@article{rocco_cao_li_lee_2024, title={Evaluating impacts of environmental stress and bioactive chemicals on the North Carolina blue crab population: An individual-based model}, volume={16}, ISSN={["1942-5120"]}, DOI={10.1002/mcf2.10286}, abstractNote={Abstract Objective Recent estimates of the North Carolina blue crab Callinectes sapidus stock found that the stock is overfished and overfishing is occurring. Threats outlined in the 2018 stock assessment include climate change and estrogenic endocrine‐disrupting chemicals (EEDCs). The objective of this study was to use an individual‐based modeling approach to simulate the long‐term effects of climate change and EEDCs on the North Carolina blue crab stock. Methods To do this, we built an individual‐based model that simulated the life history of individual blue crabs, including but not limited to growth, reproduction, and mortality. We then tested our population of blue crabs against 30 different combinations of temperature and EEDC scenarios over 50 years to determine the long‐term effects on the population. Result Our simulations suggested that the North Carolina blue crab population may be relatively resilient to climate change‐related temperature shifts but that there may be significant impacts at the population level as summer temperatures become more extreme. Endocrine‐disrupting chemical effects resulted in an alternative stable state of lower catch or the total extinction of the population. Conclusion These results suggest that management strategy changes may be necessary as temperatures become more extreme in the region. In addition, more research is necessary to fully understand the effects of EEDCs on blue crabs and other crustaceans at the individual and population level.}, number={2}, journal={MARINE AND COASTAL FISHERIES}, author={Rocco, Alex J. and Cao, Jie and Li, Yan and Lee, Laura M.}, year={2024}, month={Apr} }
 @article{shertzer_crosson_williams_cao_devictor_dumas_nesslage_2024, title={Fishery management strategies for Red Snapper in the southeastern US Atlantic: A spatial population model to compare approaches}, volume={1}, ISSN={["1548-8675"]}, DOI={10.1002/nafm.10966}, abstractNote={Abstract}, journal={NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT}, author={Shertzer, Kyle and Crosson, Scott and Williams, Erik and Cao, Jie and Devictor, Rick and Dumas, Chris and Nesslage, Genevieve}, year={2024}, month={Jan} }
 @article{guo_zhou_wan_cao_wang_2024, title={Numerical simulation-based hydrodynamic interaction of bottom-set gillnet with current and ecological implications}, volume={293}, ISSN={["1873-5258"]}, DOI={10.1016/j.oceaneng.2023.116601}, abstractNote={Bottom-set gillnets, consisting of flexible netting, are extensively utilized in coastal waters worldwide for capturing aquatic organisms. However, their efficiency and selectivity can be significantly affected by changes in shape and mesh opening due to external forces during practical operations. In this study, a comprehensive investigation of knotless nylon bottom-set gillnets under uniform current conditions was conducted using numerical simulations based on the mass-spring model. The simulations allowed us to calculate the netting configuration, mesh opening, and tension distribution of gillnets under different current velocities. The results suggest that with the increase in current velocity, the tension within the gillnet system shows a progressive increment, with higher tension observed at the diagonal corners. The vertical projection area, or effective operation area, of the netting diminishes with increasing current velocity, which is accompanied by a less uniform distribution of mesh openings. The simulation outcomes are in strong agreement with experimental measurements obtained from a set of model testing carried out in a circulating flume tank. Through simulations of structural optimization, we observed that low-profile gillnets with narrower dimensions exhibit a vertically stretched configuration resembling a wall, with meshes uniformly opened in a diamond-shaped pattern. These findings hold significant implications for the improvement of bottom-set gillnet design and the mitigation of ecological risks posed to marine fauna.}, journal={OCEAN ENGINEERING}, author={Guo, Shaojian and Zhou, Cheng and Wan, Rong and Cao, Jie and Wang, Yucheng}, year={2024}, month={Feb} }
 @article{damiano_karnauskas_merten_cao_2024, title={Spatiotemporal dynamics of dolphinfish<i> (Coryphaena</i><i> hippurus)</i> in the western Atlantic Ocean}, volume={122}, ISSN={["1937-4518"]}, DOI={10.7755/FB.122.1-2.3}, abstractNote={Dolphinfish (Coryphaena hippurus) are caught throughout the western Atlantic Ocean over varying spatial and temporal scales.Prior attempts to quantify the population dynamics of dolphinfish in this region have been inhibited by an inability to model the spatiotemporal dynamics of this stock.We fit a seasonal vector autoregressive spatiotemporal (VAST) model to quantify the spatiotemporal dynamics of western Atlantic dolphinfish, to estimate standardized relative indices of abundance during 1986-2022 at regional scales, and to estimate changes in spatial distribution.The magnitude of abundance was greatest during spring and summer in northern spatial strata and was comparable over seasons in southern spatial strata.Abundance of dolphinfish appeared to be stable during 1986-2018 and then declined during 2019-2022.This trend occurred in all regions, except for in Atlantic waters from Cape Hatteras, North Carolina, to the southern border of Georgia, where abundance remained stable during 2019-2022.No shift in the distribution of the population was detected, but regional patterns of abundance provide insight into changes in the timing of availability.This study resulted in the first standardized index of relative abundance to capture the spatiotemporal dynamics of western Atlantic dolphinfish.These results have increased our understanding of the population dynamics of this species in this region and should prove useful in future attempts to manage the population at different spatial and temporal scales.}, number={1-2}, journal={FISHERY BULLETIN}, author={Damiano, Matthew D. and Karnauskas, Mandy and Merten, Wessley and Cao, Jie}, year={2024}, pages={26–43} }
 @article{olmos_cao_thorson_punt_monnahan_alglave_szuwalski_2023, title={A step towards the integration of spatial dynamics in population dynamics models: Eastern Bering Sea snow crab as a case study}, volume={485}, ISSN={["1872-7026"]}, DOI={10.1016/j.ecolmodel.2023.110484}, abstractNote={Considering spatial processes in population dynamics models can be difficult because of data limitations and computational costs. We adapted a high-resolution spatiotemporal assessment framework to better address fine-scale spatial heterogeneities based on theories of fish population dynamics and spatiotemporal statistics. Specifically, we developed a size-based state-space model for the snow crab (Chionoecetes opilio) population in the Eastern Bering Sea (EBS) to refine the representation of spatial processes in integrated population models, facilitate understanding of the drivers of spatiotemporal population dynamics, and provide new insights for management advice. The model fits to spatial survey and fishery-dependent catch data. It implicitly accounts for seasonal movement between the time of the survey and that of fishery to estimate fine-scale spatial population dynamic and fishing impacts, including potential environmental drivers. We quantify, for the first time, spatiotemporal variation in exploitable abundance, fishing mortality, recruitment, and mature and immature abundance. The model estimated declines in exploitable abundance and in fishing mortality with variable spatial distributions, and sporadic recruitment, spatially concentrated in the northeast EBS. Few spatial assessments have been used as the basis for management advice and we consider this study as a step towards the integration of spatial dynamics in stock assessment.}, journal={ECOLOGICAL MODELLING}, author={Olmos, Maxime and Cao, Jie and Thorson, James T. and Punt, Andre E. and Monnahan, Cole C. and Alglave, Baptiste and Szuwalski, Cody}, year={2023}, month={Nov} }
