CCS Species Distribution Models for coastal pelagic species

Forage species such as Pacific sardine, northern anchovy, and market squid are critical ecological links between the planktonic food web and higher trophic levels in the California Current System, as well as supporting valuable fisheries. Environmental variability drives large fluctuations in their abundance and distribution. This dataset includes the outputs of Species Distribution Models (SDMs) for 6 key forage species, combining multiple survey datasets with environmental fields from a high-resolution Regional Ocean Modeling System (ROMS) developed at the University of California - Santa Cruz, and the Copernicus-Globcolour level 4 interpolated surface chlorophyll product (https://doi.org/10.48670/moi-00281). The sardine and anchovy SDMs also included predictors indexing stock biomass (MacCall et al. 2016; Kuriyama et al. 2022; Kuriyama et al. 2024). As temporally continuous salinity fields are not available from the UCSC ROMS, we included a measure of the distance to the nearest major river (mean > 50,000 CFS discharge) in the herring SDM, to capture the association of this species with estuaries.

The species represented are Pacific sardine (Sardinops sagax), northern anchovy (Engraulis mordax), market squid (Doryteuthis opalescens), Pacific herring (Clupea pallasii), jack mackerel (Trachurus symmetricus), and Pacific mackerel (Scomber japonicus). Results from two different SDMs are shown: Generalized Additive Models and Boosted Regression Trees, and both models predict the probability of occurrence of each species. The model outputs are generally similar, but the BRTs can be more prone to producing offshore artefacts, especially for market squid and jack mackerel. We used data from the NOAA Southwest Fisheries Science Center Coastal Pelagic Species and Columbia River Predator (Emmett et al. 2006) trawl surveys to train all SDMs, with the exception of market squid, where juvenile salmon survey data were used instead (see Chasco et al. 2022 for description of these data). More details on SDMs are available in Muhling et al. (2019); Fennie et al. (2022), and Quezada et al. (2023).

Important caveat for the sardine SDMs: these models use spawning stock biomass from the stock assessment as an indicator. Since 2022, Japanese sardine (S. melanostictus) have been detected in the California Current System in increasing numbers. These animals are excluded from the stock assessment using genetic identification, so there are likely to be more total sardine in the region than predicted by the sardine SDM.

These outputs are free to use, but we strongly recommend contacting Barbara Muhling ([e-mail]) before working with them, to ensure complete understanding of the details and caveats. Fields are updated on ERDDAP about once per year, but additional updates can be pushed upon request. Funding for this work was provided by NOAA Office of Sustainable Fisheries, and the NOAA Climate and Fisheries Adaptation program.

References

Chasco, B. E., Hunsicker, M. E., Jacobson, K. C., Welch, O. T., Morgan, C. A., Muhling, B. A., & Harding, J. A. (2022). Evidence of Temperature-Driven Shifts in Market Squid Doryteuthis opalescens Densities and Distribution in the California Current Ecosystem. Marine and Coastal Fisheries, 14(1), e10190.

Emmett, R. L., Krutzikowsky, G. K., & Bentley, P. (2006). Abundance and distribution of pelagic piscivorous fishes in the Columbia River plume during spring/early summer 1998-2003: relationship to oceanographic conditions, forage fishes, and juvenile salmonids. Progress in Oceanography, 68(1), 1-26.

Fennie, H. W., Seary, R., Muhling, B. A., Bograd, S. J., Brodie, S., Cimino, M. A., ... & Tommasi, D. (2023). An anchovy ecosystem indicator of marine predator foraging and reproduction. Proceedings of the RoyalSociety B, 290(1992), 20222326.

Kuriyama, P. T., Zwolinski, J. P., Teo, S. L. H. & Hill, K. T. (2022). Assessment of the Northern anchovy (Engraulis mordax) resource in 2021 for US management. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-665

Kuriyama, P. T., Allen Akselrud, C., Zwolinski, J. P., Hill, K. T. (2024). Assessment of the Pacific sardine resource in 2024 for US management in 2024-2025. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-698

MacCall, A. D., Sydeman, W. J., Davison, P. C., & Thayer, J. A. (2016). Recent collapse of northern anchovy biomass off California. Fisheries Research, 175, 87-94.

Muhling, B., Brodie, S., Snodgrass, O., Tommasi, D., Dewar, H., Childers, J., Jacox, M. Edwards, C. A., Xu, Y. & Snyder, S. (2019). Dynamic habitat use of albacore and their primary prey species in the California Current System. CalCOFI Reports 60: 1-15.

Quezada, F. J., Tommasi, D., Frawley, T. H., Muhling, B., Kaplan, I., & Stohs, S. (2023). Catch as catch can: Markets, availability, and fishery closures drive distinct responses among the US West Coast Coastal Pelagic Species fleet segments. Canadian Journal of Fisheries and Aquatic Sciences. https://doi.org/10.1139/cjfas-2023-009
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该数据集涵盖了太平洋鲭鱼、北鳀鱼和市售墨鱼等放牧物种的分布模型输出，这些物种在加州洋流系统中是浮游食物网与更高营养级之间的关键生态环节，同时支撑着具有重要价值的渔业。环境变化引发了它们数量和分布的巨大波动。本数据集包括针对6种关键放牧物种的物种分布模型（SDM）输出，这些模型结合了来自加州大学圣克鲁兹分校开发的具有高分辨率区域海洋模式系统（ROMS）的环境字段和Copernicus-Globcolour四级插值表面叶绿素产品（https://doi.org/10.48670/moi-00281）的多个调查数据集。鲭鱼和鳀鱼的SDM还包括指数化渔群生物量的预测因子（MacCall等，2016；Kuriyama等，2022；Kuriyama等，2024）。由于UCSC ROMS无法提供连续的时序盐度场，我们在鳕鱼的SDM中纳入了距离最近主要河流的距离指标（平均流量大于50,000立方英尺每秒），以捕捉该物种与河口之间的关联。数据集中的物种包括太平洋鲭鱼（Sardinops sagax）、北鳀鱼（Engraulis mordax）、市售墨鱼（Doryteuthis opalescens）、太平洋鳕鱼（Clupea pallasii）、鲷鱼（Trachurus symmetricus）和太平洋鲅鱼（Scomber japonicus）。展示了两种不同的SDM结果：广义加性模型和提升回归树，并且两种模型都预测了每种物种出现的概率。模型输出总体相似，但提升回归树可能更容易产生离岸伪迹，尤其是对于市售墨鱼和鲷鱼。我们使用NOAA西南渔业科学中心沿海浮游生物和哥伦比亚河捕食者（Emmett等，2006）拖网调查的数据来训练所有SDM，但市售墨鱼除外，我们使用了幼鲑鱼调查数据（参见Chasco等，2022年对这些数据的描述）。有关SDM的更多详细信息，请参阅Muhling等（2019）；Fennie等（2022）和Quezada等（2023）。对鲭鱼SDM的重要注意事项：这些模型使用种群评估中的产卵种群生物量作为指标。自2022年以来，日本鲭鱼（S. melanostictus）在加州洋流系统中数量不断增加。这些动物通过遗传鉴定被排除在种群评估之外，因此该地区可能的总鲭鱼数量可能比鲭鱼SDM预测的要多。这些输出免费使用，但我们强烈建议在处理这些数据之前联系Barbara Muhling（[e-mail]），以确保完全理解细节和注意事项。字段大约每年更新一次，但可根据请求推送额外更新。本工作的资金由NOAA可持续渔业办公室和NOAA气候与渔业适应性计划提供。