BenthosIndex.bib

@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/sarahgaichas/Zotero/storage/BDBIBD5D/Thorson and Barnett - 2017 - Comparing estimates of abundance trends and distri.pdf:application/pdf;Snapshot:/Users/sarahgaichas/Zotero/storage/F62SPRTP/2907795.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/sarahgaichas/Zotero/storage/69FKJSA6/Ng et al. - 2021 - Predator stomach contents can provide accurate ind.pdf:application/pdf;Snapshot:/Users/sarahgaichas/Zotero/storage/2X7SANRP/6145864.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 = {Climate vulnerability analysis, Distribution shift, Habitat assessment, Index standardization, Integrated ecosystem assessment, Spatio-temporal model, Stock assessment, VAST},
	pages = {143--161},
	file = {ScienceDirect Full Text PDF:/Users/sarahgaichas/Zotero/storage/38KBWBLZ/Thorson - 2019 - Guidance for decisions using the Vector Autoregres.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarahgaichas/Zotero/storage/85BILR75/S0165783618302820.html:text/html},
}

@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 = {Abundance index, Catchability coefficient, Delta model, Stock assessment, Tweedie distribution, VAST, Vector autoregressive spatio-temporal model},
	pages = {105745},
	file = {ScienceDirect Snapshot:/Users/sarahgaichas/Zotero/storage/SND4TRFL/S0165783620302629.html:text/html;Thorson et al. - 2021 - The surprising sensitivity of index scale to delta.pdf:/Users/sarahgaichas/Zotero/storage/N9EVY2WT/Thorson et al. - 2021 - The surprising sensitivity of index scale to delta.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 = {Bias correction, Epsilon estimator, Mixed-effects model, Random effects, Stock assessment, Template Model Builder (TMB)},
	pages = {66--74},
	file = {ScienceDirect Snapshot:/Users/sarahgaichas/Zotero/storage/EULWM2HW/S0165783615301399.html:text/html;Thorson and Kristensen - 2016 - Implementing a generic method for bias correction .pdf:/Users/sarahgaichas/Zotero/storage/AZC44RWT/Thorson and Kristensen - 2016 - Implementing a generic method for bias correction .pdf:application/pdf},
}

@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 = {ecosystem model, essential fish habitat, models of intermediate complexity for ecosystem assessments, spatio-temporal model, VAST},
	pages = {1083--1099},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/YJHSUG3P/Thorson et al. - 2019 - Spatio-temporal models of intermediate complexity .pdf:application/pdf;Snapshot:/Users/sarahgaichas/Zotero/storage/ENJIGEPF/faf.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 = {Abundance index, Benthic communities, Benthic ecology, Continental shelves, Disturbance, Fish feeding, Georges Bank, Gulf of Maine, Spatial distribution},
	pages = {265--275},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/QBPAZMMV/Link - 2004 - Using fish stomachs as samplers of the benthos in.pdf:application/pdf;Snapshot:/Users/sarahgaichas/Zotero/storage/CDUEEF9S/p265-275.html:text/html},
}

@article{detmer_variation_2021,
	title = {Variation in disturbance to a foundation species structures the dynamics of a benthic reef community},
	volume = {102},
	issn = {1939-9170},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ecy.3304},
	doi = {10.1002/ecy.3304},
	abstract = {Disturbance and foundation species can both have strong impacts on ecosystem structure and function, but studies of their interacting effects are hindered by the long life spans and slow growth of most foundation species. Here, we investigated the extent to which foundation species may mediate the impacts of disturbance on ecological communities, using the kelp forest ecosystem as a study system. Giant kelp (Macrocystis pyrifera) grows rapidly and experiences wave disturbance from winter storms. We developed and analyzed a model of the effects of variable storm regimes on giant kelp population dynamics and of the cascading effects on kelp-mediated competition between benthic community members in kelp forests. Simulations of severe storm regimes resulted in a greater abundance of understory macroalgae and a lower abundance of sessile invertebrates than did milder regimes. Both the cascading effects of periodic loss of giant kelp as well as the degree to which storms directly impacted the benthos (in the form of scouring) influenced the outcome of competition between benthic community members. The model’s qualitative predictions were consistent with empirical data from a 20-yr time series of community dynamics, suggesting that interannual variability in disturbance that affects giant kelp abundance can have strong consequences for benthic community structure. Our findings point to the value of long-term studies in elucidating the interacting effects of disturbance and foundation species.},
	language = {en},
	number = {5},
	urldate = {2023-03-15},
	journal = {Ecology},
	author = {Detmer, A. Raine and Miller, Robert J. and Reed, Daniel C. and Bell, Tom W. and Stier, Adrian C. and Moeller, Holly V.},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.3304},
	keywords = {competition, disturbance, foundation species, kelp forests, mathematical models},
	pages = {e03304},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/DLFFZ7G8/Detmer et al. - 2021 - Variation in disturbance to a foundation species s.pdf:application/pdf;Snapshot:/Users/sarahgaichas/Zotero/storage/TTJZBQIW/ecy.html:text/html},
}