 @article{damiano_wager_rocco_shertzer_murray_cao_2023, title={Integrating information from semi-structured interviews into management strategy evaluation: a case study for Southeast United States marine fisheries (vol 9, 1063260, 2022)}, volume={10}, ISSN={["2296-7745"]}, DOI={10.3389/fmars.2023.1205418}, abstractNote={COPYRIGHT © 2023 Damiano, Wager, Rocco, Shertzer, Murray and Cao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Correction PUBLISHED 16 May 2023 DOI 10.3389/fmars.2023.1205418}, journal={FRONTIERS IN MARINE SCIENCE}, author={Damiano, Matthew and Wager, Bethany and Rocco, Alex and Shertzer, Kyle W. W. and Murray, Grant D. D. and Cao, Jie}, year={2023}, month={May} }
 @article{zhou_hu_cao_xu_wang_wan_xiao_zhu_tang_2022, title={Comparison of nominal and standardized catch per unit effort data in quantifying habitat suitability of skipjack tuna in the equatorial Pacific Ocean}, volume={41}, ISSN={["1869-1099"]}, DOI={10.1007/s13131-021-1922-z}, number={3}, journal={ACTA OCEANOLOGICA SINICA}, author={Zhou, Cheng and Hu, Yuanyuan and Cao, Jie and Xu, Liuxiong and Wang, Xuefang and Wan, Rong and Xiao, Yu and Zhu, Jiangfeng and Tang, Hao}, year={2022}, month={Mar}, pages={1–10} }
 @article{damiano_wager_rocco_shertzer_murray_cao_2022, title={Integrating information from semi-structured interviews into management strategy evaluation: a case study for Southeast United States marine fisheries}, volume={9}, ISSN={["2296-7745"]}, DOI={10.3389/fmars.2022.1063260}, abstractNote={Management strategy evaluation (MSE) has become a more common tool for engaging stakeholders in fisheries management, and stakeholder participation in MSE is increasingly recognized as a vital component of the process. The participation of stakeholders, specifically fishers, in MSE is of particular importance because they often possess intimate knowledge of the socio-ecological management system that MSE seeks to model. When the resources to conduct a “full” MSE with direct fisher involvement are unavailable, MSEs are sometimes conducted by desk-based analysts with no fisher engagement. We propose an intermediate framework in which information collected from semi-structured interviews is used to inform a “desk-based” MSE. We demonstrate that semi-structured interviews with commercial and recreational fishers can elicit some of the same kinds of information that fishers provide during direct participation in MSE. We conducted 30 semi-structured interviews with commercial and recreational fishers from the Southeast United States participating in either Atlantic cobia (Rachycentron canadum) or black sea bass (Centropristis striata) fisheries. We collected primarily qualitative and some quantitative information about preferred conceptual objectives and management measures, and how their fishing behavior has changed in response to past management action. Commercial fishers generally preferred conceptual objectives and management measures that align with traditional MSY-based fisheries management, while recreational fishers’ responses were substantially more heterogeneous, indicating a more diverse range of desired objectives and preferred management measures. We synthesized this information to develop a suite of management procedures that employ a range of fishing mortality-based constant-catch harvest control rules and size-based management measures for simulation testing against preferred objectives by sector. We demonstrate that integrating information from semi-structured interviews with MSE in this way offers a cost-effective alternative intermediate approach to fisher participation in MSE when direct participation is not possible.}, journal={Frontiers in Marine Science}, author={Damiano, M. and Wager, B. and Rocco, A. and Shertzer, K. and Murray, G. and Cao, J.}, year={2022} }
 @article{cao_chen_2022, title={Modeling time-varying natural mortality in size-structured assessment models}, volume={250}, ISSN={0165-7836}, url={http://dx.doi.org/10.1016/j.fishres.2022.106290}, DOI={10.1016/j.fishres.2022.106290}, abstractNote={Temporal variation in natural mortality (M) has been recognized for having a degrading effect on the performance of stock assessment models when it is not accounted for in the model. However, time-invariant M has remained widely practiced in stock assessments due to the difficulties in estimation. Therefore, in this study we conducted simulation-estimation experiments to (1) evaluate the ability of a size-structured assessment model to reliably estimate time-varying M as well as other population quantities, and (2) quantify the consequences of mis-specifying M in a size-structured assessment model. We modified an existing size-structured assessment model to include three different approaches to estimate time-varying M within the model. A wide range of scenarios regarding the underlying M patterns (variation over time and length) was considered in this study. The performance of estimation methods largely depends upon whether the assumption of length-dependent/-independent M was correctly specified in the assessment model. Among the three methods, estimating time-varying M as a mean (representing an average process) and time-specific deviations using auxiliary information performed best. Estimating time-varying M as a random walk process also performed well except when underlying time-varying M had large year-to-year variation. A temporal pattern in M affected the ability of the assessment model to provide reliable estimates of M, spawning stock biomass and recruitment. Assuming a constant M (i.e., fixing M at the correct value) was quite robust over a range of actual temporal variation in underlying M.}, journal={Fisheries Research}, publisher={Elsevier BV}, author={Cao, Jie and Chen, Yong}, year={2022}, month={Jun}, pages={106290} }
 @article{cao_wang_damiano_zhou_zhu_2021, title={A Bayesian Multilevel Ordinal Regression Model for Fish Maturity Data: Difference in Maturity Ogives of Skipjack Tuna (Katsuwonus pelamis) Between Schools in the Western and Central Pacific Ocean}, volume={8}, ISSN={["2296-7745"]}, DOI={10.3389/fmars.2021.736462}, abstractNote={The maturity ogive is vital to defining the fraction of a population capable of reproduction. In this study, we proposed a novel approach, a Bayesian multilevel ordinal regression (i.e., Bayesian continuation ratio model), to model the maturity ogive. The model assumes that the observed maturity stage originates from the categorization of latent continuous variables. We demonstrated this approach by testing whether there are differences in the maturity ogive of skipjack tuna (Katsuonus pelamis) in the western and central Pacific Ocean between two school types, i.e., free-swimming and floating-object-associated schools. The model results show that K. pelamis, given the same fork length, are more likely to have a higher maturity stage in a free-swimming school than those associated with floating objects. The gonadosomatic index revealed the same conclusion. Our results indicate that fish aggregation devices (FADs) could negatively affect the maturity of K. pelamis and consequently reduce the population reproductive potential. This study provides (1) an alternative approach to analyze fisheries ordinal data; (2) important quantitative evidence to evaluate the existing ecological hypotheses; and (3) implications for tuna fisheries management.}, journal={FRONTIERS IN MARINE SCIENCE}, author={Cao, Jie and Wang, Xuefang and Damiano, Matthew D. and Zhou, Cheng and Zhu, Jiangfeng}, year={2021}, month={Dec} }
 @book{sutherland_von haefen_eggleston_cao_2021, title={Economic valuation of submerged aquatic vegetation within the Albemarle-Pamlico estuary}, institution={Albermarle-Pamlico National Estuary Partnership (APNEP)}, author={Sutherland, S.A. and von Haefen, R.H. and Eggleston, D.B. and Cao, J.}, year={2021}, month={Jun} }
