1016/j.ecolmodel.2016.05.010},
	abstract = {Understanding the role of forage fish in marine food webs is an important part of ecosystem-based fisheries management. Food web models are a common tool used to account for important characteristics of forage fish and their trophodynamics. One primary limitation of many existing food web models is that the taxonomic resolution of forage fish and their predators is overly simplified. Here, we developed a food web model with high taxonomic resolution of forage fish and their predators in the California Current to more comprehensively describe trophic linkages involving forage fish and examine the ecological role of forage fish in this system. We parameterized a mass-balanced food web model (Ecopath) with 92 living functional groups, and used this to quantify diet dependency on forage fish, determine the main predators of forage fish, identify the topological position of forage fish in the food web, and calculate an index that identifies forage species or species aggregations that have key ecological roles (Supportive Role to Fishery ecosystem, SURF). Throughout, we characterized parameter uncertainty using a Monte Carlo approach. Though diets revealed some predators had high diet dependencies on individual forage fish species, most predators consumed multiple forage fish and also had notable diet overlap with forage fish. Consequently, no single forage fish appeared to act as a vital nexus species that is characteristic of “wasp-waisted” food webs in other upwelling regions. Additionally, no single forage fish was identified as “key” by the SURF index, but if predators and fisheries view certain pairs of forage fish as functionally equivalent, some plausible pairs would be identified as key assemblages. Specifically, sardine \& anchovy (Sardinops sagax \& Engraulis mordax) and herring \& anchovy (Clupea pallasii \& E. mordax) are key when predator populations depend on the aggregate availability of these species. This food web model can be used to support generalized equilibrium trade-off analysis or dynamic modeling to identify specific predators that would be of conservation concern under conditions of future forage fish depletion.},
	language = {en},
	urldate = {2023-03-16},
	journal = {Ecological Modelling},
	author = {Koehn, Laura E. and Essington, Timothy E. and Marshall, Kristin N. and Kaplan, Isaac C. and Sydeman, William J. and Szoboszlai, Amber I. and Thayer, Julie A.},
	month = sep,
	year = {2016},
	keywords = {Forage fish, California Current, Food web model},
	pages = {87--100},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/5NB32KM5/S0304380016301909.html:text/html},
}

@article{michailidou_temperature_2021,
	title = {Temperature and {Prey} {Species} {Richness} {Drive} the {Broad}-{Scale} {Distribution} of a {Generalist} {Predator}},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1424-2818},
	url = {https://www.mdpi.com/1424-2818/13/4/169},
	doi = {10.3390/d13040169},
	abstract = {The ongoing climate change and the unprecedented rate of biodiversity loss render the need to accurately project future species distributional patterns more critical than ever. Mounting evidence suggests that not only abiotic factors, but also biotic interactions drive broad-scale distributional patterns. Here, we explored the effect of predator-prey interaction on the predator distribution, using as target species the widespread and generalist grass snake (Natrix natrix). We used ensemble Species Distribution Modeling (SDM) to build a model only with abiotic variables (abiotic model) and a biotic one including prey species richness. Then we projected the future grass snake distribution using a modest emission scenario assuming an unhindered and no dispersal scenario. The two models performed equally well, with temperature and prey species richness emerging as the top drivers of species distribution in the abiotic and biotic models, respectively. In the future, a severe range contraction is anticipated in the case of no dispersal, a likely possibility as reptiles are poor dispersers. If the species can disperse freely, an improbable scenario due to habitat loss and fragmentation, it will lose part of its contemporary distribution, but it will expand northwards.},
	language = {en},
	number = {4},
	urldate = {2023-03-17},
	journal = {Diversity},
	author = {Michailidou, Danai-Eleni and Lazarina, Maria and Sgardelis, Stefanos P.},
	month = apr,
	year = {2021},
	note = {Number: 4
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {climate change, biotic interactions, species distribution models, prey species richness},
	pages = {169},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/9QN4Y9V5/Michailidou et al. - 2021 - Temperature and Prey Species Richness Drive the Br.pdf:application/pdf},
}

@article{astarloa_role_2021,
	title = {The {Role} of {Climate}, {Oceanography}, and {Prey} in {Driving} {Decadal} {Spatio}-{Temporal} {Patterns} of a {Highly} {Mobile} {Top} {Predator}},
	volume = {8},
	issn = {2296-7745},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2021.665474},
	abstract = {Marine mammals have been proposed as ecosystem sentinels due to their conspicuous nature, wide ranging distribution, and capacity to respond to changes in ecosystem structure and functioning. In southern European Atlantic waters, their response to climate variability has been little explored, partly because of the inherent difficulty of investigating higher trophic levels and long lifespan animals. Here, we analyzed spatio-temporal patterns from 1994 to 2018 of one of the most abundant cetaceans in the area, the common dolphin (Delphinus delphis), in order to (1) explore changes in its abundance and distribution, and (2) identify the underlying drivers. For that, we estimated the density of the species and the center of gravity of its distribution in the Bay of Biscay (BoB) and tested the effect of three sets of potential drivers (climate indices, oceanographic conditions, and prey biomasses) with a Vector Autoregressive Spatio Temporal (VAST) model that accounts for changes in sampling effort resulting from the combination of multiple datasets. Our results showed that the common dolphin significantly increased in abundance in the BoB during the study period. These changes were best explained by climate indices such as the North Atlantic Oscillation (NAO) and by prey species biomass. Oceanographic variables such as chlorophyll a concentration and temperature were less useful or not related. In addition, we found high variability in the geographic center of gravity of the species within the study region, with shifts between the inner (southeast) and the outer (northwest) part of the BoB, although the majority of this variability could not be attributed to the drivers considered in the study. Overall, these findings indicate that considering temperature alone for projecting spatio-temporal patterns of highly mobile predators is insufficient in this region and suggest important influences from prey and climate indices that integrate multiple ecological influences. Further integration of existing observational datasets to understand the causes of past shifts will be important for making accurate projections into the future.},
	urldate = {2023-03-17},
	journal = {Frontiers in Marine Science},
	author = {Astarloa, Amaia and Louzao, Maite and Andrade, Joana and Babey, Lucy and Berrow, Simon and Boisseau, Oliver and Brereton, Tom and Dorémus, Ghislain and Evans, Peter G. H. and Hodgins, Nicola K. and Lewis, Mark and Martinez-Cedeira, Jose and Pinsky, Malin L. and Ridoux, Vincent and Saavedra, Camilo and Santos, M. Begoña and Thorson, James T. and Waggitt, James J. and Wall, Dave and Chust, Guillem},
	year = {2021},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/LC9AG7RJ/Astarloa et al. - 2021 - The Role of Climate, Oceanography, and Prey in Dri.pdf:application/pdf},
}