@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/sarahgaichas/Zotero/storage/N3L2RL68/Fogarty - 2014 - The art of ecosystem-based fishery management.pdf:application/pdf;NRC Research Press PDF fulltext:/Users/sarahgaichas/Zotero/storage/H3FEZEKP/Fogarty - 2013 - The art of ecosystem-based fishery management.pdf:application/pdf;NRC Research Press Snapshot:/Users/sarahgaichas/Zotero/storage/RPQVFGEI/cjfas-2013-0203.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 = {diet, foraging theory, generalized additive model, generalized linear model, metabarcoding, point process, Poisson process, predation, Tweedie distribution},
	pages = {e3637},
	annote = {e3637 ECY21-0474.R2},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/L4SMAM2H/Thorson et al. - Diet analysis using generalized linear models deri.pdf:application/pdf;Full Text PDF:/Users/sarahgaichas/Zotero/storage/8G9S6T6L/Thorson et al. - 2022 - Diet analysis using generalized linear models deri.pdf:application/pdf;Snapshot:/Users/sarahgaichas/Zotero/storage/T8TB4GK6/ecy.html:text/html},
}

@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 = {ecosystem-based fisheries management (EBFM), estuary, fish stomach contents, multivariate analysis, trophic ecology},
	pages = {967--992},
	file = {Snapshot:/Users/sarahgaichas/Zotero/storage/RIZ6PJA4/jfb.html:text/html},
}

@article{gartland_spatiotemporal_2023,
	title = {Spatiotemporal patterns in the ecological community of the nearshore {Mid}-{Atlantic} {Bight}},
	volume = {704},
	issn = {0171-8630, 1616-1599},
	url = {https://www.int-res.com/abstracts/meps/v704/p15-33/},
	doi = {10.3354/meps14235},
	abstract = {Recognition of the need for a more holistic, ecosystem approach to the assessment and management of living marine resources has renewed interest in quantitative community ecology and fueled efforts to develop ecosystem metrics to gain insight into system status. This investigation utilized 12 years (2008 to 2019) of fisheries-independent bottom trawl survey data to quantify and synthesize the spatiotemporal patterns of species assemblages inhabiting the nearshore Mid-Atlantic Bight (MAB). Assemblages were delineated by ecomorphotype (EMT), and all species collected by the survey were allocated among 9 EMTs: demersal fishes; pelagic fishes; flatfishes; skates; rays; dogfishes; other sharks; cephalopods; and benthic arthropods. Annual time series and seasonal spatial distributions of relative aggregate biomass were quantified for each EMT using delta-generalized additive models. Dynamic factor analysis (DFA) revealed that the information content of the 9 annual time series was effectively summarized by 3 common trends, and DFA model fits to each EMT time series represented a new suite of ecosystem indicators for this system. Mean sea surface temperature during winter in the MAB was included in the selected DFA model, suggesting that winter environmental conditions influence the structure of this system at an annual scale. Principal component analysis uncovered a north-to-south gradient in the seasonal spatial distributions of these EMTs and identified a distinct area of elevated biomass for several assemblages along the south shore of Long Island, NY. Taken together, these results characterize the community structure of the nearshore MAB and yield requisite information to support ongoing ecosystem-scale assessment and management activities for this region.},
	language = {en},
	urldate = {2023-04-27},
	journal = {Marine Ecology Progress Series},
	author = {Gartland, James and Gaichas, Sarah K. and Latour, Robert J.},
	month = jan,
	year = {2023},
	keywords = {Dynamic factor analysis, Ecosystem approaches, Fisheries management, Generalized additive models, Mid-Atlantic Bight, Principal component analysis, Spatiotemporal patterns, Species assemblages},
	pages = {15--33},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/SUQ2PFR3/Gartland et al. - 2023 - Spatiotemporal patterns in the ecological communit.pdf:application/pdf},
}

@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 = {Bottom trawl, Eastern Bering Sea, Empirical orthogonal function, Sea-ice extent, Vector autoregressive spatio-temporal model},
	pages = {102244},
	file = {Accepted Version:/Users/sarahgaichas/Zotero/storage/8WNQYBVI/Thorson et al. - 2020 - Defining indices of ecosystem variability using bi.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarahgaichas/Zotero/storage/XVYKNWR9/S0079661119304240.html:text/html},
}

@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/sarahgaichas/Zotero/storage/W4CMYQYY/Gaichas et al. - 2023 - Assessing small pelagic fish trends in space and t.pdf:application/pdf},
}

@article{hale_historical_2018,
	title = {Historical {Trends} of {Benthic} {Invertebrate} {Biodiversity} {Spanning} 182 {Years} in a {Southern} {New} {England} {Estuary}},
	volume = {41},
	issn = {1559-2731},
	url = {https://doi.org/10.1007/s12237-018-0378-7},
	doi = {10.1007/s12237-018-0378-7},
	abstract = {Benthic invertebrates support numerous ecosystem functions and services including shellfish production, energy flow to fishes, and biogeochemical cycles. The decline of marine biodiversity worldwide has raised concerns about effects on ecosystems. To examine biodiversity trends of Narragansett Bay over time, a list was compiled of all benthic invertebrate species collected from the bay since 1834. The list covers 104 studies spanning 182 years and currently holds 1214 unique taxa from 21 phyla, the majority of all animal phyla on Earth. A permuted estimator of number of species suggested there are about 300 more yet to be discovered. Widely varying sampling gear and sieve mesh sizes precluded the use of abundance data. Instead, multidimensional scaling and taxonomic distinctness were used with presence-absence data to examine biodiversity trends. The changes in community composition and decline of benthic biodiversity (p {\textless} 0.01) since 1855 are what would be expected of a community that gradually deteriorated in the face of increasing anthropogenic stressors. Taxonomic distinctness had negative correlations (p {\textless} 0.05) with human population in the watershed, total nitrogen inputs, and inputs of metals. This loss of benthic biodiversity has implications for ecosystem functions and services. As some of the stressors waned in the last two or three decades, following passage of environmental legislation in the 1970s, biodiversity appeared to show a partial recovery. An inventory of species, how it has changed over time, and understanding what caused those changes are important for assessing whether remediation programs are achieving improved water quality and ecosystem health.},
	language = {en},
	number = {6},
	urldate = {2024-05-28},
	journal = {Estuaries and Coasts},
	author = {Hale, Stephen S. and Hughes, Melissa M. and Buffum, Henry W.},
	month = sep,
	year = {2018},
	keywords = {Biodiversity, Historical trends, Marine benthic invertebrates, Narragansett Bay, Taxonomic distinctness},
	pages = {1525--1538},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/2Z5AL7NT/Hale et al. - 2018 - Historical Trends of Benthic Invertebrate Biodiver.pdf:application/pdf},
}

