CAFA Publications

Author(s): Thorson, J. T., W. Cheng, A. J. Hermann, J. N. Ianelli, M. A. Litzow, C. A. O’Leary, G. G. Thompson.

Project PI: Hollowed
DOI: http://doi.org/10.1111/gcb.15149

Ecologists and oceanographers inform population and ecosystem management by identifying the physical drivers of ecological dynamics. However, different research communities use different analytical tools where, for example, physical oceanographers often apply rank-reduction techniques (a.k.a. empirical orthogonal functions [EOF]) to identify indicators that represent dominant modes of physical variability, whereas population ecologists use dynamical models that incorporate physical indicators as covariates. Simultaneously modeling physical and biological processes would have several benefits, including improved communication across sub-fields; more efficient use of limited data; and the ability to compare importance of physical and biological drivers for population dynamics. Here, we develop a new statistical technique, EOF regression, which jointly models population-scale dynamics and spatially distributed physical dynamics. EOF regression is fitted using maximum-likelihood techniques and applies a generalized EOF analysis to environmental measurements, estimates one or more time series representing modes of environmental variability, and simultaneously estimates the association of this time series with biological measurements. By doing so, it identifies a spatial map of environmental conditions that are best correlated with annual variability in the biological process. We demonstrate this method using a linear (Ricker) model for early-life survival (“recruitment”) of three groundfish species in the eastern Bering Sea from 1982 to 2016, combined with measurements and end-of-century projections for bottom and sea surface temperature. Results suggest that (a) we can forecast biological dynamics while applying delta-correction and statistical downscaling to calibrate measurements and projected physical variables, (b) physical drivers are statistically significant for Pacific cod and walleye pollock recruitment, (c) separately analyzing physical and biological variables fails to identify the significant association for walleye pollock, and (d) cod and pollock will likely have reduced recruitment given forecasted temperatures over future decades.

Author(s): Whitehouse, G. A., K. Y. Aydin.

Project PI: Hollowed
DOI: http://doi.org/10.1016/j.ecolmodel.2020.109074

Ecosystem modelling is a useful tool for exploring the potential outcomes of policy options and conducting experiments that would otherwise be impractical in the real world. However, ecosystem models have been limited in their ability to engage in the management of living marine resources due in part to high levels of uncertainty in model parameters and model outputs. Additionally, for multispecies or food web models, there is uncertainty about the predator-prey functional response, which can have implications for population dynamics. In this study, we evaluate the sensitivity of large marine food webs in Alaska to parameter uncertainty, including parameters that govern the predator-prey functional response. We use Rpath, an R implementation of the food web modeling program Ecopath with Ecosim (EwE), to conduct a series of mortality-based perturbations to examine the sensitivity and recovery time of higher trophic level groups in the eastern Chukchi Sea, eastern Bering Sea, and Gulf of Alaska. We use a Monte Carlo approach to generate thousands of plausible ecosystems by drawing parameter sets from the range of uncertainty around the base model parameters. We subjected the ecosystem ensembles to a series of mortality-based perturbations to identify which functional groups the higher trophic level groups are most sensitive to when their mortality was increased, whether the food webs returned to their unperturbed configurations following a perturbation, and how long it took to return to that state. In all three ecosystems, we found that the number of disrupted ensemble food webs was positively related to the biomass and the number of trophic links of the perturbed functional group, and negatively related to trophic level. The eastern Chukchi Sea was most sensitive to perturbations to benthic invertebrate groups, the eastern Bering Sea was most sensitive to shrimp and walleye pollock, and the Gulf of Alaska was most sensitive to shrimps, pelagic forage fish, and zooplankton. Recovery time to perturbations were generally less than 5 years in all three ecosystems. The recovery times when fish groups were perturbed were generally longer than when benthic invertebrates were perturbed, and recovery times were shortest when it was pelagic invertebrates. The single model ensemble approach produced simulation results that described a range of possible outcomes to the prescribed perturbations and provided a sense for how robust the results are to parameter uncertainty.