@article{buckel_foraging_1999,
	title = {Foraging habits of bluefish, {Pomatomus} saltatrix, on the {U}.{S}. east coast continental shelf},
	abstract = {After spending summer months in estuaries, spring- and summer-spawned young-of-the-year (YOY) bluefish, Pomatomus saltatrix, migrate out to continental shelf waters of the Mid-Atlantic Bight in early autumn. Adult bluefish are found on the continental shelf throughout summer and fall. Both juveniles and adults have high food consumption rates and are generally piscivorous. To determine principal prey types on the shelf, dietary analyses were performed on YOY and adult bluefish collected from National Marine Fisheries Service autumn bottom trawl surveys in 1994 and 1995. Both spring- and summer-spawned YOY bluefish diets were dominated by bay anchovy. However, the significantly larger size of the spring-spawned cohort was associated with the consumption of other prey species such as squid, butterfish, striped anchovy, and round herring. Summer-spawned bluefish were significantly smaller in 1995 than in 1994; diet and prey size comparisons suggest that body size had a dramatic influence on the amount of piscivorous feeding in the summer-spawned cohort. Adult bluefish diet was dominated by schooling species such as squid, butterfish, and clupeids. Cannibalism was virtually nonexistent. Daily ration estimates of YOY bluefish on the shelf (4–12\% body wt/d) were similar to estuarine estimates in late summer. It is estimated that during the month of September, YOY bluefish in aggregate consumed 6.0 to 6.8 billion bay anchovies in 1994 and from 2.2 to 5.3 billion in 1995. The effect of this predatory loss on population dynamics of bay anchovy and the fish community on the continental shelf is unknown.},
	language = {en},
	journal = {Fishery Bulletin},
	author = {Buckel, Jeffrey A and Fogarty, Michael J and Conover, David O},
	year = {1999},
	file = {Buckel et al. - 1999 - Foraging habits of bluefish, Pomatomus saltatrix, .pdf:/Users/sarah.gaichas/Zotero/storage/NUGGA935/Buckel et al. - 1999 - Foraging habits of bluefish, Pomatomus saltatrix, .pdf:application/pdf},
}

@article{sanchez-jerez_interactions_2008,
	title = {Interactions between bluefish {Pomatomus} saltatrix ({L}.) and coastal sea-cage farms in the {Mediterranean} {Sea}},
	volume = {1-4},
	issn = {0044-8486},
	url = {https://www.infona.pl//resource/bwmeta1.element.elsevier-247e943a-8387-38fd-a30a-90d8fa5a0ec7},
	doi = {10.1016/j.aquaculture.2008.06.025},
	abstract = {Coastal sea-cage farms aggregate large concentrations of pelagic and demersal fish. The large numbers of cultured fish and aggregated wild fish often attract a range of marine mammal predators which may break into cages and attack the cultured fish. To date, predation by a finfish species within sea-cages has not been documented. In the Mediterranean Sea, the bluefish Pomatomus saltatrix (L.) aggregates around sea-cage farms and enters into cages to predate on the cultured fish. We obtained information about the effects of bluefish predation on aquaculture production through a questionnaire that was completed by fish farmers in Spain, Italy, Malta, Turkey, Greece and Cyprus. In addition, we identified the abundance, size and stomach contents of bluefish aggregated around three fish farms on the coast of Spain through visual counts, and from captured bluefish both inside and outside of the sea-cages. Bluefish occurred around fish farms in Spain, Italy, Malta and Turkey. Farmers in SE Spain reported its presence only inside seabream (Sparus aurata) cages, while in Turkey bluefish were reported from inside seabass (Dicentrarchus labrax) and seabream cages. Greatest aggregated biomass of bluefish reached 1049 and 3191 kg at the Altea and Guardamar farms, respectively, with abundance peaking at 4500 individuals at both farms. Size structures differed markedly between farms, with smaller individuals aggregating at Altea. Stomach content analysis revealed that bluefish on the outside of sea-cages consumed pelagic species such as Sardinella aurita and Trachurus mediterraneus, while they predated on seabream once they incurred into cages, often consuming only the tails of many fish. The interaction of bluefish with sea-cage aquaculture is, at present, a problem of local concern restricted to some areas of the Mediterranean Sea, but its widespread distribution suggests this piscivore may be a problematic predator in other regions.},
	language = {English},
	number = {282},
	urldate = {2023-03-17},
	journal = {Aquaculture},
	author = {Sanchez-Jerez, P. and Fernandez-Jover, D. and Bayle-Sempere, J. and Valle, C. and Dempster, T. and Tuya, F. and Juanes, F.},
	year = {2008},
	pages = {61--67},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/LW9CMVVE/bwmeta1.element.html:text/html},
}

