Brice X. Semmens

Legacy contaminants (DDX and PCBs) persist in fishes of the Southern California Bight, yet most consumption advisories rely on species- and region-level averages that ignore within-species variation among harvested individuals. We evaluated whether individual traits improve prediction of contaminant burden in a ”fish in hand,” and whether any gains can be achieved using information available to anglers at capture (e.g., size, region) versus traits requiring post-hoc laboratory analysis (e.g., age, stable-isotope–inferred trophic ecology). Using individually sampled, angler-caught fish collected across the Southern California Bight with associated metadata, we compared five nested predictive frameworks of increasing complexity, from species alone to models adding region, angler-measurable traits (length, lifestyle), spatially explicit sediment-contamination estimates, and laboratory-derived age and trophic-isotope metrics. Region — when informed by underlying sediment contaminant burden maps — substantially improved predictions of individual contaminant concentrations, whereas fish length contributed little additional predictive power. Among laboratory-assessed traits, isotope-derived trophic ecology provided the largest improvement, but gains were modest relative to location-based models. Overall, our results indicate limited potential for individual traits beyond catch location to meaningfully refine advisories, and support place-based guidance that leverages spatial contaminant prediction tools to inform safer consumption of recreationally caught fish.

Environmental DNA (eDNA) is an emerging tool for surveying marine organisms. Advances in molecular assay designs and bioinformatic methods provide new opportunities for detecting rare species; however, overcoming methodological challenges of rare species detection remains an important obstacle for the widespread deployment of eDNA methods for biomonitoring. Here, we provide a rigorous evaluation of eDNA sampling and processing methods to optimize eDNA capture and detection of a rare delphinid species. We applied a hierarchical Bayesian occupancy model to separate the effects of presence, capture and detection of target eDNA from Delphinus delphis and its two associated subspecies. We used a highly replicated sampling effort in the California Current Ecosystem to assess (1) the effect of water depth on the probability of D. delphis eDNA presence, (2) the effects of filtered water volume and filtration method on the likelihood of capturing D. delphis eDNA given its presence and (3) the effect of primer choice on the probability of D. delphis eDNA detection given its capture. Our results show that D. delphis eDNA is most likely to occur in surface (0–10 m) waters, and that large volume (>4 L) sampling increased the probability of capturing D. delphis eDNA on a filter. Moreover, the use of primers designed for cetaceans increased detection probabilities relative to more general primers designed for vertebrates. Our intensive replication in field sampling and laboratory assays and subsequent hierarchical modelling indicates that D. delphis eDNA was present in 90% of surface samples. Yet, since it makes up a tiny fraction of the ambient DNA pool, reliable detection requires optimized experimental design at both the sampling and processing stages. The modelling approach applied here provides an experimental design framework for eDNA studies focused on capturing rare targets. We use the results of this application to provide specific guidance on optimal experimental design for detection of delphinid eDNA.

Environmental DNA (eDNA) marker gene sequencing, or metabarcoding, can be a powerful tool for monitoring marine biodiversity. Traditional eDNA sampling methods involve manual water collection and active filtration to collect DNA. This process can be laborious and require expensive filtration equipment. To explore the possibility of making eDNA a more accessible tool, we investigated the efficacy of passive eDNA capture during citizen science SCUBA diving in the Gulf of California, Mexico. Rather than actively collecting and filtering water samples, filters that passively collected eDNA from seawater were attached to citizen scientist divers as they carried out visual surveys on fish species. eDNA metabarcoding from these filters was amplified using MiFish primers (12S rRNA gene) and sequenced to assess fish community composition and compare to visual surveys. We also investigated marine mammal detection with mitochondrial D‐loop metabarcoding primers on some of the samples. Sequencing results initially yielded 64 fish species, compared to 183 fish species observed by the divers, and shared similar biogeographic assemblage patterns. However, 95 visually observed species lacked publicly available reference sequences. To address this, we generated reference sequences for 64 fish species vouchers obtained from the Scripps Institution of Oceanography Marine Vertebrate Collection. Dedicated barcoding efforts yielded eDNA detections of 15 additional species. We discuss the relative advantages and disadvantages of this passive eDNA collection method for marine fish detection. Marine mammal sequencing results only yielded 3 species; however, one was the Guadalupe fur seal, a threatened species, which highlights the potential of eDNA for rare or threatened marine mammal detection. Our results suggest that passive capture of eDNA can be used as a tool for citizen scientists to supplement visual surveys for marine species detection and is particularly useful for species that are rare or visually inaccessible to divers.