@article{pranovi_historical_2008,
	title = {Historical changes in the structure and functioning of the benthic community in the lagoon of {Venice}},
	volume = {76},
	issn = {0272-7714},
	url = {https://www.sciencedirect.com/science/article/pii/S0272771407003678},
	doi = {10.1016/j.ecss.2007.08.006},
	abstract = {One of the main challenges in environmental management is how to manage the dynamics of natural environments. In this context, having information about historical changes of the structure of the biological communities could represent a useful tool to improve management strategies, contributing to refine the policy objectives, since it gives reference states with which to compare the present. The Venice lagoon represents an interesting case study, since it is a highly dynamic, but sensitive, environment which requires the adoption of prudent management. In its recent history the lagoon ecosystem has been exposed to different kinds of disturbance, from the discharge of pollutants and nutrients, to the invasion of alien species and the exploitation of its biological resources by using highly impacting fishing gears. The analysis of available data about the macro-benthic community, from 1935 to 2004, allows the description of changes of the community structure over almost 70 years, showing a sharp decrease in its diversity. In order to obtain information about its functioning, it is necessary to know how these changes have affected processes at the community and system level. In shallow water ecosystems, as the control is mainly due to the benthic compartment, variations in the structure of the benthic community can induce modifications in processes at different hierarchical levels. The trophic structure analysis has revealed major changes during the period; from a well-assorted structure in 1935, to an herbivore–detritivore dominated one in the 1990s, and finally to a filter feeder dominated structure during the last decade. This has produced variations in the secondary production and it has induced modifications in the type of the ecosystem control. These changes are discussed in the light of the dynamics of the main driving forces.},
	number = {4},
	urldate = {2024-05-28},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Pranovi, Fabio and Da Ponte, Filippo and Torricelli, Patrizia},
	month = mar,
	year = {2008},
	keywords = {benthic community, biological traits, exergy, lagoon of Venice, secondary production, species diversity, trophic structure},
	pages = {753--764},
	file = {Full Text:/Users/sarahgaichas/Zotero/storage/WCTWR6KP/Pranovi et al. - 2008 - Historical changes in the structure and functionin.pdf:application/pdf;ScienceDirect Snapshot:/Users/sarahgaichas/Zotero/storage/QHM33HN7/S0272771407003678.html:text/html},
}

@article{grebmeier_trends_2018,
	title = {Trends in {Benthic} {Macrofaunal} {Populations}, {Seasonal} {Sea} {Ice} {Persistence}, and {Bottom} {Water} {Temperatures} in the {Bering} {Strait} {Region}},
	volume = {31},
	issn = {10428275},
	url = {https://tos.org/oceanography/article/trends-in-benthic-macrofaunal-populations-seasonal-sea-ice-persistence-and},
	doi = {10.5670/oceanog.2018.224},
	language = {en},
	number = {2},
	urldate = {2024-05-28},
	journal = {Oceanography},
	author = {Grebmeier, Jacqueline and Frey, Karen and Cooper, Lee and Kędra, Monika},
	month = jun,
	year = {2018},
	file = {Grebmeier et al. - 2018 - Trends in Benthic Macrofaunal Populations, Seasona.pdf:/Users/sarahgaichas/Zotero/storage/BKCRIJXG/Grebmeier et al. - 2018 - Trends in Benthic Macrofaunal Populations, Seasona.pdf:application/pdf},
}

@book{theroux_quantitative_1998,
	title = {Quantitative composition anddistribution of the  macrobenthic invertebrate fauna of the continental shelf ecosystems of the northeastern {United} {States}. {U}.{S}. {Dep}. {Commer}.,{NOAA} {Tech}. {Rep}. {NMFS} 140.},
	url = {https://spo.nmfs.noaa.gov/sites/default/files/tr140opt.pdf},
	abstract = {From the mid-1950's to the mid-1960's a series ofquantitative surveys ofthe macrobenthic
invertebrate fauna were conducted in the offshore New England region (Maine to Long
Island, NewYork) . The surveys were designed to I) obtain measures of macrobenthic
standing crop expressed in terms of density and biomass; 2) determine the taxonomic
composition of the fauna (ca. 567 species); 3) map the general features of macrobenthic
distribution; and 4) evaluate the fauna's relationships to water depth, bottom type, temperature range, and sediment organic carbon content. A total of 1,076 samples, ranging from 3
to 3,974 m in depth, were obtained and analyzed.
The aggregate macrobenthic fauna consists of 44 major taxonomic groups (phyla,
classes, orders). A striking fact is that only five of those groups (belonging to four phyla)
account for over 80\% of both total biomass and number of individuals ofthe macrobenthos.
The five dominant groups are Bivalvia, Annelida, Amphipoda, Echninoidea, and
Holothuroidea.
Other salient features pertaining to the macrobenthos of the region are the following:
substantial differences in quantity exist among different geographic subareas within the
region, but with a general trend that both density and biomass increase from northeast to
southwest; both density and biomass decrease with increasing depth; the composition ofthe
bottom sediments significantly influences both the kind and quantity of macrobenthic
invertebrates, the largest quantities of both measures of abundance occurring in the coarser
grained sediments and diminishing with decreasing particle size; areas with marked seasonal changes in water temperature support an abundant and diverse fauna, whereas a
uniform temperature regime is associated with a sparse, less diverse fauna; and no detectable trends are evident in the quantitative composition of the macrobenthos in relation to
sediment organic carbon content.},
	urldate = {2024-05-28},
	author = {Theroux, Roger B and Wigley, Roland L},
	year = {1998},
	file = {tr140opt.pdf:/Users/sarahgaichas/Zotero/storage/BR4MIVPK/tr140opt.pdf:application/pdf},
}