Author(s): Gilligan Lunda, E. K., Stich, D. S., Mills, K. E., Bailey, M. M., & Zydlewski, J. D.

Project PI: Mills
DOI: https://doi.org/10.1002/tafs.10299

American Shad (Alosa sapidissima) is an anadromous species with populations ranging along the U.S. Atlantic coast. Past American Shad stock assessments have been data limited and estimating system-specific growth parameters or instantaneous natural mortality (M) was not possible. This precluded system-specific stock assessment and management due to reliance on these parameters for estimating other population dynamics (such as yield per recruit). Furthermore, climate-informed biological reference points remain a largely unaddressed need in American Shad stock assessment. Population abundance estimates of American Shad and other species often rely heavily on M derived from von Bertalanffy growth function (VBGF) parameters. Therefore, we developed Bayesian hierarchical models to estimate coastwide, regional, and system-specific VBGF parameters and M using data collected from 1982 to 2017. We tested predictive performance of models that included effects of various climate variables on VBGF parameters within these models. System-specific models were better supported than regional or coast-wide models. Mean asymptotic length (L∞) decreased with increasing mean annual sea surface temperature (SST) and degree days (DD) experienced by fish during their lifetime. Although uncertain, K (Brody growth coefficient) decreased over the same range of lifetime SST and DD. Assuming no adaptation, we projected changes in VBGF parameters and M through 2099 using modeled SST from two climate projection scenarios (Representative Concentration Pathways 4.5 and 8.5). We predicted reduced growth under both scenarios, and M was projected to increase by about 0.10. It is unclear how reduced growth and increased mortality may influence population productivity or life history adaptation in the future, but our results may inform stock assessment models to assess those trade-offs.American Shad Alosa sapidissima is an anadromous species with populations ranging along the U.S. Atlantic coast. Past American Shad stock assessments have been data limited and estimating system-specific growth parameters or instantaneous natural mortality (M) was not possible. This precluded system-specific stock assessment and management due to reliance on these parameters for estimating other population dynamics (such as yield per recruit). Furthermore, climate-informed biological reference points remain a largely unaddressed need in American Shad stock assessment. Population abundance estimates of American Shad and other species often rely heavily on M derived from von Bertalanffy growth function (VBGF) parameters. Therefore, we developed Bayesian hierarchical models to estimate coastwide, regional, and system-specific VBGF parameters and M using data collected from 1982 to 2017. We tested predictive performance of models that included effects of various climate variables on VBGF parameters within these models. System-specific models were better supported than regional or coast-wide models. Mean asymptotic length (L∞) decreased with increasing mean annual sea surface temperature (SST) and degree days (DD) experienced by fish during their lifetime. Although uncertain, K (Brody growth coefficient) decreased over the same range of lifetime SST and DD. Assuming no adaptation, we projected changes in VBGF parameters and M through 2099 using modeled SST from two climate projection scenarios (Representative Concentration Pathways 4.5 and 8.5). We predicted reduced growth under both scenarios, and M was projected to increase by about 0.10. It is unclear how reduced growth and increased mortality may influence population productivity or life history adaptation in the future, but our results may inform stock assessment models to assess those trade-offs.

Author(s): Zang, Z., Ji, R., Feng, Z., Chen, C., Li, S., Davis, C.S.

Project PI: Ji/David/Rubao
DOI: https://doi.org/10.1093/icesjms/fsab102

The signal of phytoplankton responses to climate-related forcing can be obscured by the heterogeneity of shelf seascapes, making them difficult to detect from fragmented observations. In this study, a physical–biological model was applied to the Northwest Atlantic Shelf to capture the seasonality of phytoplankton. The difference in phytoplankton seasonality between the Mid-Atlantic Bight (MAB) and the Gulf of Maine (GoM) is a result of the interplay between nutrients and temperature: In the MAB, relatively high temperature in the cold season and longer oligotrophic environment in the warm season contribute to an earlier winter bloom and a later fall bloom; in the GoM, low temperature and strong mixing limit phytoplankton growth from late fall to early spring, resulting in a later spring bloom and an earlier fall bloom. Although the temperature difference between the GoM and the MAB might decrease in the future, stratification and surface nutrient regimes in these two regions will remain different owing to distinct thermohaline structures and deep-water intrusion. The spatial heterogeneity of phytoplankton dynamics affects pelagic and benthic production through connections with zooplankton and benthic–pelagic coupling.