Passive acoustic monitoring is a cost‐effective, minimally invasive technology commonly used to study behavior and population dynamics of soniferous fish species. To understand the strengths and limitations of acoustic monitoring for this purpose at fish spawning aggregations (FSA) requires an assessment of the variability in aggregation‐associated sounds (AAS) as a function of time, space, and proximity for spawning fishes of interest. Here, we evaluate temporal and spatial trends in the detection of AAS by Nassau Grouper ( Epinephelus striatus ) using an array of six hydrophones deployed across a large Nassau Grouper FSA at Little Cayman, Cayman Islands. We collected continuous data for nine days during a winter spawning season and subsequently used an automatic classifier to extract the embedded Nassau Grouper AAS. Using these data, we analyzed variability in spatiotemporal AAS detection rates across the array with a Bayesian mixed effects model. We found high variability in the detection of AAS across the spawning site, with positive correlations among neighboring hydrophone pairs trending toward negative correlations with distances exceeding 350 m. Indeed, temporal trends in AAS rates at the spawning site were approximately inverted at the two most distant hydrophones (~600 m). Across the hydrophone network, our model predicted strong positive effects of fish proximity, spawning behavior, and crepuscular periods on detected AAS. Our findings suggest hydrophone placement can strongly influence AAS detection rates and even basic temporal patterns in AAS across the spawning season. Given both the vagaries of movement and behavior of aggregating fish at spawning sites and the limits of AAS detection using standard monitoring tools, we suggest spawning site acoustic monitoring programs deploy hydrophone arrays of sufficient size to capture the site‐wide trends in AAS rates if possible; this is particularly true if researchers hope to compare/contrast AAS rates between spawning sites or across seasons for the purpose of population assessment.

The Silky Shark (Carcharhinus falciformis) is highly vulnerable to population decline, yet leads shark bycatch in some of the world’s largest tuna fisheries. As such, this species provides an appropriate case study for regional fisheries management organizations—exemplified by the Inter-American Tropical Tuna Commission—to develop conceptual population assessment frameworks that integrate diverse data streams to elucidate population structure and dynamics of assessed species. Using genetic, movement, life history, and small- and large-scale fishery-dependent data from across much of the Silky Shark’s Pacific Ocean range, we found preliminary evidence for a three-stock model—southern, central, and northern—in the eastern Pacific Ocean (EPO). Length distributions of Silky Sharks varied with latitude and across fishery gears and strategies. The predominance of small juveniles, including neonates, caught on or near the continental shelf by small-scale fisheries and offshore by purse seines set on floating objects, including fish aggregating devices, suggested that Silky Sharks use both shelf-edge habitats and offshore areas as pupping and/or nursery areas. Finally, we showed that sex ratios favored females in oceanic and equatorial zones, where most Silky Shark bycatch in large-scale fisheries occurs. Our study serves as a roadmap to comprehensively understand spatial population dynamics of common bycatch species lacking a dispersive larval phase, such as elasmobranchs, by integrating genetic, biological, ecological, and fisheries data. Specifically, our work can inform stock assessments and management measures that may improve Silky Shark conservation in the EPO and elsewhere.