@article{gruss_developing_2019-1,
	title = {Developing spatio-temporal models using multiple data types for evaluating population trends and habitat usage},
	volume = {76},
	issn = {1054-3139},
	url = {https://doi.org/10.1093/icesjms/fsz075},
	doi = {10.1093/icesjms/fsz075},
	abstract = {Spatio-temporal models have become key tools for evaluating population trends and habitat usage. We developed a spatio-temporal modelling framework employing a combination of encounter/non-encounter, count, and biomass data collected by different monitoring programs (“combined data”). The three data types are predicted using a computationally efficient approximation to a compound Poisson-gamma process. We fitted spatio-temporal models to combined data for Gulf of Mexico (GOM) red snapper (Lutjanus campechanus) for 2006–2014. These spatio-temporal models provided insights into GOM red snapper spatial distribution patterns, which we corroborated by comparing to past predictions generated using only encounter/non-encounter data. However, relying on biomass and count data in addition to encounter/non-encounter data also allowed us to reconstruct biomass trends for GOM red snapper and to examine patterns of distribution shifts and range expansion/contraction for this population for the first time. Moreover, combining multiple data types improved the precision of reconstructed population trends and some variables quantifying habitat usage. Finally, scenarios and simulation experiments conditioned upon red snapper data showed that the improvement in fitting to combined data is greater when biomass data for the study population are lacking for an entire subregion and, to a lesser extent, for an entire time period (e.g. in early years).},
	number = {6},
	urldate = {2023-03-17},
	journal = {ICES Journal of Marine Science},
	author = {Grüss, Arnaud and Thorson, James T},
	month = dec,
	year = {2019},
	pages = {1748--1761},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/CTWJMU2D/Grüss and Thorson - 2019 - Developing spatio-temporal models using multiple d.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/IL3E9CIM/5479986.html:text/html},
}

@article{thorson_diet_2022,
	title = {Diet analysis using generalized linear models derived from foraging processes using {R} package mvtweedie},
	volume = {103},
	issn = {1939-9170},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ecy.3637},
	doi = {10.1002/ecy.3637},
	abstract = {Diet analysis integrates a wide variety of visual, chemical, and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, for example, highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package mvtweedie that extends capabilities of widely used packages in R (mgcv and ggplot2) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted Puffins (Fratercula cirrhata) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980–2000) and then Pacific herring and capelin (2000–2020), while wolves (Canis lupus ligoni) in southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines.},
	language = {en},
	number = {5},
	urldate = {2023-03-19},
	journal = {Ecology},
	author = {Thorson, James T. and Arimitsu, Mayumi L. and Levi, Taal and Roffler, Gretchen H.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3637},
	keywords = {generalized additive model, predation, diet, Tweedie distribution, foraging theory, generalized linear model, metabarcoding, point process, Poisson process},
	pages = {e3637},
	annote = {e3637 ECY21-0474.R2},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/L4SMAM2H/Thorson et al. - Diet analysis using generalized linear models deri.pdf:application/pdf;Full Text PDF:/Users/sarah.gaichas/Zotero/storage/8G9S6T6L/Thorson et al. - 2022 - Diet analysis using generalized linear models deri.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/T8TB4GK6/ecy.html:text/html},
}

@article{link_system-level_2018,
	title = {System-level optimal yield: increased value, less risk, improved stability, and better fisheries},
	volume = {75},
	issn = {0706-652X},
	shorttitle = {System-level optimal yield},
	url = {https://cdnsciencepub.com/doi/full/10.1139/cjfas-2017-0250},
	doi = {10.1139/cjfas-2017-0250},
	abstract = {The discipline and practice of fisheries science and management have had an useful, successful, and interesting history. The discipline has developed over the past century and a half into a very reductionist, highly quantitative, socially impactful endeavor. Yet given our collective successes in this field, some notable challenges remain. To address these challenges, many have proposed ecosystem-based fisheries management that takes a more systematic approach to the management of these living marine resources. Here I describe systems theory and associated constructs underlying system dynamics, elucidate how aggregate properties of systems can and have been used, contextualize these aggregate features relative to optimal yield, and note how this approach can produce useful estimates and outcomes for fisheries management. I explore two contrasting examples where this approach has and has not been considered, highlighting the benefits of applying such an approach. I conclude by discussing ways in which we might move forward with a portfolio approach for both the discipline and practice of fisheries science and management.},
	number = {1},
	urldate = {2023-03-19},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Link, Jason S.},
	month = jan,
	year = {2018},
	note = {Publisher: NRC Research Press},
	pages = {1--16},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/XAJPEGGF/Link - 2018 - System-level optimal yield increased value, less .pdf:application/pdf},
}