 @article{runde_buckel_rudershausen_mitchell_ebert_cao_taylor_2021, title={Evaluating the Effects of a Deep-Water Marine Protected Area a Decade After Closure: A Multifaceted Approach Reveals Equivocal Benefits to Reef Fish Populations}, volume={8}, ISSN={2296-7745}, url={http://dx.doi.org/10.3389/fmars.2021.775376}, DOI={10.3389/fmars.2021.775376}, abstractNote={Marine protected areas (MPAs) are increasingly used to rebuild fish populations. In 2009, eight MPAs were designated off the southeast United States with the goal of rebuilding populations of long-lived deep-water reef fishes. We tested whether reef fish within the largest of these MPAs, the Snowy Wreck Marine Protected Area (SWMPA), have increased in size and abundance relative to a nearby control area and compared to pre-closure. Hurdle models fitted through Bayesian inference on echosounder data collected in 2007–2009 and 2018–2020 yielded no evidence of an MPA effect. Comparisons of catch-per-unit-effort (CPUE) of all reef fishes yielded similar null results. However, CPUE of reef species with formal stock assessments increased 47% in the SWMPA and decreased 50% in the control area. We found significant increases in mean length of red porgy (Pagrus pagrus) inside the SWMPA but not in the control area. We also found community composition changes, including shifts away from groupers (Serranidae; Epinephelinae) and toward snappers (Lutjanidae) and tilefish (Malacanthidae) in both areas, though we did not detect an MPA effect with this analysis. Our equivocal results indicate that more time and stricter enforcement may be necessary before more biological effects of the SWMPA can be detected.}, journal={Frontiers in Marine Science}, publisher={Frontiers Media SA}, author={Runde, Brendan J. and Buckel, Jeffrey A. and Rudershausen, Paul J. and Mitchell, Warren A. and Ebert, Erik and Cao, Jie and Taylor, J. Christopher}, year={2021}, month={Nov} }
 @article{zhou_wan_cao_xu_wang_zhu_2021, title={Spatial variability of bigeye tuna habitat in the Pacific Ocean: Hindcast from a refined ecological niche model}, volume={30}, ISSN={["1365-2419"]}, DOI={10.1111/fog.12500}, abstractNote={Abstract}, number={1}, journal={FISHERIES OCEANOGRAPHY}, author={Zhou, Cheng and Wan, Rong and Cao, Jie and Xu, Liuxiong and Wang, Xuefang and Zhu, Jiangfeng}, year={2021}, month={Jan}, pages={23–37} }
 @article{huang_zhou_xu_zhu_wang_cao_2021, title={Spatial variation in bigeye tuna Thunnus obesus size at sexual maturity in the eastern Pacific Ocean}, volume={12}, ISSN={2468-550X}, url={http://dx.doi.org/10.1016/j.aaf.2021.11.003}, DOI={10.1016/j.aaf.2021.11.003}, abstractNote={Understanding the reproductive characteristics of a species is of crucial for accurate stock assessment and management plans to ensure sustainable fisheries. In this study, the size at 50% sexual maturity (L50) parameters in different bio-ecological provinces were estimated for bigeye tuna, Thunnus obesus, sampled from the Eastern Pacific Ocean tuna fisheries-dependent survey from 2013 to 2019. The overall sex ratio of the catch during the sampling differed significantly from 1:1. Bigeye tuna exhibit sexual dimorphism in the growth of males and females, with a clear shift in predominance from female to male with increasing sizes. In the North Pacific Sub-tropical Gyre (east) (NPST-east), North Pacific Tropical Gyre (NPTG), Pacific North Equatorial Countercurrent (PNEC), and Pacific Equatorial Divergence (PEQD), females (meals) reached sexual maturity round 102 cm (106 cm), 106 cm (100 cm), 125 cm (110 cm), and 113 cm (110 cm), respectively, the estimated L50 of bigeye tuna was 124.08 cm, 121.97 cm, 139.92 cm and 132.45 cm, respectively. The degree of populations mixing between equatorial (PNEC and PEQD) and high-latitude regions (NPST-east and NPTG) is extremely small, but it is reasonably high between the NPST-east and NPTG or PNEC and PEQD. These parameters were significantly different, suggesting the occurrence of a spatial difference in the size-at-maturity of bigeye tuna between these bio-ecological provinces. The findings of this study provide the key information for understanding the life history of bigeye tuna in the Eastern Pacific Ocean and will contribute to the conservation and sustainable yield of this species.}, journal={Aquaculture and Fisheries}, publisher={Elsevier BV}, author={Huang, Hongji and Zhou, Cheng and Xu, Liuxiong and Zhu, Jiangfeng and Wang, Xuefang and Cao, Jie}, year={2021}, month={Dec} }
 @article{hodgdon_tanaka_runnebaum_cao_chen_2020, title={A framework to incorporate environmental effects into stock assessments informed by fishery-independent surveys: a case study with American lobster (Homarus americanus)}, volume={77}, ISSN={["1205-7533"]}, DOI={10.1139/cjfas-2020-0076}, abstractNote={ Stock assessments for a majority of the world’s fisheries often do not explicitly consider the effects of environmental conditions on target species, which can raise model uncertainty and potentially reduce forecasting quality. Model-based abundance indices were developed using a delta generalized linear mixed model that incorporates environmental variability for use in stock assessment to understand how the incorporation of environmental variability impacts our understanding of population dynamics. For this study, multiple model-based abundance indices were developed to test the incorporation of environmental covariates in a length-structured assessment of the American lobster (Homarus americanus) stock in the Gulf of Maine – Georges Bank on the possible improvement of stock assessment quality. Comparisons reveal that modelled indices with environmental covariates appear to be more precise than traditional indices, but model performance metrics and hindcasted fishery statuses revealed that these improvements to indices may not necessarily mean an improved assessment. Model-based abundance indices are not intrinsically better than design-based indices and should be tested for each species individually. }, number={10}, journal={CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES}, author={Hodgdon, Cameron T. and Tanaka, Kisei R. and Runnebaum, Jocelyn and Cao, Jie and Chen, Yong}, year={2020}, month={Oct}, pages={1700–1710} }
 @article{runnebaum_tanaka_guan_cao_o'brien_chen_2020, title={Predicting bycatch hotspots based on suitable habitat derived from fishery-independent data}, volume={641}, ISSN={["1616-1599"]}, DOI={10.3354/meps13302}, abstractNote={Bycatch remains a global problem in managing sustainable fisheries. A critical aspect of management is understanding the timing and spatial extent of bycatch. Fisheries management often relies on observed bycatch data, which are not always available due to a lack of reporting or observer coverage. Alternatively, analyzing the overlap in suitable habitat for the target and non-target species can provide a spatial management tool to understand where bycatch interactions are likely to occur. Potential bycatch hotspots based on suitable habitat were predicted for cuskBrosme brosmeincidentally caught in the Gulf of Maine American lobsterHomarus americanusfishery. Data from multiple fisheries-independent surveys were combined in a delta-generalized linear mixed model to generate spatially explicit density estimates for use in an independent habitat suitability index. The habitat suitability indices for American lobster and cusk were then compared to predict potential bycatch hotspot locations. Suitable habitat for American lobster has increased between 1980 and 2013 while suitable habitat for cusk decreased throughout most of the Gulf of Maine, except for Georges Basin and the Great South Channel. The proportion of overlap in suitable habitat varied interannually but decreased slightly in the spring and remained relatively stable in the fall over the time series. As Gulf of Maine temperatures continue to increase, the interactions between American lobster and cusk are predicted to decline as cusk habitat continues to constrict. This framework can contribute to fisheries managers’ understanding of changes in habitat overlap as climate conditions continue to change and alter where bycatch interactions could occur.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Runnebaum, Jocelyn and Tanaka, Kisei R. and Guan, Lisha and Cao, Jie and O'Brien, Loretta and Chen, Yong}, year={2020}, month={May}, pages={159–175} }
 @article{tanaka_cao_shank_truesdell_mazur_xu_chen_2019, title={A model-based approach to incorporate environmental variability into assessment of a commercial fishery: a case study with the American lobster fishery in the Gulf of Maine and Georges Bank}, volume={76}, ISSN={["1095-9289"]}, DOI={10.1093/icesjms/fsz024}, abstractNote={Abstract}, number={4}, journal={ICES JOURNAL OF MARINE SCIENCE}, author={Tanaka, Kisei R. and Cao, Jie and Shank, Burton V and Truesdell, Samuel B. and Mazur, Mackenzie D. and Xu, Luoliang and Chen, Yong}, year={2019}, pages={884–896} }