Author(s): Smith, J. A., Muhling, B., Sweeney, J., Tommasi, D., Pozo Buil, M., Fiechter, J., & Jacox, M. G.

Project PI: Jacox
DOI: https://doi.org/10.1111/fog.12529

Many fish species are shifting spatial distributions in response to climate change, but projecting these shifts and measuring their impact at fine scales are challenging. We present a simulation that projects change in fishery landings due to spatial distribution shifts, by combining regional ocean and biogeochemical models (forced by three earth system models, ESMs: GFDL-ESM2M, HadGEM2-ES, IPSL-CM5A-MR), correlative models for species distribution and port-level landings, and a simulation framework which provides realistic values for species abundance and fishery conditions using an historical “reference period”. We demonstrate this approach for the northern subpopulation of Pacific sardine, an iconic commercial species for the U.S. West Coast. We found a northward shift in sardine landings (based on the northern subpopulation's habitat suitability), with projected declines at southern ports (20%–50% decline by 2080) and an increase (up to 50%) or no change at northern ports, and this was consistent across the three ESMs. Total sardine landings were more uncertain, with HadGEM2 indicating a 20% decline from 2000 to 15 levels by 2070 (a rate of 170 mt/y), IPSL a 10% increase (115 mt/y), and GFDL an 15% increase by the year ~2050 followed by a sharp decrease. The ESMs also differed in their projected change to the timing of the fishing season and frequency of fishery closures. Our simulation also identified key constraints on future landings that can be targeted by more tactical assessment; these included the seasonality of quota allocation and the abundance of other species in the catch portfolio.

Author(s): Amaya DJ, et al

Project PI: Jacox
DOI: 10.1175/BAMS-D-20-0144.1

Author(s): Brodie, S, et al

Project PI: Jacox
DOI: https://doi.org/10.1111/ecog.05504

Accurate forecasts of how animals respond to climate-driven environmental change are needed to prepare for future redistributions, however, it is unclear which temporal scales of environmental variability give rise to predictability of species distributions. We examined the temporal scales of environmental variability that best predicted spatial abundance of a marine predator, swordfish Xiphias gladius, in the California Current. To understand which temporal scales of environmental variability provide biological predictability, we decomposed physical variables into three components: a monthly climatology (long-term average), a low frequency component representing interannual variability, and a high frequency (sub-annual) component that captures ephemeral features. We then assessed each component's contribution to predictive skill for spatially-explicit swordfish catch. The monthly climatology was the primary source of predictability in swordfish spatial catch, reflecting the spatial distribution associated with seasonal movements in this region. Importantly, we found that the low frequency component (capturing interannual variability) provided significant skill in predicting anomalous swordfish distribution and catch, which the monthly climatology cannot. The addition of the high frequency component added only minor improvement in predictability. By examining models' ability to predict species distribution anomalies, we assess the models in a way that is consistent with the goal of distribution forecasts – to predict deviations of species distributions from their average historical locations. The critical importance of low frequency climate variability in describing anomalous swordfish distributions and catch matches the target timescales of physical climate forecasts, suggesting potential for skillful ecological forecasts of swordfish distributions across short (seasonal) and long (climate) timescales. Understanding sources of prediction skill for species environmental responses gives confidence in our ability to accurately predict species distributions and abundance, and to know which responses are likely less predictable, under future climate change. This is important as climate change continues to cause an unprecedented redistribution of life on Earth.

