Southwest Fisheries Science Center

Biases in global Earth System Models (ESMs) are an important source of errors when used to obtain boundary conditions for regional models. Here we examine historical and future conditions in the California Current System (CCS) using three different methods to force the regional model: (a) interpolation of ESM output to the regional grid with no bias correction; (b) a “seasonally‐varying” delta method that obtains a season‐dependent mean climate change signal from the ESM for a 30‐year future period; and (c) a “time‐varying” delta method that includes the interannual variability of the ESM over the 1980–2100 period. To compare these methods, we use a high‐resolution (0.1°) physical‐biogeochemical regional model to dynamically downscale an ESM projection under the RCP8.5 emission scenario. Using different downscaling methods, the sign of future changes agrees for most of the physical and ecosystem variables, but the spatial patterns and magnitudes of these changes differ, with the seasonal‐ and time‐varying delta simulations showing more similar changes. Not correcting the ESM forcing leads to amplification of biases in some ecosystem variables as well as misrepresentation of the California Undercurrent and CCS source waters. In the non‐bias corrected and time‐varying delta simulations, most of the ecosystem variables inherit trends and decadal variability from the ESM, while in the seasonally‐varying delta simulation the future variability reflects the observed historical variability (1980–2010). Our results demonstrate that bias correcting the forcing prior to downscaling improves historical simulations, and that the bias correction method may impact the spatial and temporal variability of the future projections.

Although massive biomass fluctuations of coastal-pelagic fishes are an iconic example of the impacts of climate variability on marine ecosystems, the mechanisms governing these dynamics are often elusive. We construct a 45-year record of nitrogen stable isotopes measured in larvae of Northern Anchovy (Engraulis mordax) in the California Current Ecosystem to assess patterns in food chain length. Larval trophic efficiency associated with a shortened food chain increased larval survival and produced boom periods of high adult biomass. In contrast, when larval food chain length increased, and energy transfer efficiency decreased, the population crashed. We propose the Trophic Efficiency in Early Life (TEEL) hypothesis, which states that larval fishes must consume prey that confer sufficient energy for survival, to help explain natural boom-bust dynamics of coastal pelagic fishes. Our findings illustrate a potential for trophic indicators to generally inform larval survival and adult population dynamics of coastal-pelagic fishes.

Accounting for marine stocks spatiotemporal complexity has become one of the most pressing improvements that should be added to the new generation of stock assessment. Disentangling persistent and dynamic population subcomponents and understanding their main drivers of variation are still stock-specific challenges. Here, we hypothesized that the spatiotemporal variability of two adjacent fish stocks density is associated with spatially structured environmental processes across multiple spatiotemporal scales. To test this, we applied a generalized Empirical Orthogonal Function and Dynamic Factor Analysis to fishery-independent and -dependent data of red mullet, a highly commercial species, in the Western Mediterranean Sea. Areas with persistent and dynamic high aggregations were detected for both stock units. A large-scale climatic index and local open-ocean convection were associated with both stocks while other variables exhibited stock-specific effects. We also revealed spatially structured density dynamics within the examined management units. This suggests a metapopulation structure and supports the future implementation of a spatial stock assessment. Considering the common assumptions of panmictic structure and absence of connectivity with neighbouring stock units, our methodology can be applied to other species and systems with putative spatial complexity to inform a more accurate structure of biological populations.

The sub‐Antarctic waters of South Georgia Island (Islas Georgias del Sur, SG/IG) are a regularly visited feeding ground for southern right whales ( Eubalaena australis , SRW) in the southwest Atlantic. Satellite telemetry and photo‐identification records were compared to better understand the role of SG/IG in the SRW migratory network. We present the first insights from SRW satellite‐tracked from the SG/IG feeding ground, habitat use patterns in the Scotia Arc, and movements to Antarctic habitats. Photo‐identification comparisons to calving and feeding areas across the South Atlantic and a review of sightings of cetaceans reported from Bird Island (west of SG/IG) since 1979 illuminate long‐term habitat use patterns in SG/IG. We present the first recorded migratory movement between SG/IG and multiple countries: Argentina, Uruguay, and Brazil. Photo‐identification (1) linked SG/IG to a female SRW with a long‐term sighting history in Brazil, and (2) provided the first match between SG/IG and the western Antarctic Peninsula, suggesting the latter could extend the feeding area for southwest Atlantic SRW. Satellite tracking and opportunistic sightings suggest that shelf and coastal waters west of SG/IG represent an important multi‐season SRW feeding habitat and add to our overall understanding of habitats and ranges occupied by recovering southwest Atlantic SRW.