 @article{cao_thorson_punt_szuwalski_2019, title={A novel spatiotemporal stock assessment framework to better address fine‐scale species distributions: Development and simulation testing}, volume={21}, ISSN={1467-2960 1467-2979}, url={http://dx.doi.org/10.1111/faf.12433}, DOI={10.1111/faf.12433}, abstractNote={Abstract}, number={2}, journal={Fish and Fisheries}, publisher={Wiley}, author={Cao, Jie and Thorson, James T. and Punt, André E. and Szuwalski, Cody}, year={2019}, month={Dec}, pages={350–367} }
 @article{ding_cao_chen_2019, title={Stock assessment of the western winter-spring cohort of <em>Ommastrephes bartramii</em> in the Northwest Pacific Ocean using a Bayesian hierarchical DeLury model based on daily natural mortality during 2005-2015}, volume={83}, ISSN={1886-8134 0214-8358}, url={http://dx.doi.org/10.3989/scimar.04783.10a}, DOI={10.3989/scimar.04783.10a}, abstractNote={The purpose of this study was to evaluate the effect of the intensive commercial jigging fishery on the western winter-spring cohort of neon flying squid (Ommastrephes bartramii) in the Northwest Pacific Ocean and to estimate the exploitation status of this stock during the period 2005-2015. We applied a Bayesian hierarchical DeLury depletion model to the Chinese jigging fisheries data to estimate the stock abundance and catchability for each year, and sensitivity analysis on daily natural mortality (M) was conducted. The results indicated that M values had great impacts on the overall estimates of stock size. Initial annual population sizes varied from 66 to 662 million individuals with the M value of 0.003-0.01 per day during the study period. O. bartramii suffered from a certain degree of overexploitation in 2008. The proportional escapement values (M=0.003-0.01) were 8.94% to 19.82% in 2008, with an average of 13.74%, which may have led to a low abundance of O. bartramii and annual catch since 2009. As short-lived ecological opportunists, O. bartramii are extremely sensitive to changes in multi-scale environmental conditions, especially when anomalous environmental conditions occur, and significant between-year variations in the initial abundance resulted in O. bartramii suffering from a certain degree of overexploitation in 2010. Although the proportional escapement met the management target of 40% from 2011 to 2015, the stock size and annual catch still fluctuated at relatively low levels. Improved knowledge of the influences of environmental conditions on abundance of the western winter-spring cohort of neon flying squid can contribute to the sustainable management of this stock.}, number={2}, journal={Scientia Marina}, publisher={Editorial CSIC}, author={Ding, Qi and Cao, Jie and Chen, Xinjun}, year={2019}, month={Jun}, pages={155} }
 @article{li_cao_guan_mazur_chen_wahle_2018, title={Estimating spatial non-stationary environmental effects on the distribution of species: a case study from American lobster in the Gulf of Maine}, volume={75}, ISSN={1054-3139 1095-9289}, url={http://dx.doi.org/10.1093/icesjms/fsy024}, DOI={10.1093/icesjms/fsy024}, abstractNote={Abstract}, number={4}, journal={ICES Journal of Marine Science}, publisher={Oxford University Press (OUP)}, author={Li, Bai and Cao, Jie and Guan, Lisha and Mazur, Mackenzie and Chen, Yong and Wahle, Richard A}, editor={Hidalgo, ManuelEditor}, year={2018}, month={Mar}, pages={1473–1482} }
 @article{zhao_cao_tian_chen_zhang_2018, title={Evaluating Sampling Designs for Demersal Fish Communities}, volume={10}, ISSN={2071-1050}, url={http://dx.doi.org/10.3390/su10082585}, DOI={10.3390/su10082585}, abstractNote={Fish communities play an important role in determining the dynamics of marine ecosystems, while the evaluation and formulation of protective measures for these fish communities depends on the quality and quantity of data collected from well-designed sampling programs. The ecological model was used first to predict the distribution of the demersal fish community as the “true” population for the sampling design. Four sampling designs, including simple random sampling, systematic sampling, and stratified sampling with two sampling effort allocations (proportional allocation and Neyman allocation), were compared to evaluate their performance in estimating the richness and biodiversity indices of the demersal fish community. The impacts of two different temperature change scenarios, uniform temperature and non-uniform temperature increase on the performance of the sampling designs, were also evaluated. The proportional allocation yielded the best estimates of fish community richness and biodiversity relative to a synthetic baseline. However, its performance was not always robust relative to the simulated temperature change. When the water temperature changed unevenly, systematic sampling tended to perform the best. Thus, it is important to adjust the strata for a stratified sampling when the habitat experiences large changes. This suggests that we need to carefully evaluate the appropriateness of stratification when temperature change-induced habitat changes are large enough to result in substantial changes in the fish community.}, number={8}, journal={Sustainability}, publisher={MDPI AG}, author={Zhao, Jing and Cao, Jie and Tian, Siquan and Chen, Yong and Zhang, Shouyu}, year={2018}, month={Jul}, pages={2585} }
 @article{runnebaum_guan_cao_o’brien_chen_2018, title={Habitat suitability modeling based on a spatiotemporal model: an example for cusk in the Gulf of Maine}, volume={75}, ISSN={0706-652X 1205-7533}, url={http://dx.doi.org/10.1139/cjfas-2017-0316}, DOI={10.1139/cjfas-2017-0316}, abstractNote={ Habitat use and distribution is a critical aspect in the management and conservation of a species, particularly for those in decline. Habitat suitability indices (HSI) are a common method of habitat mapping dependent on empirical data that can easily lead to misunderstanding the spatiotemporal dynamics of marine species experiencing population decline and density-dependent catchability within surveys. This is especially true when only a single monitoring program with limited spatiotemporal coverage is used. A delta-generalized linear mixed model was used to combine trawl and longline surveys to predict density estimates for cusk (Brosme brosme) in unsampled locations for use in HSIs. Catchability was estimated for longline and trawl gear without having an estimate of area fished for the longline survey. HSIs performed better using model-based density estimates from multiple surveys compared with sample-based abundance indices from a single survey. The increased spatial resolution can better inform the HSIs by providing information where the survey programs did not sample. This study provides a novel approach for integrating data from different monitoring programs for habitat modeling. }, number={11}, journal={Canadian Journal of Fisheries and Aquatic Sciences}, publisher={Canadian Science Publishing}, author={Runnebaum, Jocelyn and Guan, Lisha and Cao, Jie and O’Brien, Loretta and Chen, Yong}, year={2018}, month={Nov}, pages={1784–1797} }
 @article{wang_chen_tanaka_cao_chen_2017, title={Environmental influences on commercial oceanic ommastrephid squids: a stock assessment perspective}, volume={81}, ISSN={1886-8134 0214-8358}, url={http://dx.doi.org/10.3989/scimar.04497.25b}, DOI={10.3989/scimar.04497.25b}, abstractNote={Ommastrephid squids are short-lived ecological opportunists and their recruitment is largely driven by the surrounding environment. While recent studies suggest that recruitment variability in several squid species can be partially explained by environmental variability derived from synoptic oceanographic data, assessment of ommastrephid stocks using environmental variability is rare. In thisstudy, we modified asurplus production model to incorporate environmental variability into the assessment of threeommastrephid squids (Ommastrephes bartramii in the northwest Pacific, Illex argentinus in the southwest Atlantic and Dosidicus gigas in the southwest Pacific). We assumed that the key environmental variables—suitable sea surface temperature on spawning grounds during the spawning seasons and feeding grounds during the feeding seasons—have effects on the carrying capacity and the instantaneous population growth rate, respectively, in the surplus production model. For each squid stock, the assessment model with environmental variability had the highest fitting accuracy and the lowest mean squared error and coefficient of variation, and the management reference points based on the optimal model were more precautionary. This study advances our understanding of the interactions between the environment and ommastrephid squid population dynamics and can therefore improve the management of these commercially valuable stocks with a short life cycle.}, number={1}, journal={Scientia Marina}, publisher={Editorial CSIC}, author={Wang, Jintao and Chen, Xinjun and Tanaka, Kisei and Cao, Jie and Chen, Yong}, year={2017}, month={Mar}, pages={37} }
