California Current Large Marine Ecosystem Research Articles

Salmon shark seasonal site fidelity demonstrates the influence of scale on identifying potential high-use areas and vulnerabilities

Considering habitat use throughout the whole range of a highly mobile marine species is necessary to understand life history, identify vulnerabilities, and inform effective management. We used satellite tagging data from 128 adult female salmon sharks Lamna ditropis to identify seasonal hotspots of activity in an extended California Current region (ECCR; encompassing the California Current Large Marine Ecosystem), an area far away from their well-described primary habitat in the Alaska Downwelling Region where they have been documented, but whose utility has been poorly understood. Tag track durations had a mean of 447.7 ± 381 d, and 88 sharks (68.8%) visited the ECCR, comprising 33.6% of 28019 total daily Argos detections. Tracking data revealed that the timing and duration of migrations to the ECCR varied, but salmon shark distribution within the ECCR displayed consistent latitudinal shifts in accordance with regional oceanographic seasons. High site fidelity across multi-year tracks to high-productivity features, such as sea banks, and previously published knowledge of salmon shark life history suggest that the ECCR provides important foraging habitat which may be linked to reproductive success. The data reveal high overlap of salmon shark distribution with cumulative fishing effort collected by Global Fishing Watch for 2012-2019, particularly around seasonal hotspots, suggesting that female salmon sharks might be at risk of fisheries encounters. Collectively, our findings emphasize the importance of the ECCR in salmon shark life history and demonstrate the influence of spatial and temporal scale on interpretation of large movement data sets and identification of critical habitat outside of well-studied regions.

Trait-based indicators of resource selection by albacore tuna in the California Current Large Marine Ecosystem

As global climate change reorganizes marine ecosystems, understanding how predators will respond to variable prey resources is critical to forecasting future community dynamics. Prey traits that affect the foraging process and recur across unrelated taxa offer a means to better anticipate predator resource use by simplifying complex foraging dynamics. Here we compare taxonomic and trait-based indicators of resource use and selection for albacore tuna (Thunnus alalunga), a commercially valuable pelagic predator undergoing climate-driven range shifts. We synthesized datasets from 2005 to 2019 to evaluate diets of albacore tuna in relation to prey availability estimates from shipboard surveys in the California Current Large Marine Ecosystem. Analyses with these data reveal that albacore and trawl surveys sample different aspects of the pelagic system, with albacore consuming a subset of taxa identified within trawls. Albacore consistently selected coastal prey that are schooling, undefended, silvered and countershaded, and have high energy density — suggesting that ecological mechanisms driving albacore foraging outcomes may be conserved across time and space. Ecological traits mediating predator-prey interactions consistently distinguished albacore diets from assemblages sampled by trawls across years and regions. We demonstrate that a traits-based approach simplifies taxonomically diverse predator-prey interactions and may be a valuable tool to facilitate predictions of prey resource use in changing environments.

Trophic guilds of marine predators in the California Current Large Marine Ecosystem

Quantifying trophic relationships of marine species is fundamental to the construction and performance of ecosystem models, development of effective ecosystem-based fisheries management strategies, and support of trait-based approaches to ecological risk assessment. Accounting for food web dynamics in taxonomically diverse ecosystems, such as the California Current Large Marine Ecosystem (CCLME), is especially challenging because of the sheer number of trophic linkages and their inherent variability. Consequently, analyses that can inform the most appropriate means of aggregating species or other taxonomic groups into assemblages or guilds are critical to reducing system complexity for modeling and management, particularly when data are limited. To provide a methodological approach that is globally applicable in such cases, we define trophic guilds within biogeographic regions of the CCLME, compare results among these regions, and discuss ecological and management implications. Within each biogeographic region, predator guilds were clearly demarcated by foraging habitat (benthic, nearshore pelagic, offshore pelagic), scale of foraging movements, and trophic position. Furthermore, trophic guilds were distinctive for each region, with species composition and the noted ecological characteristics largely driving guild structure. Predator species that are reliant on continental slope and offshore foraging habitat, such as adult Pacific Hake, have diets that are representative of these areas and are similar throughout the CCLME. Generally, larger, more mobile predators that typically feed in deeper offshore waters, including swordfish, sea lions, and sharks clustered together in multiple bioregions along the coast; all reliant primarily on fishes and squids. Throughout bioregions, groundfishes preyed on benthic invertebrates (e.g., decapods, amphipods, polychaetes), while shelf-oriented pelagic predators, including smaller salmon, preyed on pelagic invertebrates (e.g., euphausiids, copepods, gelatinous zooplankton). A large number of forage taxa that are well represented in this study have dynamics largely dependent on oceanographic conditions at a regional scale (e.g., decapods), basin scale (e.g., copepods), or a combination of both (e.g., euphausiids, Northern Anchovy). Such distinctions indicate that spatial and temporal scales of coherence of predators and prey also must be considered in development of ecosystem models and evaluation of management strategies. Our study quantifies the spatial coherence of predator guilds integrated over decades within and across bioregions of the CCLME, providing an improved understanding of regional ecosystem functioning. The analytical approach we developed may be easily extended to address similar ecological and ecosystem based fisheries management priorities in other marine regions.