Salmonids are well known for their natal homing behaviour, meaning they return to breed in the same area where they originated. However, not all individuals return to their natal breeding grounds—a behavioural trait known as straying. The prevalence of straying is difficult to explore and therefore quantitative estimates for straying are seldom reported. In this study, otolith microchemistry and genetics were combined to investigate patterns of straying over ecological and evolutionary time, respectively, between neighbouring rivers flowing into Mariager fjord, Denmark. Otolith microchemistry was used to determine the river of origin for sea trout ( Salmo trutta ) upon their return to freshwater and 288 SNP markers were used to determine genetic structure among the rivers in the fjord. In this system, where the distance between rivers is short, otolith microchemistry achieved 80% accuracy in assigning juvenile brown trout to their natal river, thus allowing us to determine that approximately 43% of the adult sea trout had returned to non‐natal rivers to spawn, with a similar proportion of strayers and natal homers in all of the rivers. Genetic analysis further supported that there was substantial gene flow among individuals originating from different rivers, indicating that sea trout in Mariager fjord make up one population. The findings obtained from otolith microchemistry and genetics complement each other and provide further evidence that sea trout in this system migrate to non‐natal rivers and spawn there, which consequently affects the genetic structure of the population.

Underwater imaging enables nondestructive plankton sampling at frequencies, durations, and resolutions unattainable by traditional methods. These systems necessitate automated processes to identify organisms efficiently. Early underwater image processing used a standard approach: binarizing images to segment targets, then integrating deep learning models for classification. While intuitive, this infrastructure has limitations in handling high concentrations of biotic and abiotic particles, rapid changes in dominant taxa, and highly variable target sizes. To address these challenges, we introduce a new framework that starts with a scene classifier to capture large within-image variation, such as disparities in the layout of particles and dominant taxa. After scene classification, scene-specific Mask regional convolutional neural network (Mask R-CNN) models are trained to separate target objects into different groups. The procedure allows information to be extracted from different image types, while minimizing potential bias for commonly occurring features. Using in situ coastal plankton images, we compared the scene-specific models to the Mask R-CNN model encompassing all scene categories as a single full model. Results showed that the scene-specific approach outperformed the full model by achieving a20% accuracy improvement in complex noisy images. The full model yielded counts that were up to 78% lower than those enumerated by the scene-specific model for some small-sized plankton groups. We further tested the framework on images from a benthic video camera and an imaging sonar system with good results. The integration of scene classification, which groups similar images together, can improve the accuracy of detection and classification for complex marine biological images.

Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species’ distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) assumptions of extinction risk. Changes in agricultural practices and associated habitat loss, overharvesting, pollution and development are major threats to biodiversity. Maintaining and restoring sustainable land and water use practices is crucial to minimize future biodiversity declines.

Understanding how climate change will influence ecosystems is essential for effective climate adaptation and mitigation. Current approaches in ocean management aim to protect climate refugia, defined as areas where species will persistent over time, or areas where climatic conditions are projected to be more stable. However, these approaches overlook complex shifts in functional diversity of community assemblages resulting from climate-induced species turnover. Here, we approach climate refugia for marine megafauna in the Northeast Pacific ocean from the lens of functional diversity in comparison with species diversity. We find that species turnover explains species and functional diversity change by the year 2100 in the extreme climatic scenario better than in the moderate and intermediate scenarios. Functional diversity is more stable at temperate and tropical latitudes than at poleward latitudes. Our results show that fewer, less abundant species influence functional diversity change across ecoregions. These results highlight opportunities to target conservation on certain species in areas where they support functional diversity. Our approach can assist managers to identify and protect areas that might lose species but not functional diversity. This will help maintaining ecosystem resilience, their capacity to buffer multiple disturbances and to provide benefits to humans across future climate change scenarios.