 @article{cao_chen_richards_2017, title={Improving assessment of <i>Pandalus</i> stocks using a seasonal, size-structured assessment model with environmental variables. Part I: Model description and application}, volume={74}, ISSN={0706-652X 1205-7533}, url={http://dx.doi.org/10.1139/cjfas-2016-0020}, DOI={10.1139/cjfas-2016-0020}, abstractNote={ Pandalus species display the following features that make it difficult to apply traditional age-based stock assessment models: (i) difficulty of determining age in the absence of hard parts retained through the molt; (ii) sex change in which individuals mature first as males and then transform to females; and (iii) potentially strong influence of environmental conditions on recruitment population dynamics. In this context, we propose a seasonal, size-structured assessment model dedicated to stock assessment of hermaphroditic Pandalidae. The modeling framework incorporates a submodel for changes of length at sex transformation and functions to incorporate environmental effects on recruitment dynamics. The model can be directly fitted to length-structured data, overcoming the length to age conversion problem. The model has a seasonal time step that allows it to account for seasonal variations in biological processes and fishing patterns. The model provides stock assessment outputs, such as fishing mortality and stock biomass estimates, and sex-specific abundance-at-length. The model is applied to the exploited shrimp stock of Pandalus borealis in the Gulf of Maine as an example of its utility. The model proposed in this study is flexible and generic and can be applied to many other exploited stocks. }, number={3}, journal={Canadian Journal of Fisheries and Aquatic Sciences}, publisher={Canadian Science Publishing}, author={Cao, Jie and Chen, Yong and Richards, R. Anne}, year={2017}, month={Mar}, pages={349–362} }
 @article{cao_chen_richards_2017, title={Improving assessment of <i>Pandalus</i> stocks using a seasonal, size-structured assessment model with environmental variables. Part II: Model evaluation and simulation}, volume={74}, ISSN={0706-652X 1205-7533}, url={http://dx.doi.org/10.1139/cjfas-2016-0021}, DOI={10.1139/cjfas-2016-0021}, abstractNote={ Integrated, size-structured stock assessment models are now being used widely for assessment and management of hard-to-age species. However, few studies have attempted to evaluate their performance. A seasonal, size-structured assessment model with environmental covariates has been developed for hermaphroditic Pandalidae. We conducted simulations to evaluate its sensitivity to model configuration and performance with various misspecifications. Ignoring the seasonal fishing pattern (half-year closure) led to risk-prone assessment results of overestimating spawning stock biomass (SSB) and recruitment (R) and underestimating fishing mortality (F). Failure to incorporate environmental signals when the recruitment dynamics was environmentally driven led to bias in recent estimates of SSB, R, and F in the simulation. Ignoring annual variability in growth resulted in large estimation bias. Failing to account for time-varying natural mortality (M) led to strong biases; however, misspecifying size-specific M produced even stronger estimation bias. This result may depend on the variation of M among size classes. Under no model misspecifications, an unbiased estimate of M could be obtained by taking advantage of the seasonal fishery closure. Annual growth parameters were also estimable, but the large number of parameters with annual growth made it difficult for the model to converge. }, number={3}, journal={Canadian Journal of Fisheries and Aquatic Sciences}, publisher={Canadian Science Publishing}, author={Cao, Jie and Chen, Yong and Richards, R. Anne}, year={2017}, month={Mar}, pages={363–376} }
 @article{zhao_cao_tian_chen_zhang_zhou_2017, title={Influence of sampling frequency on detectability of fish community and fish species in a fishery-independent survey}, volume={2}, ISSN={2468-550X}, url={http://dx.doi.org/10.1016/j.aaf.2017.03.003}, DOI={10.1016/j.aaf.2017.03.003}, abstractNote={Understanding the dynamics and regulation of a particular ecological process requires monitoring of the process at appropriate spatial and temporal scales. Information collected at an inappropriate spatio-temporal scale may be insufficient for capturing spatio-temporal dynamics of fish populations and community. In this study, a Monte Carlo method was developed to evaluate the detectability performances of different sampling frequencies, sampling timings and sampling intensities on fish community indices and fish species. Species richness indices tended to decrease with an increased sampling frequency, while species diversity indices had small changes in response to changes in sampling frequency. The diversity index was more likely to be influenced by the choice of sampling timing compared to the richness index. The total number of species, especially seasonal and rare species present in the simulated sampling, increased with sampling frequency. Although sampling frequency is more important than sampling intensity, sampling intensity is also important for the detectability of fish species. This study showed that sampling frequency and intensity could greatly influence the estimation of fish community. Choices of sampling timing, sampling frequency and intensity may result in different estimates of fish species compositions and community structure. It is very necessary to consider the importance of sufficient sampling frequency and intensity in a survey program.}, number={2}, journal={Aquaculture and Fisheries}, publisher={Elsevier BV}, author={Zhao, Jing and Cao, Jie and Tian, Siquan and Chen, Yong and Zhang, Shouyu and Zhou, Xijie}, year={2017}, month={Mar}, pages={94–102} }
 @article{cao_thorson_richards_chen_2017, title={Spatiotemporal index standardization improves the stock assessment of northern shrimp in the Gulf of Maine}, volume={74}, ISSN={0706-652X 1205-7533}, url={http://dx.doi.org/10.1139/cjfas-2016-0137}, DOI={10.1139/cjfas-2016-0137}, abstractNote={ Estimated trends in relative stock abundance are a primary input to fish stock assessments. Accurate and precise estimates are essential for successful conservation and management. Scientifically designed data collection ensures that estimates of relative abundance are unbiased. However, the statistical efficiency of a design-based estimator may be low under certain circumstances. We apply a recently developed spatiotemporal model that incorporates habitat variables to estimate a model-based abundance index for northern shrimp (Pandalus borealis) in the Gulf of Maine. We contrast this spatiotemporal index with a classical design-based index and evaluate the impacts of differences between the two abundance indices on the stock assessment. We show that using the spatiotemporal index in the assessment model greatly alters the estimates of recruitment and spawning stock biomass and the determination of stock status. Also, incorporating the spatiotemporal index leads to less retrospective bias and outperforms the model with design-based index in terms of predictive performance through a retrospective cross-validation test. Our results suggest that temporal variability of population abundance could be exaggerated by the design-based estimator, and such imprecision may greatly affect the performance of a stock assessment and subsequent development of management decisions. }, number={11}, journal={Canadian Journal of Fisheries and Aquatic Sciences}, publisher={Canadian Science Publishing}, author={Cao, Jie and Thorson, James T. and Richards, R. Anne and Chen, Yong}, year={2017}, month={Nov}, pages={1781–1793} }