@article{fogarty_art_2014,
	title = {The art of ecosystem-based fishery management},
	volume = {71},
	issn = {0706-652X},
	url = {https://cdnsciencepub.com/doi/full/10.1139/cjfas-2013-0203},
	doi = {10.1139/cjfas-2013-0203},
	abstract = {The perception that ecosystem-based fishery management is too complex and poorly defined remains a primary impediment to its broadscale adoption and implementation. Here, I attempt to offer potential solutions to these concerns. Specifically, I focus on pathways that can contribute to overall simplification by moving toward integrated place-based management plans and away from large numbers of species-based plans; by using multispecies or ecosystem models and indicators that permit the simultaneous and consistent assessment of ecosystem components while also incorporating broader environmental factors; and by consolidating individual administrative and regulatory functions now mostly dealt with on a species-by-species basis into a more integrated framework for system-wide decision-making. The approach focuses on emergent properties at the community and ecosystem levels and seeks to identify simpler modeling and analysis tools for evaluation. Adoption of ecosystem-based management procedures relying on simple decision rules and metrics is advocated. It is recommended that we replace static concepts for individual species focusing on maximum sustainable yield with a dynamic ecosystem yield framework that involves setting system-wide reference points along with constraints to protect individual species, habitats, and nontarget organisms in a dynamic environmental setting.},
	number = {3},
	urldate = {2023-03-19},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Fogarty, Michael J.},
	month = mar,
	year = {2014},
	note = {Publisher: NRC Research Press},
	pages = {479--490},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/N3L2RL68/Fogarty - 2014 - The art of ecosystem-based fishery management.pdf:application/pdf;NRC Research Press PDF fulltext:/Users/sarah.gaichas/Zotero/storage/H3FEZEKP/Fogarty - 2013 - The art of ecosystem-based fishery management.pdf:application/pdf;NRC Research Press Snapshot:/Users/sarah.gaichas/Zotero/storage/RPQVFGEI/cjfas-2013-0203.html:text/html},
}

@misc{lucey_survdat_2022,
	title = {survdat: {Tools} for working with {NEFSC} survey data},
	shorttitle = {survdat},
	url = {https://github.com/NOAA-EDAB/survdat, https://noaa-edab.github.io/survdat/},
	author = {Lucey, Sean and Beet, Andrew},
	year = {2022},
}

@misc{noauthor_resilience_nodate,
	title = {Resilience and stability of a pelagic marine ecosystem},
	url = {https://royalsocietypublishing.org/doi/epdf/10.1098/rspb.2015.1931},
	language = {en},
	urldate = {2023-03-22},
	doi = {10.1098/rspb.2015.1931},
	file = {Full Text:/Users/sarah.gaichas/Zotero/storage/HSJLJG25/Resilience and stability of a pelagic marine ecosy.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/CRC4TZ4S/rspb.2015.html:text/html},
}

@article{landi_complexity_2018,
	title = {Complexity and stability of ecological networks: a review of the theory},
	volume = {60},
	issn = {1438-390X},
	shorttitle = {Complexity and stability of ecological networks},
	url = {https://doi.org/10.1007/s10144-018-0628-3},
	doi = {10.1007/s10144-018-0628-3},
	abstract = {Our planet is changing at paces never observed before. Species extinction is happening at faster rates than ever, greatly exceeding the five mass extinctions in the fossil record. Nevertheless, our lives are strongly based on services provided by ecosystems, thus the responses to global change of our natural heritage are of immediate concern. Understanding the relationship between complexity and stability of ecosystems is of key importance for the maintenance of the balance of human growth and the conservation of all the natural services that ecosystems provide. Mathematical network models can be used to simplify the vast complexity of the real world, to formally describe and investigate ecological phenomena, and to understand ecosystems propensity of returning to its functioning regime after a stress or a perturbation. The use of ecological-network models to study the relationship between complexity and stability of natural ecosystems is the focus of this review. The concept of ecological networks and their characteristics are first introduced, followed by central and occasionally contrasting definitions of complexity and stability. The literature on the relationship between complexity and stability in different types of models and in real ecosystems is then reviewed, highlighting the theoretical debate and the lack of consensual agreement. The summary of the importance of this line of research for the successful management and conservation of biodiversity and ecosystem services concludes the review.},
	language = {en},
	number = {4},
	urldate = {2023-03-22},
	journal = {Population Ecology},
	author = {Landi, Pietro and Minoarivelo, Henintsoa O. and Brännström, Åke and Hui, Cang and Dieckmann, Ulf},
	month = oct,
	year = {2018},
	keywords = {Biodiversity, Ecosystem, Community, Complex networks, Resilience},
	pages = {319--345},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/3X3AJIV6/Landi et al. - 2018 - Complexity and stability of ecological networks a.pdf:application/pdf},
}