Author(s): Ding, H., Alexander, MA, Jacox, MG

Project PI: Jacox
DOI: https://doi.org/10.1029/2020GL090768

Given the importance of coastal upwelling in the California Current System (CCS), there is a considerable interest in predicting its response to global warming. However, upwelling changes are often treated as synonymous with changes in upwelling-favorable winds, while the role of geostrophic transport is unaccounted for. Here, we examine the respective roles of Ekman and geostrophic transports using the Community Earth System Model Large Ensemble. In some parts of the CCS, the contribution of geostrophic transport to long-term changes in upwelling is equal or greater than the contribution from Ekman transport. The combination of the two transports nearly close the momentum budget, and thus reproduce the mean state, interannual variability, and long-term changes in upwelling. These results highlight the importance of accounting for ocean circulation when quantifying upwelling and its variability and change.

Author(s): Fiechter, J, Pozo Buil, M, Jacox, M, Alexander, M, Rose, K,

Project PI: Jacox
DOI: https://doi.org/10.3389/fmars.2021.685241

Predicting changes in the abundance and distribution of small pelagic fish species in response to anthropogenic climate forcing is of paramount importance due to the ecological and socioeconomic importance of these species, especially in eastern boundary current upwelling regions. Coastal upwelling systems are notorious for the wide range of spatial (from local to basin) and temporal (from days to decades) scales influencing their physical and biogeochemical environments and, thus, forage fish habitat. Bridging those scales can be achieved by using high-resolution regional models that integrate global climate forcing downscaled from coarser resolution earth system models. Here, “end-to-end” projections for 21st century sardine population dynamics and catch in the California Current system (CCS) are generated by coupling three dynamically downscaled earth system model solutions to an individual-based fish model and an agent-based fishing fleet model. Simulated sardine population biomass during 2000–2100 exhibits primarily low-frequency (decadal) variability, and a progressive poleward shift driven by thermal habitat preference. The magnitude of poleward displacement varies noticeably under lower and higher warming conditions (500 and 800 km, respectively). Following the redistribution of the sardine population, catch is projected to increase by 50–70% in the northern CCS and decrease by 30–70% in the southern and central CCS. However, the late-century increase in sardine abundance (and hence, catch) in the northern CCS exhibits a large ensemble spread and is not statistically identical across the three downscaled projections. Overall, the results illustrate the benefit of using dynamical downscaling from multiple earth system models as input to high-resolution regional end-to-end (“physics to fish”) models for projecting population responses of higher trophic organisms to global climate change.

Author(s): Frawley, T, et al

Project PI: Jacox
DOI: https://doi.org/10.1111/faf.12519

Marine fisheries around the globe are increasingly exposed to external drivers of social and ecological change. Though diversification and flexibility have historically helped marine resource users negotiate risk and adversity, much of modern fisheries management treats fishermen as specialists using specific gear types to target specific species. Here, we describe the evolution of harvest portfolios amongst Pacific Northwest fishermen over 35+ years with explicit attention to changes in the structure and function of the albacore (Thunnus alalunga, Scombridae) troll and pole-and-line fishery. Our analysis indicates that recent social–ecological changes have had heterogenous impacts upon the livelihood strategies favoured by different segments of regional fishing fleets. As ecological change and regulatory reform have restricted access to a number of fisheries, many of the regional small (<45 ft) and medium (45–60 ft) boat fishermen who continue to pursue diverse livelihood strategies have increasingly relied upon the ability to opportunistically target albacore in coastal waters while retaining more of the value generated by such catch. In contrast, large vessels (>60 ft) targeting albacore are more specialized now than previously observed, even as participation in multiple fisheries has become increasingly common for this size class. In describing divergent trajectories associated with the albacore fishery, one of the US West Coast's last open-access fisheries, we highlight the diverse strategies and mechanisms utilized to sustain fisheries livelihoods in the modern era while arguing that alternative approaches to management and licensing may be required to maintain the viability of small-scale fishing operations worldwide moving forward.