 @article{guan_chen_staples_cao_li_2017, title={The influence of complex structure on the spatial dynamics of Atlantic cod (Gadus morhua) in the Gulf of Maine}, volume={74}, ISSN={1054-3139 1095-9289}, url={http://dx.doi.org/10.1093/icesjms/fsx064}, DOI={10.1093/icesjms/fsx064}, abstractNote={Abstract}, number={9}, journal={ICES Journal of Marine Science}, publisher={Oxford University Press (OUP)}, author={Guan, Lisha and Chen, Yong and Staples, Kevin W and Cao, Jie and Li, Bai}, editor={Hidalgo, ManuelEditor}, year={2017}, month={Apr}, pages={2379–2388} }
 @article{cao_guan_truesdell_chen_tian_2016, title={An individual-based probabilistic model for simulating fisheries population dynamics}, volume={1}, ISSN={2468-550X}, url={http://dx.doi.org/10.1016/j.aaf.2016.10.001}, DOI={10.1016/j.aaf.2016.10.001}, abstractNote={The purpose of stock assessment is to support managers to provide intelligent decisions regarding removal from fish populations. Errors in assessment models may have devastating impacts on the population fitness and negative impacts on the economy of the resource users. Thus, accuracte estimations of population size, growth rates are critical for success. Evaluating and testing the behavior and performance of stock assessment models and assessing the consequences of model mis-specification and the impact of management strategies requires an operating model that accurately describe the dynamics of the target species, and can resolve spatial and seasonal changes. In addition, the most thorough evaluations of assessment models use an operating model that takes a different form than the assessment model. This paper presents an individual-based probabilistic model used to simulate the complex dynamics of populations and their associated fisheries. Various components of population dynamics are expressed as random Bernoulli trials in the model and detailed life and fishery histories of each individual are tracked over their life span. The simulation model is designed to be flexible so it can be used for different species and fisheries. It can simulate mixing among multiple stocks and link stock-recruit relationships to environmental factors. Furthermore, the model allows for flexibility in sub-models (e.g., growth and recruitment) and model assumptions (e.g., age- or size-dependent selectivity). This model enables the user to conduct various simulation studies, including testing the performance of assessment models under different assumptions, assessing the impacts of model mis-specification and evaluating management strategies.}, journal={Aquaculture and Fisheries}, publisher={Elsevier BV}, author={Cao, Jie and Guan, Wenjiang and Truesdell, Samuel and Chen, Yong and Tian, Siquan}, year={2016}, month={Dec}, pages={34–40} }
 @book{li_cao_zhu_2016, title={Analyzing population dynamics of Indian Ocean albacore (Thunnus alalunga) using Bayesian state-space production model}, number={IOTC-2016-WPTmT06-24}, institution={Indian Ocean Tuna Commission}, author={Li, B. and Cao, J. and Zhu, J.F.}, year={2016} }
 @article{li_cao_zou_chen_runnebaum_2016, title={Modeling habitat suitability index for Chilean jack mackerel (Trachurus murphyi) in the South East Pacific}, volume={178}, ISSN={0165-7836}, url={http://dx.doi.org/10.1016/j.fishres.2015.11.012}, DOI={10.1016/j.fishres.2015.11.012}, abstractNote={Habitat models, such as the habitat suitable index (HSI), have been extensively used to estimate the spatial distribution of fish species based on the quality of habitat. Fishery dependent data from commercial fishing vessels are an important or potentially the only source of scientific information available in these fisheries, especially for the highly migratory stocks in the high seas. In this study we use catch and effort data from the Chinese trawl fishery combined with remote sensing data including sea surface temperature (SST), sea surface height (SSH) and sea surface chlorophyll-a concentration (Chl-a) to define suitable index (SI) for jack mackerel (Trachurus murphyi) in the South East Pacific Ocean. Observed SI values were calculated based on the frequency distribution of fishing effort for each environmental variable, and parameters of the SI models were estimated using nonlinear regression. SI models for SST, SSH, and Chl-a were combined into two empirical HSI models, the arithmetic mean model (AMM) and the geometric mean model (GMM). Results indicate that the AMM performs better than the GMM model to quantify the scale of best available habitat for jack mackerel. Catch distribution fit well with the predicted high-quality habitat in 2013: 85.5%, 100.0% and 97.0% of total catch in fall, winter and spring respectively, were caught in areas predicted with better habitat. The seasonal variation of suitable habitat in latitude is consistent with that of the gravity centers of fishing effort and the 15 °C isotherm. There is strong agreement between annual total catch by the international trawl fishery and mean suitable habitat area during the period 2001–2010, but an opposite tendency from 2011 to 2013. This may be related to the lowest biomass of jack mackerel and catch quota introduced by the South Pacific Regional Fisheries Management Organization since 2010.}, journal={Fisheries Research}, publisher={Elsevier BV}, author={Li, Gang and Cao, Jie and Zou, Xiaorong and Chen, Xinjun and Runnebaum, Jocelyn}, year={2016}, month={Jun}, pages={47–60} }
 @article{liu_cao_truesdell_chen_chen_tian_2016, title={Reconstructing cephalopod migration with statolith elemental signatures: a case study using Dosidicus gigas}, volume={82}, ISSN={0919-9268 1444-2906}, url={http://dx.doi.org/10.1007/s12562-016-0978-8}, DOI={10.1007/s12562-016-0978-8}, number={3}, journal={Fisheries Science}, publisher={Springer Science and Business Media LLC}, author={Liu, Bi Lin and Cao, Jie and Truesdell, Samuel B. and Chen, Yong and Chen, Xin Jun and Tian, Si Quan}, year={2016}, month={Mar}, pages={425–433} }
 @inproceedings{cao_chen_dai_zhu_2016, title={Stock Assessment for south Pacific albacore tuna using stock synthesis}, booktitle={Western and Central Pacific Fisheries Commission, scientific committee twelfth regular session}, author={Cao, J. and Chen, Y. and Dai, X.J. and Zhu, J.F.}, year={2016} }
 @inproceedings{cao_runnebaum_tanaka_boenish_dayton_guan_li_li_mazur_olson_et al._2016, place={Orono, ME}, title={Technical Minutes of the Review Group on the Bay of Biscay and Iberian Waters Advice Drafting Group: Review of ICES Bay of Biscay and Iberian Waters Ecoregion Working Group 2015}, publisher={ICES Bay of Biscay and Iberian Waters Ecoregion Working Group}, author={Cao, J. and Runnebaum, J. and Tanaka, K. and Boenish, R. and Dayton, A. and Guan, L. and Li, B. and Li, Z. and Mazur, M. and Olson, D. and et al.}, year={2016} }
 @inproceedings{cao_runnebaum_tanaka_boenish_dayton_guan_li_li_mazur_olson_et al._2016, place={Orono, ME}, title={Technical Minutes of the Review Group on the Joint NAFO/ICES Pandalus Assessment Working group on the three Pandulas stocks in Skagerrak and Norwegian Deep, Barent Sea, and Fladen Ground}, publisher={Joint NAFO/ICES Pandalus Assessment Working group}, author={Cao, J. and Runnebaum, J. and Tanaka, K. and Boenish, R. and Dayton, A. and Guan, L. and Li, B. and Li, Z. and Mazur, M. and Olson, D. and et al.}, year={2016} }
 @article{li_cao_chang_wilson_chen_2015, title={Evaluation of Effectiveness of Fixed-Station Sampling for Monitoring American Lobster Settlement}, volume={35}, ISSN={0275-5947 1548-8675}, url={http://dx.doi.org/10.1080/02755947.2015.1074961}, DOI={10.1080/02755947.2015.1074961}, abstractNote={Abstract}, number={5}, journal={North American Journal of Fisheries Management}, publisher={Wiley}, author={Li, Bai and Cao, Jie and Chang, Jui-Han and Wilson, Carl and Chen, Yong}, year={2015}, month={Sep}, pages={942–957} }