@book{wigley_atlantic_1981,
	title = {Atlantic {Continental} {Shelf} and {Slope} of the {United} {StatesMacro} benthic {Invertebrate} {Fauna} of the {Middle} {Atlantic} {Bight} {Region}-{Faunal} {Composition} and {Quantitative} {Distribution}. {GEOLOGICAL} {SURVEY} {PROFESSIONAL} {PAPER} 529-{N}},
	url = {https://pubs.usgs.gov/pp/0529n/report.pdf},
	abstract = {In the early 1960's, a quantitative survey of the macrobenthic invertebrate fauna was conducted in the Middle
Atlantic Bight region. Purposes of this survey were to
obtain a preliminary measure of the macrobenthic standing
crop, particularly of biomass, and secondarily, to determine
the principal taxonomic components of the fauna and the
general features of their distribution. Sampling was conducted at 563 locations; water depths ranged from 4 to
3,080 m. An analysis of f'aunal composition and of quantitative distributions from the survey is presented in this
report. Quantities are expressed in terms of density and
biomass.
Dominant taxonomic components in numbers of individuals
were (in percentage of total fauna): Arthropoda (46),
Mollusca (25), Annelida (21), Echinodermata (4), and
Coelenterata (1). Dominant in biomass were (in percentage
of total fauna): Mollusca (71), Echinodermata (12), Annelida (7), Arthropoda (5), and Ascidiace·a (2). The quantity
of fauna, both density and biomass, decreased substantially
from shallow to deep water. Another major trend was the
marked decrease in quantity from north to south within the
Middle Atlantic Bight. Bottom sediment composition strongly
influenced both the kind and the quantity of macrobenthic
animals. Coarse-grained sediments generally supported the
largest quantities of animals, including many sessile forms.
Fine-grained sediments usually contained a depauperate
fauna; attached organisms were uncommon. No obvious correlations were detected between the amount of organic carbon
in bottom sediments and the quantity of benthic animals
present. Marked seasonal changes in bottom water temperature were associated with an abundant fauna composed of
diverse forms, whereas uniform temperatures throughout the
year were associated with a sparse fauna composed of a
moderate variety of species. Taxonomic groups that were
dominant in a significant number of s·amples, in terms of
number of individuals, were: Bivalvia, Annelida, Echinoidea,
Ophiuroidea, Crustacea, and the bathyal assemblage. Groups
dominant in terms of biomass were: Bivalvia, Annelida,
Echinoidea, Ophiuroidea, Holothuroidea, and the bathyal
assemblage.},
	urldate = {2024-05-28},
	author = {Wigley, Roland L and Theroux, Roger B},
	year = {1981},
	file = {report.pdf:/Users/sarahgaichas/Zotero/storage/YCNG76A5/report.pdf:application/pdf},
}

@article{stratmann_benbioden_2020,
	title = {The {BenBioDen} database, a global database for meio-, macro- and megabenthic biomass and densities},
	volume = {7},
	copyright = {2020 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-020-0551-2},
	doi = {10.1038/s41597-020-0551-2},
	abstract = {Benthic fauna refers to all fauna that live in or on the seafloor, which researchers typically divide into size classes meiobenthos (32/64 µm–0.5/1 mm), macrobenthos (250 µm–1 cm), and megabenthos ({\textgreater}1 cm). Benthic fauna play important roles in bioturbation activity, mineralization of organic matter, and in marine food webs. Evaluating their role in these ecosystem functions requires knowledge of their global distribution and biomass. We therefore established the BenBioDen database, the largest open-access database for marine benthic biomass and density data compiled so far. In total, it includes 11,792 georeferenced benthic biomass and 51,559 benthic density records from 384 and 600 studies, respectively. We selected all references following the procedure for systematic reviews and meta-analyses, and report biomass records as grams of wet mass, dry mass, or ash-free dry mass, or carbon per m2 and as abundance records as individuals per m2. This database provides a point of reference for future studies on the distribution and biomass of benthic fauna.},
	language = {en},
	number = {1},
	urldate = {2024-06-04},
	journal = {Scientific Data},
	author = {Stratmann, Tanja and van Oevelen, Dick and Martínez Arbizu, Pedro and Wei, Chih-Lin and Liao, Jian-Xiang and Cusson, Mathieu and Scrosati, Ricardo A. and Archambault, Philippe and Snelgrove, Paul V. R. and Ramey-Balci, Patricia A. and Burd, Brenda J. and Kenchington, Ellen and Gilkinson, Kent and Belley, Rénald and Soetaert, Karline},
	month = jun,
	year = {2020},
	note = {Publisher: Nature Publishing Group},
	keywords = {Ecosystem services, Marine biology},
	pages = {206},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/9FWEZ2DH/Stratmann et al. - 2020 - The BenBioDen database, a global database for meio.pdf:application/pdf},
}