A multi-predator trophic database for the California Current Large Marine Ecosystem

The California Current Trophic Database (CCTD) was developed at NOAA Southwest Fisheries Science Center in collaboration with numerous diet data contributors. We compiled the CCTD from twenty-four data sets, representing both systematic collections and directed trophic studies. Diet composition data, including stomach and scat samples, were obtained from 105,694 individual predators among 143 taxa collected throughout the California Current Large Marine Ecosystem (CCLME) from 1967–2019. Predator taxa consist of squids (n = 5), elasmobranchs (n = 13), bony fishes (n = 118), and marine mammals (n = 7). Extensive time series are available for some predators (e.g., California Sea Lion, Pacific Hake, Chinook Salmon). The CCTD represents the largest compilation of raw trophic data within the CCLME, allowing for more refined analyses and modeling studies within this region. Our intention is to further augment and periodically update the dataset as additional historical or contemporary data become available to increase its utility and impact.

Archived DNA reveals marine heatwave‐associated shifts in fish assemblages

AbstractMarine heatwaves can drive large‐scale shifts in marine ecosystems, but studying their impacts on whole species assemblages is difficult. Analysis combining microscopic observations with environmental DNA (eDNA) metabarcoding of the ethanol preservative of an ichthyoplankton biorepository spanning a 23 years time series captures major and sometimes unexpected changes to fish assemblages in the California Current Large Marine Ecosystem during and after the 2014–2016 Pacific Marine Heatwave. Joint modeling efforts reveal patterns of tropicalization with increases in southern, mesopelagic species and associated declines in commercially important temperate fish species (e.g., North Pacific Hake [Merluccius productus] and Pacific Sardine [Sardinops sagax]). Data show shifts in fisheries assemblages (e.g., Northern Anchovy, Engraulis mordax) even after the return to average water temperatures, corroborating ecosystem impacts found through multiple traditional surveys of this study area. Our innovative approach of metabarcoding preservative eDNA coupled with quantitative modeling leverages the taxonomic breadth and resolution of DNA sequences combined with microscopy‐derived ichthyoplankton identification to yield higher‐resolution, species‐specific quantitative abundance estimates. This work opens the door to economically reconstruct the historical dynamics of assemblages from modern and archived samples worldwide.

Juvenile Albacore tuna (Thunnus alalunga) foraging ecology varies with environmental conditions in the California Current Large Marine Ecosystem

AbstractJuvenile North Pacific Albacore tuna (Thunnus alalunga) support commercial and recreational fisheries in the California Current Large Marine Ecosystem (CCLME), where they forage during summer and fall. The distributions of the commercial and recreational fisheries and estimates of forage availability have varied substantially over the past century. Time‐series quantifying Albacore diet can help link forage composition to variability in Albacore abundance and distribution and, consequently, their availability to fishers. Previous diet studies in the CCLME are of relatively short duration, and long‐term variability in Albacore diet remains poorly understood. We describe the diets of juvenile Albacore from three regions in the CCLME from 2007 to 2019 and use classification and regression tree analysis to explore environmental drivers of variability. Important prey include Northern Anchovy (Engraulis mordax), rockfishes (Sebastes spp.), Boreal Clubhook Squid (Onychoteuthis borealijaponica), euphausiids (Order: Euphausiidae), and amphipods (Order: Amphipoda), each contributing >5% mean proportional abundance. Most prey items were short lived species or young‐of‐the‐year smaller than 10 cm. Diet variability was related to environmental conditions over the first 6 months of the year (PDO, sea surface temperature, and NPGO) and conditions concurrent with Albacore capture (region and surface nitrate flux). We describe foraging flexibility over regional and annual scales associated with these environmental influences. Continuous, long‐term studies offer the opportunity to identify flexibility in Albacore foraging behavior and begin to make a predictive link between environmental conditions early in the year and Albacore foraging during summer and fall.