 @inproceedings{cao_tanaka_runnebaum_boenish_guan_li_mazur_olson_rodrigue_ritchie_et al._2015, place={Orono, ME}, title={Technical Minutes of the Review Group for the Celtic Sea Advice Drafting Group: Review of ICES Widely Working Group 2014}, publisher={Celtic Sea Advice Drafting Group}, author={Cao, J. and Tanaka, K. and Runnebaum, J. and Boenish, R. and Guan, L. and Li, B. and Mazur, M. and Olson, D. and Rodrigue, M. and Ritchie, M. and et al.}, year={2015} }
 @article{cao_chen_tian_2014, title={A Bayesian hierarchical DeLury model for stock assessment of the west winter-spring cohort of neon flying squid (<i>Ommastrephes bartramii</i>) in the northwest Pacific Ocean}, volume={91}, ISSN={0007-4977}, url={http://dx.doi.org/10.5343/bms.2014.1020}, DOI={10.5343/bms.2014.1020}, abstractNote={DeLury depletion models are commonly used in the stock assessment of short-lived species, such as squid of the family Ommastrephidae. However, this type of model may be misleading if its input data are not informative. Here, we applied and compared both Bayesian hierarchical and non-hierarchical DeLury depletion models to conduct stock assessment of the west winter-spring cohort of neon flying squid, Ommastrephes bartramii (LeSueur, 1821), in the North Pacific Ocean. Fishery data from the Chinese squid jigging fleets from 1996 to 2004 were examined. The Bayesian hierarchical model yielded reasonable estimates, but the Bayesian non-hierarchical model did not successfully estimate the initial abundance for certain years. This suggests that the Bayesian hierarchical DeLury depletion model can produce more reliable estimates than a similar non-hierarchical model, especially because it uses the data more efficiently by combining all sets of time-series data hierarchically in the same model.}, number={1}, journal={Bulletin of Marine Science}, publisher={Bulletin of Marine Science}, author={Cao, Jie and Chen, Xinjun and Tian, Siquan}, year={2014}, month={Jan}, pages={1–13} }
 @article{zhao_cao_tian_chen_zhang_wang_zhou_2014, title={A comparison between two GAM models in quantifying relationships of environmental variables with fish richness and diversity indices}, volume={48}, ISSN={1386-2588 1573-5125}, url={http://dx.doi.org/10.1007/s10452-014-9484-1}, DOI={10.1007/s10452-014-9484-1}, number={3}, journal={Aquatic Ecology}, publisher={Springer Science and Business Media LLC}, author={Zhao, Jing and Cao, Jie and Tian, Siquan and Chen, Yong and Zhang, Shouyu and Wang, Zhenhua and Zhou, Xijie}, year={2014}, month={May}, pages={297–312} }
 @article{cao_chen_chang_chen_2014, title={An evaluation of an inshore bottom trawl survey design for American lobster (<i>Homarus americanus</i>) using
computer simulations}, volume={46}, ISSN={0250-6408 1682-9786 1811-8224}, url={http://dx.doi.org/10.2960/j.v46.m696}, DOI={10.2960/j.v46.m696}, abstractNote={This paper evaluates the performance of six possible sampling designs to estimate the population abundance index for American lobster using computer simulations. These designs include simple random sampling (SRS), systematic sampling (SYS) and stratified random sampling with four stratification schemes (i.e., based on region, depth, sediment and region × depth). For the stratified random design with region and depth being used for stratification, we evaluated the performances of different strategies for allocating sampling efforts. Simulations were implemented on the “true” populations which were estimated annually from 2002 to 2008 for both spring and fall based on a general additive model model developed in a separate study. Relative Estimation Error (REE), Relative Bias (RB) and design effect were used to measure the precision, accuracy and efficiency of mean estimation for different designs. On average, SYS tended to yield the most precise and efficient estimate of mean with specified sample size. However, its estimates tended to be biased and its performance varied with sample sizes and realizations of “true” population, thus changed with lobster distribution. Appropriate stratification, such as using depth to determine strata, significantly improved the precision and efficiency over SRS. Sediment, which is related to lobster distribution, was found to have little contribution to the improvement of the performance over SRS when it is used to determine strata. Also, allocating samples to each stratum based on variance or mean of previous year improved precision and efficiency. This study suggests that current design ( i.e., region-depth stratified design) used in the survey had stable performance across years and seasons.}, journal={Journal of Northwest Atlantic Fishery Science}, publisher={Northwest Atlantic Fisheries Organization (NAFO)}, author={Cao, J and Chen, Y and Chang, J-H and Chen, X}, year={2014}, month={Jul}, pages={27–39} }
 @article{cao_truesdell_chen_2014, title={Impacts of seasonal stock mixing on the assessment of Atlantic cod in the Gulf of Maine}, volume={71}, ISSN={1054-3139 1095-9289}, url={http://dx.doi.org/10.1093/icesjms/fsu066}, DOI={10.1093/icesjms/fsu066}, abstractNote={Atlantic cod (Gadus morhua) in the Northwest Atlantic off New England and southern Atlantic Canada exhibit a complex population structure. This region has three independently assessed stocks [Georges Bank, Gulf of Maine (GOM), and the 4X stock], all of which are known to mix with each other. Assessments of these stocks, however, assume no interpopulation mixing. Using simulations, we evaluated impacts of ignoring mixing resulting from seasonal migrations on the GOM assessment. The dynamics of the three stocks were simulated according to different scenarios of interstock mixing, and a statistical catch-at-age stock assessment model was fitted to the simulated GOM data with and without mixing. The results suggest that, while mixing causes measurable bias in the assessment, under the conditions tested, this model still performed well. Of the bias that does exist, spawning-stock biomass estimates are relatively sensitive to mixing compared with estimates of recruitment and exploitation rate. The relative timing of seasonal migration of the three stocks plays a critical role in determining the magnitude of bias. The scale and trends among years in the bias were driven by how representative the catch and survey data were for the GOM stock; this representation changed with the mixing rates.}, number={6}, journal={ICES Journal of Marine Science}, publisher={Oxford University Press (OUP)}, author={Cao, Jie and Truesdell, Samuel B. and Chen, Yong}, year={2014}, month={Apr}, pages={1443–1457} }
 @inproceedings{truesdell_cao_dayton_guan_li_liu_olson_runnebaum_staples_tanaka_et al._2014, place={Orono, ME}, title={Technical Minutes of the Review Group for the Celtic Sea Advice Drafting Group: Review of ICES Celtic Sea Working Group 2013}, publisher={ICES Celtic Sea Working Group}, author={Truesdell, S. and Cao, J. and Dayton, A. and Guan, L. and Li, B. and Liu, B. and Olson, D. and Runnebaum, J. and Staples, K. and Tanaka, K. and et al.}, year={2014} }
 @article{wang_chen_truesdell_xu_cao_guan_2014, title={The Large-Scale Deployment of Fish Aggregation Devices Alters Environmentally-Based Migratory Behavior of Skipjack Tuna in the Western Pacific Ocean}, volume={9}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0098226}, DOI={10.1371/journal.pone.0098226}, abstractNote={Fish aggregation devices (FADs) have been used extensively in the tuna purse seine fishery since the 1980s. This long-term modification of natural habitat has generated discussions as to whether FADs impact movement patterns of tuna species. We examined this question using data collected from the skipjack tuna (Katsuwonus pelamis) fishery. We used the longitudinal gravitational center of catch (G) to examine temporal variability in skipjack movement in the Western and Central Pacific Ocean, and related this to El Niño Southern Oscillation (ENSO) events. We found that in most cases G for free-swimming school sets changed with the onset of ENSO events, while G for floating-object-associated school sets remained relatively constant. This suggests that skipjack exhibit distinguishable behavioral strategies in response to ENSO events: they either react by moving long distances or they associate with floating objects. There has been no previous attempt to evaluate the interaction between FADs and the environmentally-determined movement of skipjack; this study shows evidence of an interaction, which should be considered when managing skipjack populations.}, number={5}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Wang, Xuefang and Chen, Yong and Truesdell, Samuel and Xu, Liuxiong and Cao, Jie and Guan, Wenjiang}, editor={Buckel, JeffreyEditor}, year={2014}, month={May}, pages={e98226} }