@misc{noauthor_nefsc_nodate,
	title = {{NEFSC} {Benthic} {Database} - {Ocean} {Biodiversity} {Information} {System}},
	url = {https://www.obis.org/dataset/e7c86904-aac7-4a17-a895-99a54c430d80},
	urldate = {2024-06-10},
	file = {NEFSC Benthic Database - Ocean Biodiversity Information System:/Users/sarahgaichas/Zotero/storage/WPBG3CEG/e7c86904-aac7-4a17-a895-99a54c430d80.html:text/html},
}

@article{fuchs_wrong-way_2020,
	title = {Wrong-way migrations of benthic species driven by ocean warming and larval transport},
	volume = {10},
	copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {1758-6798},
	url = {https://www.nature.com/articles/s41558-020-0894-x},
	doi = {10.1038/s41558-020-0894-x},
	abstract = {Ocean warming has predictably driven some marine species to migrate polewards or to deeper water, matching rates of environmental temperature change (climate velocity) to remain at tolerable temperatures. Most species conforming to expectations are fish and other strong swimmers that can respond to temperature change by migrating as adults. On the Northwest Atlantic continental shelf, however, many benthic invertebrates’ ranges have instead shifted southwards and into shallower, warmer water. We tested whether these ‘wrong-way’ migrations could arise from warming-induced changes in the timing of spawning (phenology) and transport of drifting larvae. The results showed that larvae spawned earlier in the year encounter more downwelling-favourable winds and river discharge that drive transport onshore and southwards. Phenology and transport explained most observed range shifts, whereas climate velocity was a poor predictor. This study reveals a physical mechanism that counterintuitively pushes benthic species, including commercial shellfish, into warmer regions with higher mortality.},
	language = {en},
	number = {11},
	urldate = {2024-06-10},
	journal = {Nature Climate Change},
	author = {Fuchs, Heidi L. and Chant, Robert J. and Hunter, Elias J. and Curchitser, Enrique N. and Gerbi, Gregory P. and Chen, Emily Y.},
	month = nov,
	year = {2020},
	note = {Publisher: Nature Publishing Group},
	keywords = {Marine biology, Phenology, Physical oceanography},
	pages = {1052--1056},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/H5ABKPCN/Fuchs et al. - 2020 - Wrong-way migrations of benthic species driven by .pdf:application/pdf},
}

@article{hale_subtidal_2017,
	title = {Subtidal {Benthic} {Invertebrates} {Shifting} {Northward} {Along} the {US} {Atlantic} {Coast}},
	volume = {40},
	issn = {1559-2731},
	url = {https://doi.org/10.1007/s12237-017-0236-z},
	doi = {10.1007/s12237-017-0236-z},
	abstract = {Numerous marine and terrestrial species have shifted their ranges poleward in response to warming from global climate change. However, few studies have examined range shifts of subtidal benthic communities in estuarine and nearshore waters. This study examined 20 years (1990–2010) of occurrence and abundance data of soft-bottom, benthic invertebrates along the Atlantic coast of the USA. Data from two biogeographic provinces (Carolinian and Virginian), which spanned 15° of latitude from mid-Florida to Cape Cod, were extracted from a national coastal assessment program. Mean water temperatures increased significantly during the study period, bottom water by 1.6 °C and surface water by 1.7 °C. Of 25 species with significant changes in centers of abundance (out of the 30 most prevalent), 18 (60\%) shifted northward and 7 (23\%) shifted southward. Species that shifted north moved an average distance of 181 km, in contrast with 65 km for species that shifted south. The southern limits of 22 species showed significant northward shifts; because there was little change in northern limits, this resulted in an average 25\% range contraction. Community composition changed during the study period, most notably in southern latitudes. Five Carolinian species surmounted their northerly biogeographic boundary. Consequences of these range shifts include changes in benthic community structure and function, which have strong implications for ecosystem functioning and services including changes in fisheries dependent upon benthic prey.},
	language = {en},
	number = {6},
	urldate = {2024-08-30},
	journal = {Estuaries and Coasts},
	author = {Hale, Stephen S. and Buffum, Henry W. and Kiddon, John A. and Hughes, Melissa M.},
	month = nov,
	year = {2017},
	keywords = {Benthic invertebrates, Carolinian Biogeographic Province, Climate change, Species’ range shifts, US Atlantic coast, Virginian Biogeographic Province},
	pages = {1744--1756},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/EKD3G3GC/Hale et al. - 2017 - Subtidal Benthic Invertebrates Shifting Northward .pdf:application/pdf},
}

@incollection{lopez-gappa_impact_2022,
	address = {Cham},
	title = {The {Impact} of {Global} {Change} on {Marine} {Benthic} {Invertebrates}},
	isbn = {978-3-030-86676-1},
	url = {https://doi.org/10.1007/978-3-030-86676-1_8},
	abstract = {Marine biogeographers divide the coastal areas of the southern Southwest Atlantic in two main biogeographic units: the warm-temperate Argentine and the cold-temperate Magellanic provinces, with a transition at 43°–44°S. Biodiversity decreases with latitude in decapod crustaceans but increases southward in most benthic invertebrate groups. Patagonian rocky shores are exposed to harsh physical conditions resulting in intense desiccation of intertidal organisms, which can be expected to get worse in future scenarios of global climate change. A change to be anticipated in the Patagonian coast is the southward range shift of warm-temperate species, which can already be perceived in San Jorge gulf, where recent southward range extensions were detected in the distribution of several species. The most important changes during the last decades in the Patagonian coast were caused by the invasion of nonindigenous benthic invertebrates. The arrivals of the intertidal barnacle Balanus glandula, the crab Carcinus maenas, the sea slug Pleurobranchaea maculata, the tunicate Styela clava, and the reef-forming oyster Magallana gigas were the main invasions of marine invertebrates recorded in the region. Massive mortalities of the yellow clam Amarilladesma mactroides occurred in Buenos Aires Province and northern Patagonia in the 1990s. Future perspectives for the region are briefly discussed.},
	language = {en},
	urldate = {2024-08-30},
	booktitle = {Global {Change} in {Atlantic} {Coastal} {Patagonian} {Ecosystems}: {A} {Journey} {Through} {Time}},
	publisher = {Springer International Publishing},
	author = {López-Gappa, Juan},
	editor = {Helbling, E. Walter and Narvarte, Maite A. and González, Raul A. and Villafañe, Virginia E.},
	year = {2022},
	doi = {10.1007/978-3-030-86676-1_8},
	pages = {177--204},
}