@article{pikitch_global_2014,
	title = {The global contribution of forage fish to marine fisheries and ecosystems},
	volume = {15},
	issn = {1467-2979},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12004},
	doi = {10.1111/faf.12004},
	abstract = {Forage fish play a pivotal role in marine ecosystems and economies worldwide by sustaining many predators and fisheries directly and indirectly. We estimate global forage fish contributions to marine ecosystems through a synthesis of 72 published Ecopath models from around the world. Three distinct contributions of forage fish were examined: (i) the ecological support service of forage fish to predators in marine ecosystems, (ii) the total catch and value of forage fisheries and (iii) the support service of forage fish to the catch and value of other commercially targeted predators. Forage fish use and value varied and exhibited patterns across latitudes and ecosystem types. Forage fish supported many kinds of predators, including fish, seabirds, marine mammals and squid. Overall, forage fish contribute a total of about \$16.9 billion USD to global fisheries values annually, i.e. 20\% of the global ex-vessel catch values of all marine fisheries combined. While the global catch value of forage fisheries was \$5.6 billion, fisheries supported by forage fish were more than twice as valuable (\$11.3 billion). These estimates provide important information for evaluating the trade-offs of various uses of forage fish across ecosystem types, latitudes and globally. We did not estimate a monetary value for supportive contributions of forage fish to recreational fisheries or to uses unrelated to fisheries, and thus the estimates of economic value reported herein understate the global value of forage fishes.},
	language = {en},
	number = {1},
	urldate = {2023-03-30},
	journal = {Fish and Fisheries},
	author = {Pikitch, Ellen K and Rountos, Konstantine J and Essington, Timothy E and Santora, Christine and Pauly, Daniel and Watson, Reg and Sumaila, Ussif R and Boersma, P Dee and Boyd, Ian L and Conover, David O and Cury, Philippe and Heppell, Selina S and Houde, Edward D and Mangel, Marc and Plagányi, Éva and Sainsbury, Keith and Steneck, Robert S and Geers, Tess M and Gownaris, Natasha and Munch, Stephan B},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12004},
	keywords = {ecosystem-based management, forage fish, trade-offs, Ecosystem service, ecosystem‐based management, fisheries value, supportive values, trade‐offs},
	pages = {43--64},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/AT9D9ARZ/Pikitch et al. - 2014 - The global contribution of forage fish to marine f.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/W8QK3NUW/faf.html:text/html},
}

@misc{smith_fish_2022,
	title = {Fish trophic ecology of the northeast {US} continental shelf. {Shiny} {Application}.},
	url = {https://fwdp.shinyapps.io/tm2020/},
	author = {Smith, Brian E. and Rowe, Stacey},
	month = sep,
	year = {2022},
}

@article{galili_dendextend_2015,
	title = {dendextend: an {R} package for visualizing, adjusting and comparing trees of hierarchical clustering},
	volume = {31},
	issn = {1367-4803},
	shorttitle = {dendextend},
	url = {https://doi.org/10.1093/bioinformatics/btv428},
	doi = {10.1093/bioinformatics/btv428},
	abstract = {Summary:  dendextend is an R package for creating and comparing visually appealing tree diagrams. dendextend provides utility functions for manipulating dendrogram objects (their color, shape and content) as well as several advanced methods for comparing trees to one another (both statistically and visually). As such, dendextend offers a flexible framework for enhancing R's rich ecosystem of packages for performing hierarchical clustering of items.Availability and implementation: The dendextend R package (including detailed introductory vignettes) is available under the GPL-2 Open Source license and is freely available to download from CRAN at: (http://cran.r-project.org/package=dendextend)Contact:  Tal.Galili@math.tau.ac.il},
	number = {22},
	urldate = {2023-03-31},
	journal = {Bioinformatics},
	author = {Galili, Tal},
	month = nov,
	year = {2015},
	pages = {3718--3720},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/PFLDL7XV/Galili - 2015 - dendextend an R package for visualizing, adjustin.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/LBL6CWUA/240978.html:text/html},
}

@misc{massicotte_rnaturalearth_2023,
	title = {rnaturalearth: {World} {Map} {Data} from {Natural} {Earth}},
	url = {https://docs.ropensci.org/rnaturalearth/ https://github.com/ropensci/rnaturalearth},
	author = {Massicotte, Philippe and South, Andy},
	year = {2023},
}

@article{buchheister_diets_2015,
	title = {Diets and trophic-guild structure of a diverse fish assemblage in {Chesapeake} {Bay}, {U}.{S}.{A}.},
	volume = {86},
	issn = {1095-8649},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jfb.12621},
	doi = {10.1111/jfb.12621},
	abstract = {Dietary habits and trophic-guild structure were examined in a fish assemblage (47 species) of the Chesapeake Bay estuary, U.S.A., using 10 years of data from {\textgreater}25 000 fish stomachs. The assemblage was comprised of 10 statistically significant trophic guilds that were principally differentiated by the relative amounts of Mysida, Bivalvia, Polychaeta, Teleostei and other Crustacea in the diets. These guilds were broadly aggregated into five trophic categories: piscivores, zooplanktivores, benthivores, crustacivores and miscellaneous consumers. Food web structure was largely dictated by gradients in habitat (benthic to pelagic) and prey size. Size classes within piscivorous species were more likely to be classified into different guilds, reflecting stronger dietary changes through ontogeny relative to benthivores and other guilds. Relative to predator species and predator size, the month of sampling had negligible effects on dietary differences within the assemblage. A majority of sampled fishes derived most of their nutrition from non-pelagic prey sources, suggesting a strong coupling of fish production to benthic and demersal food resources. Mysida (predominantly the opossum shrimp Neomysis americana) contributed substantially to the diets of over 25\% of the sampled predator groups, indicating that this species is a critical, but underappreciated, node in the Chesapeake Bay food web.},
	language = {en},
	number = {3},
	urldate = {2023-03-31},
	journal = {Journal of Fish Biology},
	author = {Buchheister, A. and Latour, R. J.},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jfb.12621},
	keywords = {trophic ecology, ecosystem-based fisheries management (EBFM), estuary, fish stomach contents, multivariate analysis},
	pages = {967--992},
	file = {Snapshot:/Users/sarah.gaichas/Zotero/storage/RIZ6PJA4/jfb.html:text/html},
}