 @article{guan_cao_chen_cieri_2013, title={Impacts of population and fishery spatial structures on fishery stock assessment}, volume={70}, ISSN={0706-652X 1205-7533}, url={http://dx.doi.org/10.1139/cjfas-2012-0364}, DOI={10.1139/cjfas-2012-0364}, abstractNote={ Fish populations and fishing efforts in most fisheries exhibit spatial heterogeneity. However, spatial considerations are generally ignored in fishery stock assessment and management because of a lack of spatially explicit data and poor understanding of the spatial dynamics of most fisheries. This study uses a simulation approach to evaluate the consequences of misspecifying spatial structure and migration during the assessment process. We developed an operating model to simulate a fishery using US Atlantic herring (Clupea harengus) as our model species. This population consists of two well-defined spawning substocks distributed and mixed in four management areas. Simulations were done for three alternative “true” populations, each having a different spatial structure both biologically and with regard to the geographic distribution of fishing effort. Stock assessments were then performed for the three simulated “true” populations using standard methodologies and assumptions currently used. Management-area-based assessments lead to overestimation of spawning stock biomass and underestimation of fishing mortality because of the interaction within the management area between the spatial structure of the population and that of the spatially heterogeneous fishery removals. In contrast, when fishing is spatially homogeneous, movement across management boundaries may not be relevant to modeling population dynamics. Such an idealized situation does not typically hold, however. }, number={8}, journal={Canadian Journal of Fisheries and Aquatic Sciences}, publisher={Canadian Science Publishing}, author={Guan, Wenjiang and Cao, Jie and Chen, Yong and Cieri, Matthew}, editor={Quinn, Terrance, IIEditor}, year={2013}, month={Aug}, pages={1178–1189} }
 @article{chen_cao_chen_liu_tian_2012, title={Effect of the Kuroshio on the Spatial Distribution of the Red Flying Squid <I>Ommastrephes Bartramii</I> in the Northwest Pacific Ocean}, volume={88}, ISSN={0007-4977}, url={http://dx.doi.org/10.5343/bms.2010.1098}, DOI={10.5343/bms.2010.1098}, abstractNote={As a dominant current in the northwest Pacific Ocean, the Kuroshio influences the population dynamics and species distributions in this region. Using catch per fishing day (CPUE, t/d) of the red flying squid Ommastrephes bartramii (LeSueur, 1821) from the chinese mainland squid jigging fleets on the feeding ground (150°E-165°E, 38°N-46°N) from August to October of 1998-2007, we calculated the monthly latitudinal center of gravity of CPUE (LATGj) and analyzed the relationship between the strength and position of the Kuroshio and the spatial distribution of O. bartramii. The LATGj for this species differed significantly from month to month. Regression modeling of the LATG vs Kuroshio transport also revealed a significant influence of Kuroshio strength on the north-south movement of O. bartramii. We suggest that the varying strength of the Kuroshio leads to changes in environmental conditions at 150°E-155°E, 40°n-43°n. The environmental variable most significantly correlated with LATGj was sea surface temperature, suggesting that the distribution of O. bartramii is controlled by optimal thermal habitat. We conclude that the spatial distribution of O. bartramii on their feeding grounds from august to october can be forecast using the path and transport of the Kuroshio.}, number={1}, journal={Bulletin of Marine Science}, publisher={Bulletin of Marine Science}, author={Chen, Xinjun and Cao, Jie and Chen, Yong and Liu, Bilin and Tian, Siquan}, year={2012}, month={Jan}, pages={63–71} }
 @article{chen_cao_chen_liu_ma_li_2011, title={Generalized linear Bayesian models for standardizing CPUE: an application to a squid-jigging fishery in the northwest Pacific Ocean}, volume={75}, ISSN={1886-8134 0214-8358}, url={http://dx.doi.org/10.3989/scimar.2011.75n4679}, DOI={10.3989/scimar.2011.75n4679}, abstractNote={Generalized linear Bayesian (GLBM) non-hierarchical and hierarchical models were developed for standardization of catch per unit effort (CPUE). The GLBM containing the covariates of month, latitude, sea surface temperature (SST), sea surface salinity (SSS) and sea level height (SLH) had the best fit for the Chinese squid-jigging fishery of Ommastrephes bartramii in the northwest Pacific Ocean based on deviance information criteria. This best-fitting model tends to be more ecologically sound than other CPUE standardization models, such as generalized linear models and generalized additive models. GLBM was also used to deal with the problems of estimating stock abundance index (i.e. standardized CPUE) resulting from increased spatial heterogeneity of spatial dynamics of fishing efforts in the squid fishery by predicting the standardized CPUE for unfished areas. The standardized CPUE based on data including predicted CPUE of unfished areas was lower than the derived CPUE based on data with observed CPUE alone, in particular during the fishing peak of August to October. This study indicates that it is more appropriate to use the standardized CPUE derived from data including both predicted CPUE of unfished areas and observed CPUE of fished area as a stock abundance index. We suggest that the proposed method be used in CPUE standardization to account for impacts of large spatial heterogeneity of fishing efforts in fisheries.}, number={4}, journal={Scientia Marina}, publisher={Editorial CSIC}, author={Chen, Xinjun and Cao, Jie and Chen, Yong and Liu, Bilin and Ma, Jin and Li, Siliang}, year={2011}, month={Jul}, pages={679–689} }
 @article{cao_chen_chen_2009, title={Influence of surface oceanographic variability on abundance of the western winter-spring cohort of neon flying squid Ommastrephes bartramii in the NW Pacific Ocean}, volume={381}, ISSN={0171-8630 1616-1599}, url={http://dx.doi.org/10.3354/meps07969}, DOI={10.3354/meps07969}, abstractNote={Abundance of the Ommastrephes bartramii winter-spring cohort fluctuated greatly from 1995 to 2004. To understand how abundance was influenced by sea surface conditions, we examined the variations in the proportion of thermal habitats with favourable sea surface tempera- ture (SST). The SST data of both the spawning and feeding grounds were used to calculate the monthly proportion of favourable-SST areas (PFSSTA). Catch per fishing day per fishing boat (catch per unit effort, CPUE) of the Chinese mainland squid-jigging fleet was used as squid abundance index. The relationships between CPUE and monthly PFSSTA at spawning and feeding grounds were analyzed, and the relationship between CPUE and selected PFSSTA was quantified with a mul- tiple linear regression model. Results showed that February PFSSTA at the spawning ground and August to November PFSSTA at the feeding ground could account for about 60% of the variability in O. bartramii abundance between 1995 and 2004, that February was the most important period influ- encing squid recruitment during the spawning season, and that feeding ground PFSSTA during the fishing season would influence CPUE by causing squid to aggregate. Our forecast model was found to perform well when we compared the model-predicted CPUEs and the average CPUEs observed during August to November in 2005 and 2006 from the Chinese squid-jigging fishery.}, journal={Marine Ecology Progress Series}, publisher={Inter-Research Science Center}, author={Cao, J and Chen, X and Chen, Y}, year={2009}, month={Apr}, pages={119–127} }
 @article{influence of surface oceanographic variability on abundance of the western winter-spring cohort of neon flying squid ommastrephes bartramii in the nw pacific ocean }