@article{rivetti_global_2014,
	title = {Global {Warming} and {Mass} {Mortalities} of {Benthic} {Invertebrates} in the {Mediterranean} {Sea}},
	volume = {9},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115655},
	doi = {10.1371/journal.pone.0115655},
	abstract = {Satellite data show a steady increase, in the last decades, of the surface temperature (upper few millimetres of the water surface) of the Mediterranean Sea. Reports of mass mortalities of benthic marine invertebrates increased in the same period. Some local studies interpreted the two phenomena in a cause-effect fashion. However, a basin-wide picture of temperature changes combined with a systematic assessment on invertebrate mass mortalities was still lacking. Both the thermal structure of the water column in the Mediterranean Sea over the period 1945–2011 and all documented invertebrate mass mortality events in the basin are analysed to ascertain if: 1- documented mass mortalities occurred under conditions of positive temperature trends at basin scale, and 2- atypical thermal conditions were registered at the smaller spatial and temporal scale of mass mortality events. The thermal structure of the shallow water column over the last 67 years was reconstructed using data from three public sources: MEDAR-MEDATLAS, World Ocean Database, MFS-VOS programme. A review of the mass mortality events of benthic invertebrates at Mediterranean scale was also carried out. The analysis of in situ temperature profiles shows that the Mediterranean Sea changed in a non-homogeneous fashion. The frequency of mass mortalities is increasing. The areas subjected to these events correspond to positive thermal anomalies. Statistically significant temperature trends in the upper layers of the Mediterranean Sea show an increase of up to 0.07°C/yr for a large fraction of the basin. Mass mortalities are consistent with both the temperature increase at basin scale and the thermal changes at local scale, up to 5.2°C. Our research supports the existence of a causal link between positive thermal anomalies and observed invertebrate mass mortalities in the Mediterranean Sea, invoking focused mitigation initiatives in sensitive areas.},
	language = {en},
	number = {12},
	urldate = {2024-08-30},
	journal = {PLOS ONE},
	author = {Rivetti, Irene and Fraschetti, Simonetta and Lionello, Piero and Zambianchi, Enrico and Boero, Ferdinando},
	month = dec,
	year = {2014},
	note = {Publisher: Public Library of Science},
	keywords = {Climate change, Invertebrates, Islands, Marine ecosystems, Mediterranean Sea, Ocean temperature, Sponges, Water columns},
	pages = {e115655},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/QXZ4LLPD/Rivetti et al. - 2014 - Global Warming and Mass Mortalities of Benthic Inv.pdf:application/pdf},
}

@article{hiddink_temperature_2015,
	title = {Temperature tracking by {North} {Sea} benthic invertebrates in response to climate change},
	volume = {21},
	copyright = {© 2014 John Wiley \& Sons Ltd},
	issn = {1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.12726},
	doi = {10.1111/gcb.12726},
	abstract = {Climate change is a major threat to biodiversity and distributions shifts are one of the most significant threats to global warming, but the extent to which these shifts keep pace with a changing climate is yet uncertain. Understanding the factors governing range shifts is crucial for conservation management to anticipate patterns of biodiversity distribution under future anthropogenic climate change. Soft-sediment invertebrates are a key faunal group because of their role in marine biogeochemistry and as a food source for commercial fish species. However, little information exists on their response to climate change. Here, we evaluate changes in the distribution of 65 North Sea benthic invertebrate species between 1986 and 2000 by examining their geographic, bathymetric and thermal niche shifts and test whether species are tracking their thermal niche as defined by minimum, mean or maximum sea bottom (SBT) and surface (SST) temperatures. Temperatures increased in the whole North Sea with many benthic invertebrates showing north-westerly range shifts (leading/trailing edges as well as distribution centroids) and deepening. Nevertheless, distribution shifts for most species (3.8–7.3 km yr−1 interquantile range) lagged behind shifts in both SBT and SST (mean 8.1 km yr−1), resulting in many species experiencing increasing temperatures. The velocity of climate change (VoCC) of mean SST accurately predicted both the direction and magnitude of distribution centroid shifts, while maximum SST did the same for contraction of the trailing edge. The VoCC of SBT was not a good predictor of range shifts. No good predictor of expansions of the leading edge was found. Our results show that invertebrates need to shift at different rates and directions to track the climate velocities of different temperature measures, and are therefore lagging behind most temperature measures. If these species cannot withstand a change in thermal habitat, this could ultimately lead to a drop in benthic biodiversity.},
	language = {en},
	number = {1},
	urldate = {2024-08-30},
	journal = {Global Change Biology},
	author = {Hiddink, Jan G. and Burrows, Michael T. and García Molinos, Jorge},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.12726},
	keywords = {benthic invertebrate, benthos, distribution shifts, North Sea, sea bottom temperature, sea surface temperature, velocity of climate change},
	pages = {117--129},
	file = {Snapshot:/Users/sarahgaichas/Zotero/storage/6DWM8PTX/gcb.html:text/html},
}

