Dovi Kacev’s research while affiliated with University of California, San Diego and other places

Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve the monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding the application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non-annual breeding dynamics are present, or if year-specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long-lived data-limited species.

Marine 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. K E Y W O R D S amplicon sequencing, CalCOFI, California Current Ecosystem, eDNA, ichthyoplankton, joint model, marine heatwave, quantitative metabarcoding

On September 11, 2022, two megamouth sharks ( Megachasma pelagios ), estimated at 3.7–4.6 m TL, were observed swimming together near the surface about 39 km off the coast of San Diego, CA, USA. Megamouth sharks are rarely observed pelagic sharks, and the film from this encounter provided new insight into the social behavior of this species. We attempt to put the behavior of these two individuals into the context of past sightings, known megamouth shark biology, and with analogous behavior observed in other shark and pelagic fish species.

Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that have been challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and sampling strategy affect the accuracy and precision of CKMR parameter estimates, and present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a relatively simple CKMR model produces robust estimates of population abundance when key assumptions including annual breeding and stable population size are met; however, if strong population declines or non-annual breeding dynamics are present, a more complex CKMR model must be constructed to avoid biased parameter estimates. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed. Finally, we apply our adapted CKMR model to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas to demonstrate how juvenile-focused CKMR can be used to expand monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, and provides recommendations for sampling design and model construction that can aid biologists in planning and implementing an effective CKMR experiment, particularly for long-lived data-limited species.

The zebrafish lateral line is an established model for hair cell organ damage, yet few studies link mechanistic disruptions to changes in biologically relevant behavior. We used larval zebrafish to determine how damage via ototoxic compounds impact rheotaxis. Larvae were treated with CuSO 4 or neomycin to disrupt lateral line function then exposed to water flow stimuli. Their swimming behavior was recorded on video then DeepLabCut and SimBA software were used to track movements and classify rheotaxis behavior, respectively. Lateral line-disrupted fish performed rheotaxis, but they swam greater distances, for shorter durations, and with greater angular variance than controls. Furthermore, spectral decomposition analyses confirmed that lesioned fish exhibited ototoxic compound-specific behavioral profiles with distinct changes in the magnitude, frequency, and cross-correlation between fluctuations in linear and angular movements. Our observations demonstrate that lateral line input is needed for fish to hold their station in flow efficiently and reveals that commonly used lesion methods have unique effects on rheotaxis behavior.

Marine heatwaves can drive large-scale shifts in marine ecosystems but studying their impacts on whole species assemblages can be difficult. Here, we leverage the taxonomic breadth and resolution of DNA sequences derived from environmental DNA (eDNA) in the ethanol of a set of 23-year longitudinal ichthyoplankton samples, combining these with microscopy-derived ichthyoplankton identification to yield higher-resolution, species-specific quantitative abundance estimates of fish assemblages in the California Current Large Marine Ecosystem during and after the 2014–16 Pacific marine heatwave. This integrated dataset reveals patterns of tropicalization with increases in southern, mesopelagic species and associated declines in important temperate fisheries targets (e.g., North Pacific Hake ( Merluccius productus ) and Pacific Sardine ( Sardinops sagax )). We observed novel assemblages of southern, mesopelagic fishes and temperate species (e.g., Northern Anchovy, Engraulis mordax ) even after the return to average water temperatures. Our innovative preservative derived eDNA metabarcoding and quantitative modeling approaches open the door to reconstructing the historical dynamics of assemblages from modern and archived samples worldwide. Summary Novel quantitative abundance estimates from archived DNA reveals marine heatwave-associated shifts in fish assemblages.

The 2014-2016 Northeast Pacific marine heatwave (MHW) induced the warmest 3-year period on record in the California Current Ecosystem. We tested whether lar-val fish assemblage structure, phenology, and diversity dynamics were comparable to past warming events from 1951 to 2013. First, we hypothesized, based on past observations of biological effect of warming, that mesopelagic species with southern distributions relative to southern California and Pacific sardine Sardinops sagax (a coastal pelagic species) would increase during the MHW while northern mesopelagics and northern anchovy Engraulis mordax (coastal pelagic) abundances would decline. Similar to past warming, southern mesopelagics increased and northern mesopelag-ics decreased. Unexpectedly, however, a common southern mesopelagic, Mexican lampfish Triphoturus mexicanus, was approximately three times more abundant than the previous annual high. Furthermore, whereas sardine abundance did not increase, larval anchovy abundance rose to near-record highs in summer 2016. Second, we hypothesized that fishes would spawn earlier during the MHW. Fishes did not spawn in an earlier season within a year, but five of six southern mesopelagic taxa spawned earlier than typical within winter and spring. Third, we predicted that species richness would increase moderately due to an influx of southern and exodus of northern species. Richness, however, was very high in all seasons and the highest ever during the summer as multiple species with primarily southern distributions were recorded spawning for the first time in southern California. The richness of northern species was also unexpectedly high during the MHW. Northern species likely persisted in the study area because in addition to the warm water, pockets of cold water were consistently present. If, as predicted, conditions similar to the MHW become more common as oceans warm, this unique and largely unexpected combination of fishes may reflect future biological conditions.

Zebrafish lateral line is an established model for hair cell organ damage, yet few studies link mechanistic disruptions to changes in biologically relevant behavior. We used larval zebrafish to determine how damage via ototoxic chemicals impact rheotaxis. Larvae were treated with CuSO4 or neomycin to disrupt lateral line function then exposed to water flow stimuli. Their swimming behavior was recorded, and DeepLabCut and SimBA software were used to track movements and classify rheotaxis behavior. Lateral line-disrupted fish performed rheotaxis, but they swam greater distances, for shorter durations, and with greater angular variance than controls. Further, spectral decomposition analyses demonstrated that lesioned fish exhibited toxin-specific behavioral profiles with distinct fluctuations in the magnitude, timing, and cross-correlation between changes in linear and angular movements. Our observations support that lateral-line input is needed for fish to perform rheotaxis efficiently in flow and reveals commonly used lesion methods have unique effects on behavior.