Ocean forecasting is now widely recognized as an important approach to improve the resilience of marine ecosystems, coastal communities, and economies to climate variability and change. In particular, regionally tailored forecasts may serve as the foundation for a wide range of applications to facilitate proactive decision making. Here, we describe and assess ~30 years of retrospective seasonal (1–12 month) forecasts for the California Current System, produced by forcing a regional ocean model with output from a global forecast system. Considerable forecast skill is evident for surface and bottom temperatures, sea surface height, and upper ocean stratification. In contrast, mixed layer depth, surface wind stress, and surface currents exhibit little predictability. Ocean conditions tend to be more predictable in the first half of the year, owing to greater persistence for forecasts initialized in winter and dynamical forecast skill consistent with winter/spring influence of the El Niño–Southern Oscillation (ENSO) for forecasts initialized in summer. Forecast skill above persistence appears to come through the ocean more than through the atmosphere. We also test the sensitivity of forecast performance to downscaling method; bias correcting global model output before running the regional model greatly reduces bias in the downscaled forecasts, but only marginally improves prediction of interannual variability. We then tailor the physical forecast evaluation to a suite of potential ecological applications, including species distribution and recruitment, bycatch and ship-strike risk, and indicators of ecosystem change. This evaluation serves as a template for identifying promising ecological forecasts based on the physical parameters that underlie them. Finally, we discuss suggestions for developing operational forecast products, including methodological considerations for downscaling as well as the respective roles of regional and global forecasts.

Fishers often target multiple species. More diverse harvest portfolios may reduce income risk, increasing resilience to climate-driven changes in target species’ spatial distributions and availability. Moreover, different effects can be observed across vessels in response to the same shocks and stressors, as fishers are heterogeneous. Evaluation of climate risk within a particular fishery requires consideration of heterogeneous climate impacts on the availability of multiple target species and how such changes may impact substitution behavior. Here we analyze how historical climate-driven changes in forage species distribution and the closure of the Pacific sardine fishery affected landings per vessel of three coastal pelagic species (CPS): Pacific sardine (Sardinops sagax), market squid (Doryteuthis opalescens), and northern anchovy (Engraulis mordax) targeted by the U.S. West Coast CPS fleet from 2000-2020. Using cluster analysis, we grouped vessels into different fleet segments and estimated heterogeneous responses by fleet segment and port area. Our results show that considering heterogeneity is essential in the development of equitable and effective adaptation policies designed to mitigate the impact of change in these fisheries.

Protected areas are typically managed as a network of sites exposed to varying anthropogenic conditions. Managing these networks benefits from monitoring of conditions across sites to help prioritize coordinated efforts. Monitoring marine vessel activity and related underwater noise impacts across a network of protected areas, like the U.S. National Marine Sanctuary system, helps managers ensure the quality of habitats used by a wide range of marine species. Here, we use underwater acoustic detection of vessels to quantify vessel noise at 25 locations within eight marine sanctuaries including the Hawaiian Archipelago and the U.S. east and west coasts. Vessel noise metrics were paired with Automatic Identification System (AIS) vessel tracking data to derive a suite of robust vessel noise indicators for use across the network of marine protected areas. Network-wide comparisons revealed a spectrum of vessel noise conditions that closely matched AIS vessel traffic composition. Shifts in vessel noise were correlated with the decrease in vessel activity in early COVID-19 pandemic and vessel speed reduction initiatives. Improving our understanding of vessel noise conditions in these protected areas can help direct opportunities for reducing vessel noise, such as establishing and maintaining noise-free periods, enhancing port efficiency, engaging with regional and international vessel quieting initiatives, and leveraging co-benefits of management actions for reducing ocean noise.

Age‐, region‐, and year‐specific estimates of reproduction are needed for monitoring wildlife populations during periods of ecosystem change. Population dynamics of Steller sea lions ( Eumetopias jubatus ) in Southeast Alaska varied regionally (with high population growth and survival in the north vs. the south) and annually (with reduced adult female survival observed following a severe marine heatwave event), but reproductive performance is currently unknown. We used mark‐resighting data from 1006 Steller sea lion females marked as pups at ~3 weeks of age from 1994 to 1995 and from 2001 to 2005 and resighted from 2002 to 2019 (to a maximum age of 25) to examine age‐, region‐, and year‐specific reproduction. In the north versus the south, age of first reproduction was earlier (beginning at age 4 vs. age 5, respectively) but annual birth probabilities of parous females were reduced by 0.05. In an average year pre‐heatwave, the proportion of females with pup at the end of the pupping season peaked at ages 12–13 with ~0.60/0.65 (north/south) with pup, ~0.30/0.25 with juvenile, and ~0.10 (both regions) without a dependent. In both regions, reproductive senescence was gradual after age 12: ~0.40, 0.40, and 0.20 of females were in these reproductive states, respectively, by age 20. Correcting for neonatal mortality, true birth probabilities at peak ages were 0.66/0.72 (north/south). No cost of reproduction on female survival was detected, but pup production remained lower (−0.06) after the heatwave event, which if sustained could result in population decline in the south. Reduced pup production and greater retention of juveniles during periods of poor prey conditions may be an important strategy for Steller sea lions in Southeast Alaska, where fine‐tuning reproduction based on nutritional status may improve the lifetime probability of producing pups under good conditions in a variable and less productive environment.