@article{przeslawski_beyond_2008,
	title = {Beyond corals and fish: the effects of climate change on noncoral benthic invertebrates of tropical reefs},
	volume = {14},
	copyright = {© 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd},
	issn = {1365-2486},
	shorttitle = {Beyond corals and fish},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2486.2008.01693.x},
	doi = {10.1111/j.1365-2486.2008.01693.x},
	abstract = {Climate change is threatening tropical reefs across the world, with most scientists agreeing that the current changes in climate conditions are occurring at a much faster rate than in the past and are potentially beyond the capacity of reefs to adapt and recover. Current research in tropical ecosystems focuses largely on corals and fishes, although other benthic marine invertebrates provide crucial services to reef systems, with roles in nutrient cycling, water quality regulation, and herbivory. We review available information on the effects of environmental conditions associated with climate change on noncoral tropical benthic invertebrates, including inferences from modern and fossil records. Increasing sea surface temperatures may decrease survivorship and increase the developmental rate, as well as alter the timing of gonad development, spawning, and food availability. The broad latitudinal distribution and associated temperature ranges of several pantropical taxa suggest that some reef communities may have an in-built adaptive capacity. Tropical benthic invertebrates will also show species-specific sublethal and lethal responses to sea-level rise, ocean acidification, physical disturbance, runoff, turbidity, sedimentation, and changes in ocean circulation. In order to accurately predict a species' response to these stressors, we must consider the magnitude and duration of exposure to each stressor, as well as the physiology, mobility, and habitat requirements of the species. Stressors will not act independently, and many organisms will be exposed to multiple stressors concurrently, including anthropogenic stressors. Environmental changes associated with climate change are linked to larger ecological processes, including changes in larval dispersal and recruitment success, shifts in community structure and range extensions, and the establishment and spread of invasive species. Loss of some species will trigger economic losses and negative effects on ecosystem function. Our review is intended to create a framework with which to predict the vulnerability of benthic invertebrates to the stressors associated with climate change, as well as their adaptive capacity. We anticipate that this review will assist scientists, managers, and policy-makers to better develop and implement regional research and management strategies, based on observed and predicted changes in environmental conditions.},
	language = {en},
	number = {12},
	urldate = {2024-08-30},
	journal = {Global Change Biology},
	author = {Przeslawski, Rachel and Ahyong, Shane and Byrne, Maria and Wörheide, Gert and Hutchings, Pat},
	year = {2008},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2486.2008.01693.x},
	keywords = {Caribbean, Great Barrier Reef, habitat loss, invasive species, larvae, ocean acidification, reproduction, salinity, temperature, tropical invertebrates},
	pages = {2773--2795},
	file = {Snapshot:/Users/sarahgaichas/Zotero/storage/XHQSCG7P/j.1365-2486.2008.01693.html:text/html},
}

@article{prather_invertebrates_2013,
	title = {Invertebrates, ecosystem services and climate change},
	volume = {88},
	copyright = {© 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society},
	issn = {1469-185X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/brv.12002},
	doi = {10.1111/brv.12002},
	abstract = {The sustainability of ecosystem services depends on a firm understanding of both how organisms provide these services to humans and how these organisms will be altered with a changing climate. Unquestionably a dominant feature of most ecosystems, invertebrates affect many ecosystem services and are also highly responsive to climate change. However, there is still a basic lack of understanding of the direct and indirect paths by which invertebrates influence ecosystem services, as well as how climate change will affect those ecosystem services by altering invertebrate populations. This indicates a lack of communication and collaboration among scientists researching ecosystem services and climate change effects on invertebrates, and land managers and researchers from other disciplines, which becomes obvious when systematically reviewing the literature relevant to invertebrates, ecosystem services, and climate change. To address this issue, we review how invertebrates respond to climate change. We then review how invertebrates both positively and negatively influence ecosystem services. Lastly, we provide some critical future directions for research needs, and suggest ways in which managers, scientists and other researchers may collaborate to tackle the complex issue of sustaining invertebrate-mediated services under a changing climate.},
	language = {en},
	number = {2},
	urldate = {2024-08-30},
	journal = {Biological Reviews},
	author = {Prather, Chelse M. and Pelini, Shannon L. and Laws, Angela and Rivest, Emily and Woltz, Megan and Bloch, Christopher P. and Del Toro, Israel and Ho, Chuan-Kai and Kominoski, John and Newbold, T. A. Scott and Parsons, Sheena and Joern, A.},
	year = {2013},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/brv.12002},
	keywords = {biodiversity, bioindicator species, climate change, ecosystem engineers, ecosystem services, insects, invertebrates, sustainability},
	pages = {327--348},
	file = {Snapshot:/Users/sarahgaichas/Zotero/storage/K2LZNIRX/brv.html:text/html},
}

