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Scholarly Works (4 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2022)

Tuna purse seine vessels fishing for Thunnus albacares was a cause for significant incidental bycatch of dolphins and subsequent depletion of their populations in the Eastern Tropical Pacific (ETP) in the 1960s and 1970s, until the establishment of the United States Marine Mammal Protection Act (US MMPA) in 1972. Some of the most heavily affected species are spotted dolphins (Stenella attenuata), the abundances of which have been estimated to have been reduced by up to one-fifth of their size. Despite a marked decrease in dolphin mortality and incidental take post implementation of the US MMPA, populations have not been recovering at expected rates. One hypothesis for this is that repeated chase, encirclement, and release by purse seiners affects reproduction or population growth rates in ways other than directly observed mortality. Since these effects are related to how often a given dolphin is likely to interact with the fishery and the fishery is more likely to target large schools that carry large amounts of tuna, it is imperative to understand how schools of pelagic dolphins arrange themselves in the ETP. This study uses data from the Stenella Abundance Research Line Transect and Ecosystem (STAR-LITE) cruise from 2007 to determine how schools of different sizes are arrayed in space and time. We then illustrate how these results can improve estimates of indirect effects of purse seine fishing on the recovery of these depleted populations.

    Cover page: Temporal and Spatial Variability of Pantropical Spotted Dolphin (Stenella attenuata) Group Size in the Eastern Tropical Pacific
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2023)
    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.
      Cover page: The genomic footprint of whaling and isolation in fin whale populations.
      • Article
      UC San Francisco Previously Published Works (2020)
      AbstractThe vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.
        Creative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2021)
        The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.
          Creative Commons 'BY-NC-ND' version 4.0 license
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