Larval rockfish growth and survival in response to anomalous ocean conditions

Understanding how future ocean conditions will affect populations of marine species is integral to predicting how climate change will impact both ecosystem function and fisheries management. Fish population dynamics are driven by variable survival of the early life stages, which are highly sensitive to environmental conditions. As global warming generates extreme ocean conditions (i.e., marine heatwaves) we can gain insight into how larval fish growth and mortality will change in warmer conditions. The California Current Large Marine Ecosystem experienced anomalous ocean warming from 2014 to 2016, creating novel conditions. We examined the otolith microstructure of juveniles of the economically and ecologically important black rockfish (Sebastes melanops) collected from 2013 to 2019 to quantify the implications of changing ocean conditions on early growth and survival. Our results demonstrated that fish growth and development were positively related to temperature, but survival to settlement was not directly related to ocean conditions. Instead, settlement had a dome-shaped relationship with growth, suggesting an optimal growth window. Our results demonstrated that the dramatic change in water temperature caused by such extreme warm water anomalies increased black rockfish growth in the larval stage; however, without sufficient prey or with high predator abundance these extreme conditions contributed to reduced survival.

Effects of ocean acidification on the early life history processes of the breadcrumb sponge Halichondria panicea

AbstractOcean acidification (OA) is predicted to result in reduced survival, growth, reproduction, and overall biodiversity of marine invertebrates, and yet we lack information about the response to OA of some major groups of marine organisms. In particular, we know relatively little about how OA will impact temperate sponges, which will experience more extreme low pH conditions than tropical species. In this study, we quantified OA‐induced changes in early life history patterns (larval mortality and condition, settlement rate, recruit survival, and size) in the non‐calcifying breadcrumb sponge Halichondria panicea collected from a temperate intertidal site in the California Current Large Marine Ecosystem. Sponge larvae were exposed to OA conditions for 15 days, and early life history patterns were observed. Compared with baseline (“present”) conditions, larval mortality and settlement rates increased in the acidified treatment (“future”). This effect was restricted to larval stages; treatment had no effect on the growth and survival of recruits. This study is significant in that it shows that H. panicea may be particularly vulnerable to changes in ocean pH during the larval stage, which could ultimately reduce total sponge abundance by diminishing the number of larvae that survive to settlement.

Vulnerability to climate change of managed stocks in the California Current large marine ecosystem

IntroductionUnderstanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes.MethodsThis study applies the NOAA (National Oceanic and Atmospheric Administration) Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions.ResultsOverall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges.DiscussionAs climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information can inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially effective to protect or restore.

Multiscale relationships between humpback whales and forage species hotspots within a large marine ecosystem.

Fluctuations in prey abundance, composition, and distribution can impact predators, and when predators and fisheries target the same species, predators become essential to ecosystem-based management. Because of the difficulty in collecting concomitant predator-prey data at appropriate scales in patchy environments, few studies have identified strong linkages between cetaceans and prey, especially across large geographic areas. During summer 2018, a line-transect survey for cetaceans and coastal pelagic species was conducted over the continental shelf and slope of British Columbia, Canada, and the US West Coast, allowing for a large-scale investigation of predator-prey spatial relationships. We report on a case study of humpback whales (Megaptera novaeangliae) and their primary prey-Pacific herring (Clupea pallasii), northern anchovy (Engraulis mordax), and krill-using generalized additive models to explore the relationships between whale abundance on 10-km transect segments and prey metrics. Prey metrics included direct measures of biomass densities on segments and an original hotspot metric. For each prey species, segments in the upper fifth percentile for biomass density (across all segments) were designated hotspots, and whale counts on a segment were evaluated for their relationship to number of hotspot segments (species-specific and multispecies) within 25, 50, or 100 km. Whale abundance was not strongly related to direct measures of biomass densities, whereas models using hotspot metrics were more effective at describing variation in whale abundance, underscoring that evaluating prey at relevant and measurable scales is critical in patchy, dynamic marine environments. Our analysis highlighted differences in the distribution and prey availability for three humpback whale distinct population segments (DPSs) as defined under the US Endangered Species Act, including threatened and endangered DPSs that forage within the California Current Large Marine Ecosystem. These linkages provide insights into which prey species whales may be targeting in different regions and across multiple scales and, consequently, how climatic variability and anthropogenic risks may differentially impact these distinct predator-prey assemblages. By identifying scale-appropriate prey hotspots that co-occur with humpback whale aggregations, and with targeted, consistent prey sampling and estimations of potential consumption rates by whales, these findings can help inform the conservation and management of humpback whales within an ecosystem-based management framework.