@incollection{roberts_benthic_2012,
	title = {Benthic invertebrates in a high- {CO2} world},
	isbn = {978-0-429-10938-6},
	abstract = {Abstract Ocean acidižcation (OA), whereby increases in atmospheric carbon dioxide (CO2) over 
the past 200 years have led to a decline in the pH and carbonate ion availability of the oceans, has 
emerged as one of the major drivers of twenty-žrst century marine scientižc research. Here we 
describe the current understanding of OA effects on benthic marine invertebrates, in particular the 
calcižers thought to be most sensitive to altered carbonate chemistry. We describe the responses of 
benthic invertebrates to OA conditions predicted up to the end of the century, examining individual 
organism response through to ecosystem-level impacts. Research over the past decade has found 
great variability in the physiological and functional response of different species and communities to OA, with further variability evident between life stages. Over both geological and recent 
timescales, the presence and calcižcation rates of marine calcižers have been inextricably linked 
to the carbon chemistry of the oceans. Under short-term experimentally enhanced CO2 conditions, 
many organisms have shown trade-offs in their physiological responses, such as reductions in calcižcation rate and reproductive output. In addition, carry-over effects from fertilization, larval and 
juvenile stages, such as enhanced development time and morphological changes, highlight the need 
for broad-scale studies over multiple life stages. These organism-level responses may propagate 
through to altered benthic communities under naturally enhanced CO2 conditions, evident in studies 
of upwelling regions and at shallow-water volcanic CO2 vents. Only by establishing which benthic 
invertebrates have the ability to acclimate or adapt, via natural selection, to changes from OA, in 
combination with other environmental stressors, can we begin to predict the consequences of future 
climate change for these communities.},
	booktitle = {Oceanography and {Marine} {Biology}},
	publisher = {CRC Press},
	author = {Roberts, Laura C. Wicks \& J. Murray},
	year = {2012},
	note = {Num Pages: 62},
}

@article{bianchi_benthic_2023,
	title = {Benthic {Invertebrates} on the {Move}: {A} {Tale} of {Ocean} {Warming} and {Sediment} {Carbon} {Storage}},
	volume = {32},
	copyright = {© 2023 Association for the Sciences of Limnology and Oceangraphy.},
	issn = {1539-6088},
	shorttitle = {Benthic {Invertebrates} on the {Move}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/lob.10544},
	doi = {10.1002/lob.10544},
	abstract = {Ongoing effects of climate change create a dual challenge of shifting distributions of organisms and concerns about the fate of organic carbon in nature. Marine sediments store vast amounts of organic carbon, but the fate of that material hinges on the biology of organisms associated with the seafloor and how they influence rates of carbon decomposition and burial. Shifts in large megafauna that disturb and thus help to oxygenate sediments could have important ramifications regarding whether sediments release or store carbon for long periods of time. We consider snow crab and lobster, two commercially important seafloor species in the Northeastern Atlantic, and the potential effects of ongoing changes in their distributions and that of their fisheries for future climate scenarios. These ongoing biogeographic shifts, considered in tandem with areas of seabed legislatively protected from fishing impacts and thus not confounded by cumulative effects of fishing gear disturbance, offer an opportunity to study how newly arrived species that disturb large areas of the seafloor might influence the global carbon cycle.},
	language = {en},
	number = {1},
	urldate = {2024-08-30},
	journal = {Limnology and Oceanography Bulletin},
	author = {Bianchi, Thomas S. and Brown, Craig J. and Snelgrove, Paul V. R. and Stanley, Ryan R. E. and Cote, David and Morris, Corey},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/lob.10544},
	pages = {1--5},
	file = {Full Text PDF:/Users/sarahgaichas/Zotero/storage/U8X9LWZC/Bianchi et al. - 2023 - Benthic Invertebrates on the Move A Tale of Ocean.pdf:application/pdf;Snapshot:/Users/sarahgaichas/Zotero/storage/NSCVD7WP/lob.html:text/html},
}

@article{birchenough_climate_2015,
	title = {Climate change and marine benthos: a review of existing research and future directions in the {North} {Atlantic}},
	volume = {6},
	copyright = {© 2015 John Wiley \& Sons, Ltd},
	issn = {1757-7799},
	shorttitle = {Climate change and marine benthos},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/wcc.330},
	doi = {10.1002/wcc.330},
	abstract = {There is growing evidence that climate change could affect marine benthic systems. This review provides information of climate change-related impacts on the marine benthos in the North Atlantic. We cover a number of related research aspects, mainly in connection to two key issues. First, is the relationship between different physical aspects of climate change and the marine benthos. This section covers: (a) the responses to changes in seawater temperature (biogeographic shifts and phenology); (b) altered Hydrodynamics; (c) ocean acidification (OA); and (d) sea-level rise-coastal squeeze. The second major issue addressed is the possible integrated impact of climate change on the benthos. This work is based on relationships between proxies for climate variability, notably the North Atlantic Oscillation (NAO) index, and the long-term marine benthos. The final section of our review provides a series of conclusions and future directions to support climate change research on marine benthic systems. WIREs Clim Change 2015, 6:203–223. doi: 10.1002/wcc.330 This article is categorized under: Climate, Ecology, and Conservation {\textgreater} Modeling Species and Community Interactions},
	language = {en},
	number = {2},
	urldate = {2024-08-30},
	journal = {WIREs Climate Change},
	author = {Birchenough, Silvana N.R. and Reiss, Henning and Degraer, Steven and Mieszkowska, Nova and Borja, Ángel and Buhl-Mortensen, Lene and Braeckman, Ulrike and Craeymeersch, Johan and De Mesel, Ilse and Kerckhof, Francis and Kröncke, Ingrid and Parra, Santiago and Rabaut, Marijn and Schröder, Alexander and Van Colen, Carl and Van Hoey, Gert and Vincx, Magda and Wätjen, Kai},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/wcc.330},
	pages = {203--223},
	file = {Snapshot:/Users/sarahgaichas/Zotero/storage/WB4MASJ8/wcc.html:text/html},
}