R: Objective: Early life success of fishes is considered one of the most important drivers of recruitment to adult populations, and elucidating the governing mechanisms is important for management efforts. Many hypotheses over the past century have been proposed to explain recruitment fluctuation, with the recently postulated Trophic Efficiency in Early Life (TEEL) hypothesis arguing that a shorter food chain length equals greater energy transfer efficiency from primary producers to larval fishes, thereby reducing early-life mortality and ultimately leading to stronger recruitment. Under TEEL it would then be assumed that feeding low in the food chain would improve growth and body condition, as these are often shown to be associated with increased survival in larval fishes. The objective of this study was to test this aspect of the TEEL hypothesis by quantifying condition, growth, and trophic level of larval Shortbelly Rockfish Sebastes jordani collected by the California Cooperative Oceanic Fisheries Investigations program and archived at the Ichthyoplankton Collection. Methods: The trophic level on larval Shortbelly Rockfish was assessed with compound-specific isotopic analysis of amino acids. Their size at age and survival were estimated with otolith microstructure. Their diet was examined through stomach content analysis. Result: Observations indicate that larvae consuming prey at a lower trophic level have greater body weight and exhibit faster growth rates. However, feeding at a lower trophic level did not influence body length. The ingested prey responsible for the lower trophic level within larval rockfish could not be determined. Conclusion: Larval Shortbelly Rockfish consuming prey at a lower trophic level garnered greater body weight and exhibited faster growth rates and provides support for the TEEL hypothesis. However, further research is needed to identify the preferred prey(s) responsible for the more efficient energy transfer.

Globally, ocean dumping of chemical waste is a common method of disposal and relies on the assumption that dilution, diffusion, and dispersion at ocean scales will mitigate human exposure and ecosystem impacts. In southern California, extensive dumping of agrochemical waste, particularly chlorinated hydrocarbon contaminants such as DDT, via sewage outfalls and permitted offshore barging occurred for most of the last century. This study compiled a database of existing sediment and fish DDT measurements to examine how this unique legacy of regional ocean disposal translates into the contemporary contamination of the coastal ocean. We used spatiotemporal modeling to derive continuous estimates of sediment DDT contamination and show that the spatial signature of disposal (i.e., high loadings near historic dumping sites) is highly conserved in sediments. Moreover, we demonstrate that the proximity of fish to areas of high sediment loadings explained over half of the variation in fish DDT concentrations. The relationship between sediment and fish contamination was mediated by ecological predictors (e.g., species, trophic ecology, habitat use), and the relative influence of each predictor was context-dependent, with habitat exhibiting greater importance in heavily contaminated areas. Thus, despite more than half a century since the cessation of industrial dumping in the region, local ecosystem contamination continues to mirror the spatial legacy of dumping, suggesting that sediment can serve as a robust predictor of fish contamination, and general ecological characteristics offer a predictive framework for unmeasured species or locations.

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380–1800 mL) collected at depths of 0–2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.

Feeding success and maternal effects on larval size have long been hypothesized as important contributors to interannual recruitment variability in marine fishes. This study examined the feeding ecology and influences of diet and size-at-birth on length and growth of larval rockfishes ( Sebastes spp.). Prey carbon biomass and selection were calculated from gut contents, size-at-birth was estimated using otolith core size, and recent growth was derived from outer otolith increment widths. Biomass contributions of preferred prey and otolith data were integrated into Bayesian hierarchical models predicting length and growth. Larvae primarily fed on and selected for copepod nauplii and Calanoid copepodites, modulating feeding with ontogeny and in response to prey availability. Based on carbon weight, the relative contribution of Calanoid copepodites to the diet was more strongly and positively correlated with length and growth than that of nauplii. Younger larvae experienced faster growth in association with Calanoid copepodite consumption than older larvae. Positive effects of core radius suggest that initial larval size, believed to be mediated by maternal provisioning, increases the likelihood of survival, larger size and faster growth. These findings ultimately provide evidence that selective feeding and size-at-birth mediate rockfish survival in early life stages.

A variety of criteria may influence the efficacy of networks of marine protected areas (MPA) designed to enhance biodiversity conservation and provide fisheries benefits. Meta‐analyses have evaluated the influence of MPA attributes on abundance, biomass, and size structure of harvested species, reporting that MPA size, age, depth, and connectivity influence the strength of MPA responses. However, few empirical MPA evaluation studies have used consistent sampling methodology across multiple MPAs and years. Our collaborative fisheries research program systematically sampled 12 no‐take or highly protective limited‐take MPAs and paired fished reference areas across a network spanning 1100 km of coastline to evaluate the factors driving MPA efficacy across a large geographic region. We found that increased size and age consistently contributed to increased fish catch, biomass, and positive species responses inside MPAs, while accounting for factors such as latitude, primary productivity, and distance to the nearest MPA. Our study provides a model framework to collaboratively engage diverse stakeholders in fisheries research and provide high‐quality data to assess the success of conservation strategies.