Marine bird mass mortality events as an indicator of the impacts of ocean warming

The frequency and severity of marine heatwaves (MHWs), an emergent property of global warming, has led to large-scale disruptions to marine ecosystems. As upper trophic species, marine birds reflect shifts in trophic structure and stability; therefore, a sharp increase in marine bird mortality is a clear signal of ecosystem impact. In this study, we analyzed 29 yr (1993-2021) of beached bird monitoring data (~90000 surveys) to identify marine bird mortality events throughout the Northeast Pacific and Alaska, USA, and examined linkages to ocean-climate variability. Mortality events were documented throughout the study period, but massive events (>500 km in extent, >10 carcasses km-1) occurred infrequently (n = 5), with an unprecedented sequence from 2014-2019. Event characteristics, including encounter rate (carcasses km-1), duration, and spatial extent, were positively related to prior-year averaged sea surface temperature anomaly, with event magnitude (product of encounter rate, extent, and duration) displaying a step-like transition, increasing 5-fold between +0°C and +1°C above baseline (1981-2010) temperatures. Mortality events occurred more frequently following MHWs, and a common sequence of mortality events (at 1-6 and 10-16 mo after heatwave onset) was observed in the California Current large marine ecosystem following 3 prolonged MHW events. Following the second wave of mortality at 10-16 mo after MHW onset, a consistent 16 mo period of depressed carcass encounter rates ensued. Given continued global warming, our results point to more frequent large-scale mortality events and the potential for a new lower carrying capacity for marine birds in the Northeast Pacific.

After Two Decades, Argo at PMEL, Looks to the Future

The NOAA Pacific Environmental Laboratory (PMEL) has contributed to the revolutionary Argo ocean observing system since its inception, developing CTD calibration algorithms and software that have been adopted by the international Argo community. PMEL has provided over 1,440 Argo floats—~13% of the global array—with ~500 currently active. PMEL scientific contributions using Argo data have ranged from regional to global analyses of ocean circulation and water-mass variability, to ocean warming and its contributions to sea level rise and Earth’s energy imbalance, to estimates of global ocean deoxygenation. In recent years, PMEL has initiated both Deep Argo (with a regional pilot array of full-ocean-depth profiling floats in the rapidly changing and dynamic western South Atlantic) and Biogeochemical (BGC) Argo (with a pilot array in the biogeochemically diverse and economically important California Current Large Marine Ecosystem). PMEL is also developing innovative near-global maps of ocean physical and biogeochemical parameters using machine learning algorithms that enable investigations of societally important oceanographic phenomena, and an Adopt-A-Float program. Future challenges include growing the financial, infrastructure, and human resources necessary to take the Deep and BGC Argo missions global and to fulfill the One Argo mission of a global, full-depth, multidisciplinary ocean observing array.

An evaluation of high-resolution ocean reanalyses in the California current system

Sparse and inconsistent coverage of ocean observations makes analysis of climate impacts on ocean physics and marine ecosystems challenging. As a result, ocean reanalyses (i.e., ocean models constrained by observations through data assimilation) were developed to provide historical ocean state estimates that are spatially and temporally uniform. Recent advances in high performance computing and the number and quality of observations have led to the development of high-resolution ocean reanalyses, which offer an opportunity to investigate coastal ocean variability with enhanced fidelity. In this study, we evaluate the ability of three high-resolution ocean reanalyses, including the Global Ocean Reanalysis and Simulations (GLORYS), the Ocean Reanalysis System version 5 (ORAS5), and the California Current System Reanalysis (CCSRA), to accurately represent ocean temperature and salinity (from the surface to the bottom), sea surface height, and mesoscale activity in the California Current Large Marine Ecosystem (CCLME). Specifically, we compare these reanalyses to a variety of assimilated and independent in situ and satellite derived observations along the U.S. west coast. We find that the reanalyses generally reproduce large-scale variability in temperature and sea surface height within the CCLME, including effects of major ENSO events and recent marine heatwaves. We also show that GLORYS and CCSRA, with their finer horizontal resolution, have enhanced fidelity in simulating nearshore ocean parameters such as coastal sea level and bottom temperature along the continental shelf. Our results suggest that these tools can be used to study the fine-scale features of the California Current System over the past several decades.