@article{maunder_review_2013,
	title = {A review of integrated analysis in fisheries stock assessment},
	volume = {142},
	issn = {0165-7836},
	url = {https://www.sciencedirect.com/science/article/pii/S0165783612002627},
	doi = {10.1016/j.fishres.2012.07.025},
	abstract = {Limited data, and the requirement to provide science-based advice for exploited populations, have led to the development of statistical methods that combine several sources of information into a single analysis. This approach, “integrated analysis”, was first formulated by Fournier and Archibald in 1982. Contemporary use of integrated analysis involves using all available data, in as raw a form as appropriate, in a single analysis. Analyses that were traditionally carried out independently are now conducted simultaneously through likelihood functions that include multiple data sources. For example, the traditional analysis of converting catch-at-length data into catch-at-age data for use in an age-structured population dynamics models can be avoided by including the basic data used in this conversion, length-frequency and conditional age-at-length data, in the likelihood function. This allows for consistency in assumptions and permits the uncertainty associated with both data sources to be propagated to final model outputs, such as catch limits under harvest control rules. The development of the AD Model Builder software has greatly facilitated the use of integrated analyses, and there are now several general stock assessment models (e.g., Stock Synthesis) that allow many data types and model assumptions to be analyzed simultaneously. In this paper, we define integrated analysis, describe its history and development, give several examples, and describe the advantages of and problems with integrated analysis.},
	language = {en},
	urldate = {2023-07-21},
	journal = {Fisheries Research},
	author = {Maunder, Mark N. and Punt, André E.},
	month = may,
	year = {2013},
	keywords = {Fisheries stock assessment, Meta-analysis, Bayesian, Data assimilation, Integrated analysis, Maximum likelihood, Multivariate nonlinear regression},
	pages = {61--74},
	file = {ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/WDDEFTXN/S0165783612002627.html:text/html},
}

@article{wilberg_incorporating_2009-1,
	title = {Incorporating {Time}-{Varying} {Catchability} into {Population} {Dynamic} {Stock} {Assessment} {Models}},
	volume = {18},
	issn = {1064-1262},
	url = {https://doi.org/10.1080/10641260903294647},
	doi = {10.1080/10641260903294647},
	abstract = {Catchability is an important parameter in many stock assessment models because it relates an index of abundance to stock size. We review the theory and evidence for time-varying catchability, its effects on stock assessment estimates, and methods to include time-varying catchability in stock assessments. Numerous studies provide strong evidence that time-varying catchability is common in most fisheries and many fishery-independent surveys and can be caused by anthropogenic, environmental, biological, and management processes. Trends in catchability over time can cause biased estimates of stock size and fishing mortality rates in stock assessment models that do not compensate for them. Methods that use descriptive and functional relationships have been developed to incorporate time-varying catchability in stock assessment models. We recommend that the default assumption for stock assessments should be that catchability varies over time and that multiple methods of including time-varying catchability should be applied. Additional studies are needed to determine relative performance of alternative methods and to develop methods for selecting among models.},
	number = {1},
	urldate = {2023-07-21},
	journal = {Reviews in Fisheries Science},
	author = {Wilberg, Michael J. and Thorson, James T. and Linton, Brian C. and Berkson, Jim},
	month = dec,
	year = {2009},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/10641260903294647},
	keywords = {catch per unit effort, catch rate, density-dependent catchability, index of abundance, relative abundance},
	pages = {7--24},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/BCLQG7TG/Wilberg et al. - 2009 - Incorporating Time-Varying Catchability into Popul.pdf:application/pdf},
}

@article{goetsch_surface_2023,
	title = {Surface and subsurface oceanographic features drive forage fish distributions and aggregations: {Implications} for prey availability to top predators in the {US} {Northeast} {Shelf} ecosystem},
	volume = {13},
	issn = {2045-7758},
	shorttitle = {Surface and subsurface oceanographic features drive forage fish distributions and aggregations},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.10226},
	doi = {10.1002/ece3.10226},
	abstract = {Forage fishes are a critical food web link in marine ecosystems, aggregating in a hierarchical patch structure over multiple spatial and temporal scales. Surface-level forage fish aggregations (FFAs) represent a concentrated source of prey available to surface- and shallow-foraging marine predators. Existing survey and analysis methods are often imperfect for studying forage fishes at scales appropriate to foraging predators, making it difficult to quantify predator–prey interactions. In many cases, general distributions of forage fish species are known; however, these may not represent surface-level prey availability to predators. Likewise, we lack an understanding of the oceanographic drivers of spatial patterns of prey aggregation and availability or forage fish community patterns. Specifically, we applied Bayesian joint species distribution models to bottom trawl survey data to assess species- and community-level forage fish distribution patterns across the US Northeast Continental Shelf (NES) ecosystem. Aerial digital surveys gathered data on surface FFAs at two project sites within the NES, which we used in a spatially explicit hierarchical Bayesian model to estimate the abundance and size of surface FFAs. We used these models to examine the oceanographic drivers of forage fish distributions and aggregations. Our results suggest that, in the NES, regions of high community species richness are spatially consistent with regions of high surface FFA abundance. Bathymetric depth drove both patterns, while subsurface features, such as mixed layer depth, primarily influenced aggregation behavior and surface features, such as sea surface temperature, sub-mesoscale eddies, and fronts influenced forage fish diversity. In combination, these models help quantify the availability of forage fishes to marine predators and represent a novel application of spatial models to aerial digital survey data.},
	language = {en},
	number = {7},
	urldate = {2023-07-28},
	journal = {Ecology and Evolution},
	author = {Goetsch, Chandra and Gulka, Julia and Friedland, Kevin D. and Winship, Arliss J. and Clerc, Jeff and Gilbert, Andrew and Goyert, Holly F. and Stenhouse, Iain J. and Williams, Kathryn A. and Willmott, Julia R. and Rekdahl, Melinda L. and Rosenbaum, Howard C. and Adams, Evan M.},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.10226},
	keywords = {predator–prey interactions, forage fish aggregation, hierarchical Bayesian model, joint species distribution model, trophodynamics},
	pages = {e10226},
	annote = {e10226 ECE-2022-12-01863.R1},
}