Knowledge of cetacean life history, morphology, and social behavior provides clues to the niche-specific adaptations that have evolved to maximize reproductive fitness. An essential component of a species’ life history is mating, particularly the sex-specific mating strategies that have evolved. Mating strategies vary within and among species reflecting phylogenetic constraints and the interplay of selective forces molding each species’ adaptations. The suite of cetacean mating strategies that have evolved ultimately determines how a species’ mating system operates. Thus, mating systems provide a unifying framework to compare and contrast cetacean strategies for reproduction and mating. Theory predicts that the degree of sexual size dimorphism (SSD) and the relative testes size of mammalian species will be good indicators of their mating system. However, interspecific and intraspecific variability in SSD and relative testes size reveal unique tradeoffs made in response to evolutionary pressures and ecological processes that result in exceptions to the theoretical predictions. In this chapter, we review current knowledge of cetacean reproductive biology and how that information furthers our understanding of their mating systems.

Gray whale sexual behavior and copulation are observed throughout their range. The most prominent period for reproductive behavior is during the southward migration from summer feeding areas to wintering areas where some breeding occurs and calves of the year are reared. The seasonal migrations of gray whales are believed to function, in part, to bring together individuals that are otherwise widely distributed during the period of estrus to facilitate mating and reproduction. Sexual behaviors and sexual strategies for this species appear to align closely with those of balaenid (not rorqual) whales, although such comparisons need further investigation. Gray whales are polygynandrous (multi-mate) breeders. There does not appear to be female choice of mates, as groups of numerous females and males aggregate, and multiple copulations occur. Female estrus begins in mid-November and continues to early December; females may undergo a second estrus, extending into February, if they fail to conceive during their first cycle. Male gray whales have large testes and concomitantly produce large volumes of sperm, so they are believed to be sperm competitors; that is, they rely on multiple copulations (and sperm volume) to produce offspring. Multiple copulations with different males during the female estrus period may increase the likelihood that the timing of conception results in the birth of a calf approximately 13 months later near or in the wintering area(s). Mating bouts can last for minutes to hours, interspersed with surface-active-social-sexual behavior. Some all-male groups have been observed with erect penises engaged in social-sexual behavior in the absence of any females. Instances of male aggression toward postpartum females with calves of the year, sometimes resulting in injury or death, have been reported. As a result of dedicated long-term research in the past several decades, the state of knowledge on gray whale reproduction has greatly expanded and updated information on this topic is summarized in this chapter.

The management and conservation of tuna and other transboundary marine species have to date been limited by an incomplete understanding of the oceanographic, ecological and socioeconomic factors mediating fishery overlap and interactions, and how these factors vary across expansive, open ocean habitats. Despite advances in fisheries monitoring and biologging technology, few attempts have been made to conduct integrated ecological analyses at basin scales relevant to pelagic fisheries and the highly migratory species they target. Here, we use vessel tracking data, archival tags, observer records, and machine learning to examine inter‐ and intra‐annual variability in fisheries overlap (2013–2020) of five pelagic longline fishing fleets with North Pacific albacore tuna ( Thunnus alalunga , Scombridae). Although progressive declines in catch and biomass have been observed over the past several decades, the North Pacific albacore is one of the only Pacific tuna stocks primarily targeted by pelagic longlines not currently listed as overfished or experiencing overfishing. We find that fishery overlap varies significantly across time and space as mediated by (1) differences in habitat preferences between juvenile and adult albacore; (2) variation of oceanographic features known to aggregate pelagic biomass; and (3) the different spatial niches targeted by shallow‐set and deep‐set longline fishing gear. These findings may have significant implications for stock assessment in this and other transboundary fishery systems, particularly the reliance on fishery‐dependent data to index abundance. Indeed, we argue that additional consideration of how overlap, catchability, and size selectivity parameters vary over time and space may be required to ensure the development of robust, equitable, and climate‐resilient harvest control rules.