Habitat compression indices for monitoring ocean conditions and ecosystem impacts within coastal upwelling systems

Upwelling ecosystems are characterized by intense seasonal productivity that supports highly dynamic species populations, high diversity of mid and upper trophic levels, and a myriad of important fisheries. Climate variability and long-term change will impact upwelling intensity, timing and persistence, thereby potentially threatening resilience of coastal food webs and stability of ecosystem services. The spatial footprint of cool upwelled waters in the surface mixed-layer supports trophic transfer and ultimately the productivity of fisheries. The spatial area of upwelled water in eastern boundary upwelling systems can vary dramatically in response to both local and remote atmospheric forcing. These variations contribute to dynamic habitats that impact the structure, function, and spatial characteristics of marine ecosystems. We quantified the variability in “cool-water thermal habitat” area as a new ecological indicator, the Habitat Compression Index (HCI), for the nearshore (within 150 km of the coast) waters of the California Current Large Marine Ecosystem (CCLME). The HCI can be easily updated from ocean model products and satellite observations of sea surface temperature. We describe standardization of the HCI, regional variability, and evaluate HCI relationships with other indicators commonly used to inform ecosystem context within the CCLME. Importantly, our approach to calculating the HCI is easily extendable to other upwelling ecosystems. Further, we discuss the management context of the HCI such as assessing risk of whale entanglement in a highly profitable fishery, and implications for monitoring ecosystem shifts in coastal upwelling systems and the fisheries they support.

Social-ecological vulnerability of fishing communities to climate change: A U.S. West Coast case study.

Climate change is already impacting coastal communities, and ongoing and future shifts in fisheries species productivity from climate change have implications for the livelihoods and cultures of coastal communities. Harvested marine species in the California Current Large Marine Ecosystem support U.S. West Coast communities economically, socially, and culturally. Ecological vulnerability assessments exist for individual species in the California Current but ecological and human vulnerability are linked and vulnerability is expected to vary by community. Here, we present automatable, reproducible methods for assessing the vulnerability of U.S. West Coast fishing dependent communities to climate change within a social-ecological vulnerability framework. We first assessed the ecological risk of marine resources, on which fishing communities rely, to 50 years of climate change projections. We then combined this with the adaptive capacity of fishing communities, based on social indicators, to assess the potential ability of communities to cope with future changes. Specific communities (particularly in Washington state) were determined to be at risk to climate change mainly due to economic reliance on at risk marine fisheries species, like salmon, hake, or sea urchins. But, due to higher social adaptive capacity, these communities were often not found to be the most vulnerable overall. Conversely, certain communities that were not the most at risk, ecologically and economically, ranked in the category of highly vulnerable communities due to low adaptive capacity based on social indicators (particularly in Southern California). Certain communities were both ecologically at risk due to catch composition and socially vulnerable (low adaptive capacity) leading to the highest tier of vulnerability. The integration of climatic, ecological, economic, and societal data reveals that factors underlying vulnerability are variable across fishing communities on the U.S West Coast, and suggests the need to develop a variety of well-aligned strategies to adapt to the ecological impacts of climate change.

Dissimilar Sensitivities of Ocean Acidification Metrics to Anthropogenic Carbon Accumulation in the Central North Pacific Ocean and California Current Large Marine Ecosystem

AbstractWe analyze and compare changes in ocean acidification metrics caused by anthropogenic carbon (Canth) accumulation in the North Pacific Ocean and California Current Large Marine Ecosystem (CCLME). The greatest declines in pH and carbonate mineral saturation state occur near the surface, coincident with the highest Canth concentrations. However, maximal increases in the partial pressure of carbon dioxide (pCO2) and hydrogen ion concentration occur subsurface where Canth values are lower. We attribute dissimilar sensitivities of these metrics to background ocean chemistry, which has naturally high pCO2 and low buffering capacity in subsurface waters due to accumulated byproducts of organic matter respiration, which interacts with Canth. In the CCLME, rising subsurface pCO2 has increased the frequency, duration, and intensity of hypercapnia (pCO2 ≥ 1,000 μatm) on the continental shelf. Our findings suggest that hypercapnia induced by Canth accumulation can co‐occur with hypoxia in the CCLME and is an additional modern stressor for marine organisms.

Large-scale, multidecade monitoring data from kelp forest ecosystems in California and Oregon (USA).