@article{friedland_forage_2023,
	title = {Forage {Fish} {Species} {Prefer} {Habitat} within {Designated} {Offshore} {Wind} {Energy} {Areas} in the {U}.{S}. {Northeast} {Shelf} {Ecosystem}},
	volume = {15},
	copyright = {© 2023 The Authors. Marine and Coastal Fisheries published by Wiley Periodicals LLC on behalf of American Fisheries Society.},
	issn = {1942-5120},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mcf2.10230},
	doi = {10.1002/mcf2.10230},
	abstract = {As the world develops sources of renewable energy, there is an intensifying interest in offshore wind energy production. The Northeast U.S. Continental Shelf (NES) ecosystem has favorable wind dynamics, with active development of wind energy. In this study, we present species distribution models that consider both occupancy and biomass responses for a broad spectrum of fish and macroinvertebrate taxa (n = 177). Building upon prior analyses, habitat was differentiated into overall and core habitats based on statistical distributions of habitat scores. Overall habitat was used to show each species' regional distribution based on fishery-independent survey captures between 1976 and 2019, whereas core habitat represented where the focus of the species' abundance was located as a subset of overall habitat. Wind energy developments may modify the water column in ways that impact lower-trophic-level productivity; therefore, added attention was given to the response of forage species. Over 20\% of species showed preferential use of putative and potential wind development areas, including a disproportionate number of forage taxa. Principal usage varied by season, with forage species like Atlantic Menhaden Brevoortia tyrannus and Atlantic Mackerel Scomber scombrus preferentially using the lease areas in spring and Round Herring Etrumeus teres and longfin inshore squid Doryteuthis pealeii using lease areas in autumn. For species with relatively low usage of the lease areas, there was a tendency for the usage related to overall habitat to be lower than usage for core habitat; in contrast, for species with high usage of the lease areas, that usage was higher for overall habitat than for core habitat. The area of habitat tended to have positive trends across species, with these positive trends being disproportionately higher among forage taxa. These results frame the importance of wind lease areas for species in the NES, particularly forage taxa that fulfill many important ecological functions.},
	language = {en},
	number = {2},
	urldate = {2023-08-07},
	journal = {Marine and Coastal Fisheries},
	author = {Friedland, Kevin D. and Adams, Evan M. and Goetsch, Chandra and Gulka, Julia and Brady, Damian C. and Rzeszowski, Everett and Crear, Daniel P. and Gaichas, Sarah and Gill, Andrew B. and McManus, M. Conor and Methratta, Elizabeth T. and Morano, Janelle L. and Staudinger, Michelle D.},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/mcf2.10230},
	pages = {e10230},
	annote = {e10230 UMCF-2022-0033.R1},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/NSHY2THP/Friedland et al. - 2023 - Forage Fish Species Prefer Habitat within Designat.pdf:application/pdf;Snapshot:/Users/sarah.gaichas/Zotero/storage/U5UD4ETL/mcf2.html:text/html},
}

@article{thorson_defining_2020,
	title = {Defining indices of ecosystem variability using biological samples of fish communities: {A} generalization of empirical orthogonal functions},
	volume = {181},
	issn = {0079-6611},
	shorttitle = {Defining indices of ecosystem variability using biological samples of fish communities},
	url = {https://www.sciencedirect.com/science/article/pii/S0079661119304240},
	doi = {10.1016/j.pocean.2019.102244},
	abstract = {Multivariate data reduction techniques are widely used to describe modes of variability in atmospheric and oceanographic conditions for the world’s oceans. Dominant modes of variability such as the Pacific Decadal Oscillation (PDO) are typically defined as a statistical summary of physical measurements, and include both principle components representing modes of variability over time, and an empirical orthogonal function (EOF) giving the spatial pattern associated with a positive or negative phase for each mode. Typically, these indices are compared with biological conditions to describe or predict physical drivers of ecological dynamics. In some circumstances, however, it may instead be useful to apply EOF analysis directly to biological measurements, estimating indices of biological variability as well as maps of biological response associated with each index. We therefore develop a generalization of EOF analysis that can be applied directly to multispecies biological samples using a multivariate spatio-temporal model. These biologically derived indices can then be compared with relevant indices derived from physical data, or used as covariates in spatially-varying coefficient models. We first show that a spatio-temporal model can replicate previous EOF estimates of the PDO and North Pacific Gyre Oscillation. We then identify three axes of variability in the eastern Bering Sea using biomass-sampling data for fourteen bottom-associated fishes and decapod crustaceans from 1982 to 2017. The first axis represents habitat preferences that are stable over time, and the second represents a multi-decadal trend in distribution for most species; for example, showing an increasing density for Alaska skate and arrowtooth flounder in the middle and inner domain. Finally, the third axis shows high interannual variability from 1982 to 1998 switching to multiyear stanzas from 1999 to 2017 and is highly correlated (0.87) with the extent of the cold bottom temperatures in this region and associated impacts on Alaska pollock and Pacific cod. These axes represent ecological dynamics for adult fishes and therefore integrate the impact of bottom-up and top-down processes, and they also confirm the importance of cold-pool extent for fish distribution in the Bering Sea while visualizing its varied impact on individual species. Moreover, this spatio-temporal approach allows oceanographers to define annual indices representing modes of variability in diverse biological communities from widely available field-sampling data.},
	language = {en},
	urldate = {2023-08-11},
	journal = {Progress in Oceanography},
	author = {Thorson, James T. and Ciannelli, Lorenzo and Litzow, Michael A.},
	month = feb,
	year = {2020},
	keywords = {Eastern Bering Sea, Vector autoregressive spatio-temporal model, Bottom trawl, Empirical orthogonal function, Sea-ice extent},
	pages = {102244},
	file = {Accepted Version:/Users/sarah.gaichas/Zotero/storage/8WNQYBVI/Thorson et al. - 2020 - Defining indices of ecosystem variability using bi.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarah.gaichas/Zotero/storage/XVYKNWR9/S0079661119304240.html:text/html},
}