Improving our understanding of the effects of satellite tags on large whales is a critical step in ongoing tag development to minimise potential health effects whilst addressing important research questions that enhance conservation management policy. In 2014, satellite tags were deployed on 9 female southern right whales Eubalaena australis accompanied by a calf off Australia. Photo-identification resights (n = 48) of 4 photo-identified individuals were recorded 1 to 2894 d (1-8 yr) post-tagging. Short-term (<22 d) effects observed included localised and regional swelling, depression at the tag site, blubber extrusion, skin loss and pigmentation colour change. Broad swelling observable from lateral but not aerial imagery (~1.2 m diameter or ~9% of body length) and depression at the tag site persisted up to 1446 d post-tagging for 1 individual, indicating a persistent foreign-body response or infection. Two tagged individuals returned 4 yr post-tagging in 2018 with a calf, and the medium-term effects were evaluated by comparing body condition of tagged whales with non-tagged whales. These females calved in a typical 4 yr interval, suggesting no apparent immediate impact of tagging on reproduction for these individuals, but longer-term monitoring is needed. There was no observable difference in the body condition between the 2 tagged and non-tagged females. Ongoing monitoring post-tagging is required to build on the sample size and statistical power. We demonstrate the value of long-term monitoring programmes and a collaborative approach for evaluating effects from satellite-tagging cetaceans to support species management.

Seascape genomics provides a powerful framework to evaluate the presence and strength of environmental pressures on marine organisms, as well as to forecast long term species stability under various perturbations. In the highly productive North Pacific, forage fishes, key trophic links across ecosystems, are also contending with a rapidly warming climate and a litany of associated oceanographic changes (e.g., changes in salinity, dissolved oxygen, pH, primary production, etc.). These changes can place substantial selective pressures on populations over space and time. While several population genomics studies have targeted forage fishes in the North Pacific, none have formally analyzed the interactions between genotype and environment. However, when population genomics studies provide collection location information and other critical data, it is possible to supplement a published genomic dataset with environmental data from existing public databases and perform “ post hoc seascape genomics” analyses. In reviewing the literature, we find pertinent metadata (dates and locations of sample collection) are rarely provided. We identify specific factors that may impede the application of seascape genomics methods in the North Pacific. Finally, we present an approach for supplementing data in a reproducible way to allow for post hoc seascape genomics analysis, in instances when metadata are reported. Overall, our goal is to demonstrate – via literature review – the utility and importance of seascape genomics to understanding the long term health of forage fish species in the North Pacific.

Twentieth century industrial whaling pushed several species to the brink of extinction, with fin whales being the most impacted. However, a small, resident population in the Gulf of California was not targeted by whaling. Here, we analyzed 50 whole-genomes from the Eastern North Pacific (ENP) and Gulf of California (GOC) fin whale populations to investigate their demographic history and the genomic effects of natural and human-induced bottlenecks. We show that the two populations diverged~16,000 years ago, after which the ENP population expanded and then suffered a 99% reduction in effective size during the whaling period. In contrast, the GOC population remained small and isolated, receiving less than one migrant per generation. However, this low level of migration has been crucial for maintaining its viability. Our study exposes the severity of whaling, emphasizes the importance of migration, and demonstrates the use of genome-based analyses and simulations to inform conservation strategies.

Marine heatwaves cause widespread environmental, biological, and socioeconomic impacts, placing them at the forefront of 21st-century management challenges. However, heatwaves vary in intensity and evolution, and a paucity of information on how this variability impacts marine species limits our ability to proactively manage for these extreme events. Here, we model the effects of four recent heatwaves (2014, 2015, 2019, 2020) in the Northeastern Pacific on the distributions of 14 top predator species of ecological, cultural, and commercial importance. Predicted responses were highly variable across species and heatwaves, ranging from near total loss of habitat to a twofold increase. Heatwaves rapidly altered political bio-geographies, with up to 10% of predicted habitat across all species shifting jurisdictions during individual heatwaves. The variability in predicted responses across species and heatwaves portends the need for novel management solutions that can rapidly respond to extreme climate events. As proof-of-concept, we developed an operational dynamic ocean management tool that predicts predator distributions and responses to extreme conditions in near real-time. Long-term climate trends (e.g., global warming) and short-term extreme events (e.g., heatwaves) have global impacts on ecosystem structure and functioning, and human well-being 1-3. The impacts of long-term climate trends have received considerable attention through the examination of the warming signal in both historical observations and future climate projections 4-9. However, mounting evidence indicates that episodic events like fires, floods, and heatwaves can have catastrophic ecosystem and socioeconomic impacts 1,10-12 .