Kelp forests are among the most productive ecosystems on Earth. In combination with their close proximity to the shore, the productivity and biodiversity of these ecosystems generate a wide range of ecosystem services including supporting (e.g., primary production, habitat), regulating (e.g., water flow, coastal erosion), provisioning (e.g., commercial and recreational fisheries), and cultural (e.g., recreational, artisanal) services. For these reasons, kelp forests have long been the target of ecological studies. However, with few exceptions, these studies have been localized and short term (<5 years). In 1999, recognizing the importance of large-scale, long-term studies for understanding the structure, functioning, and dynamics of coastal marine ecosystems, and for informing policy, the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) designed and initiated a large-scale, long-term monitoring study of kelp forest ecosystems along 1400 km of coast stretching from southern California to southern Oregon, USA. The purpose of the study has been to characterize the spatial and temporal patterns of kelp forest ecosystem structure and evaluate the relative contributions of biological and environmental variables derived from external sources (e.g., sea otter density, Chl-a concentration, sea surface temperature, wave energy) in explaining observed spatial and temporal patterns. For this purpose, the ecological community (i.e., density, percent cover, or biomass of conspicuous fishes, invertebrates, and macroalgae) and geomorphological attributes (bottom depth, substratum type, and vertical relief) of kelp forest ecosystems have been surveyed annually using SCUBA divers trained in both scientific diving and data collection techniques and the identification of kelp forest species. The study region spans distinct ecological and biogeographic provinces, which enables investigations of how variation in environmental drivers and distinctive species compositions influence community structure, and its response to climate-related environmental change across a portion of the California Current Large Marine Ecosystem. These data have been used to inform fisheries management, design and evaluate California's state-wide network of marine protected areas (MPAs), and assess the ecological consequences of climate change (e.g., marine heatwaves). Over time, the spatial and temporal design of the monitoring program was adapted to fill its role in evaluating the ecological responses to the establishment of MPAs. There are no copyright restrictions; please cite this paper when data are used.

Diverse integrated ecosystem approach overcomes pandemic-related fisheries monitoring challenges

The COVID-19 pandemic caused unprecedented cancellations of fisheries and ecosystem-assessment surveys, resulting in a recession of observations needed for management and conservation globally. This unavoidable reduction of survey data poses challenges for informing biodiversity and ecosystem functioning, developing future stock assessments of harvested species, and providing strategic advice for ecosystem-based management. We present a diversified framework involving integration of monitoring data with empirical models and simulations to inform ecosystem status within the California Current Large Marine Ecosystem. We augment trawl observations collected from a limited fisheries survey with survey effort reduction simulations, use of seabird diets as indicators of fish abundance, and krill species distribution modeling trained on past observations. This diversified approach allows for evaluation of ecosystem status during data-poor situations, especially during the COVID-19 era. The challenges to ecosystem monitoring imposed by the pandemic may be overcome by preparing for unexpected effort reduction, linking disparate ecosystem indicators, and applying new species modeling techniques.

Natal origin and age-specific egress of Pacific bluefin tuna from coastal nurseries revealed with geochemical markers

Geochemical chronologies were constructed from otoliths of adult Pacific bluefin tuna (PBT) to investigate the timing of age-specific egress of juveniles from coastal nurseries in the East China Sea or Sea of Japan to offshore waters of the Pacific Ocean. Element:Ca chronologies were developed for otolith Li, Mg, Mn, Zn, Sr, and Ba, and our assessment focused on the section of the otolith corresponding to the age-0 to age-1 + interval. Next, we applied a common time-series approach to geochemical profiles to identify divergences presumably linked to inshore-offshore migrations. Conspicuous geochemical shifts were detected during the juvenile interval for Mg:Ca, Mn:Ca, and Sr:Ca that were indicative of coastal-offshore transitions or egress generally occurring for individuals approximately 4–6 mo. old, with later departures (6 mo. or older) linked to overwintering being more limited. Changepoints in otolith Ba:Ca profiles were most common in the early age-1 period (ca. 12–16 mo.) and appear associated with entry into upwelling areas such as the California Current Large Marine Ecosystem following trans-Pacific migrations. Natal origin of PBT was also predicted using the early life portion of geochemical profile in relation to a baseline sample comprised of age-0 PBT from the two primary spawning areas in the East China Sea and Sea of Japan. Mixed-stock analysis indicated that the majority (66%) of adult PBT in our sample originated from the East China Sea, but individuals of Sea of Japan origin were also detected in the Ryukyu Archipelago.

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem.

DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597species using the MiFish 12S primers, adding 252species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.