@book{murdy_fishes_1997,
	address = {Washington and London},
	title = {Fishes of {Chesapeake} {Bay}},
	url = {https://www.amazon.com/Fishes-Chesapeake-Bay-Edward-Murdy/dp/1588340457},
	urldate = {2023-08-11},
	publisher = {Smithsonian Institution Press},
	author = {Murdy, Edward O. and Birdsong, Ray S. and Musick, John A.},
	year = {1997},
	file = {Fishes of Chesapeake Bay\: Edward O. Murdy, Ray S. Birdsong, John A. Musick\: 9781588340450\: Amazon.com\: Books:/Users/sarah.gaichas/Zotero/storage/JHYKQP9I/1588340457.html:text/html},
}

@book{bivand_spatial_2023,
	address = {New York},
	title = {Spatial {Data} {Science}: {With} {Applications} in {R}},
	isbn = {978-0-429-45901-6},
	shorttitle = {Spatial {Data} {Science}},
	abstract = {Spatial Data Science introduces fundamental aspects of spatial data that every data scientist should know before they start working with spatial data. These},
	publisher = {Chapman and Hall/CRC},
	author = {Bivand, Roger, Edzer Pebesma},
	month = may,
	year = {2023},
	doi = {10.1201/9780429459016},
}

@article{pebesma_simple_2018,
	title = {Simple {Features} for {R}: {Standardized} {Support} for {Spatial} {Vector} {Data}},
	volume = {10},
	issn = {2073-4859},
	shorttitle = {Simple {Features} for {R}},
	url = {https://journal.r-project.org/archive/2018/RJ-2018-009/index.html},
	doi = {10.32614/RJ-2018-009},
	abstract = {Simple features are a standardized way of encoding spatial vector data (points, lines, polygons) in computers. The sf package implements simple features in R, and has roughly the same capacity for spatial vector data as packages sp, rgeos, and rgdal. We describe the need for this package, its place in the R package ecosystem, and its potential to connect R to other computer systems. We illustrate this with examples of its use.},
	language = {en},
	number = {1},
	urldate = {2023-09-20},
	journal = {The R Journal},
	author = {Pebesma, Edzer},
	year = {2018},
	pages = {439},
	file = {Pebesma - 2018 - Simple Features for R Standardized Support for Sp.pdf:/Users/sarah.gaichas/Zotero/storage/86PCQULA/Pebesma - 2018 - Simple Features for R Standardized Support for Sp.pdf:application/pdf},
}


@article{gaichas_assessing_2023,
	title = {Assessing small pelagic fish trends in space and time using piscivore stomach contents},
	issn = {0706-652X, 1205-7533},
	url = {https://cdnsciencepub.com/doi/10.1139/cjfas-2023-0093},
	doi = {10.1139/cjfas-2023-0093},
	abstract = {Changing distribution and abundance of small pelagic fishes may drive changes in predator distributions, affecting predator availability to fisheries and surveys. However, small pelagics are difficult to survey directly, so we developed a novel method of assessing the aggregate abundance of 21 small pelagic forage taxa via predator stomach contents. We used stomach contents collected from 22 piscivore species captured by multiple bottom trawl surveys within a vector autoregressive spatio-temporal model to assess trends of small pelagics on the Northeast US shelf. The goal was to develop a spatial “forage index” to inform survey and (or) fishery availability in the western North Atlantic bluefish ( Pomatomus saltatrix) stock assessment. This spatially resolved index compared favorably with more traditional design-based survey biomass indices for forage species well sampled by surveys. However, our stomach content-based index better represented smaller unmanaged forage species that surveys are not designed to capture. The stomach-based forage index helped explain bluefish availability to the recreational fishery for stock assessment and provided insight into pelagic forage trends throughout the regional ecosystem.},
	language = {en},
	urldate = {2024-02-15},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Gaichas, Sarah K. and Gartland, James and Smith, Brian E. and Wood, Anthony D. and Ng, Elizabeth L. and Celestino, Michael and Drew, Katie and Tyrell, Abigail S. and Thorson, James T.},
	month = oct,
	year = {2023},
	pages = {cjfas--2023--0093},
	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/W4CMYQYY/Gaichas et al. - 2023 - Assessing small pelagic fish trends in space and t.pdf:application/pdf},
}