Dataset Information

The Genome of the Steller Sea Lion (Eumetopias jubatus).

ABSTRACT: The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabases. As a measure of completeness, 95.1% of 4104 highly conserved mammalian genes were found to be complete within the assembly. Further annotation identified 19,668 protein coding genes. The assembled genome sequence and underlying sequence data can be found at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA475770.

SUBMITTER: Kwan HH

PROVIDER: S-EPMC6678222 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Publications

The Genome of the Steller Sea Lion (<i>Eumetopias jubatus</i>).

Kwan Harwood H HH Culibrk Luka L Taylor Gregory A GA Leelakumari Sreeja S Tan Ryan R Jackman Shaun D SD Tse Kane K MacLeod Tina T Cheng Dean D Chuah Eric E Kirk Heather H Pandoh Pawan P Carlsen Rebecca R Zhao Yongjun Y Mungall Andrew J AJ Moore Richard R Birol Inanc I Marra Marco A MA Rosen David A S DAS Haulena Martin M Jones Steven J M SJM

Genes 20190626 7

The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabase ...[more]

PMID: 31248052

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Project description:BackgroundA utilization distribution quantifies the temporal and spatial probability of space use for individuals or populations. These patterns in movement arise from individuals' internal state and from their response to the external environment, and thus can provide insights for assessing factors associated with the management of threatened populations. The Western Distinct Population Segment of the Steller sea lion (Eumetopias jubatus) has declined to approximately 20% of levels encountered 40 years ago. At the height of the decline, juvenile survival appeared to be depressed and currently there is evidence that juvenile mortality due to predation may be constraining recovery in some regions. Therefore, our objectives were to identify what spaces are biologically important to juvenile Steller sea lions in the Kenai Fjords and Prince William Sound regions of the Gulf of Alaska.MethodsWe examined geospatial location data from juvenile sea lions tagged between 2000 and 2014 (n = 84) and derived individual and pooled-population utilization distributions (UDs) from their movements. Core areas were defined from the UDs using an individual-based approach; this quantitatively confirmed that all individuals in our sample exhibited concentrated use within their home range (95% UD). Finally, we explored if variation in UD characteristics were associated with sex, season, age, or region.ResultsWe found evidence that individual juvenile home ranges were region and sex-specific, with males having larger home ranges on average. Core space characteristics were also sex-specific, and exhibited seasonal patterns of reduced size, increased proximity to haulouts, and increased intensity of use in the summer, but only in the Kenai Fjords-Gulf of Alaska region.ConclusionsThis study highlights the areas of biological importance during this vulnerable life history stage, and the demographic, seasonal, and spatial factors associated with variation in movement patterns for a marine mesopredator. This can be useful information for promoting species recovery, and for future efforts to understand ecological patterns such as predator-prey interactions.

Project description:The two stocks of Steller sea lions (Eumetopias jubatus) in Alaska include an endangered western stock, recently recovering in parts of its range following decades of decline, and an eastern stock which was removed from the U.S. Endangered Species List in 2013 following increasing numbers since the 1970s. Information on overlapping distributions of eastern and western sea lions is needed for management considerations. We analyzed >30,000 sightings collected from 2000-2014 of 2,385 sea lions that were branded as pups at 10 Alaskan rookeries to examine mesoscale (mostly <500km) spatial distribution, geographic range, and geographic population structure based on natal rookery, sex, and age during breeding and non-breeding seasons. Analyses of summary movement measures (e.g., natal rookery, sex, and age-class differences in spatial distribution and geographic range) indicate wide variation in rookery-specific movement patterns. Correlations between movement measures and population dynamics suggested movement patterns could be a function of density dependence. Animals from larger rookeries, and rookeries with slower population growth and lower survival, had wider dispersion than animals from smaller rookeries, or rookeries with high growth and survival. Sea lions from the largest rookery, Forrester Island, where survival and population trends are lowest, were the most widely distributed. Analysis of geographic population structure indicated that animals born in the eastern Aleutian Islands had the most distinct movements and had little overlap with other western sea lions. Northern Southeast Alaska, within the eastern stock, is the area of greatest overlap between stocks, and is important to western animals, especially those born in Prince William Sound. Detailed knowledge of distribution and movements of western sea lions is useful for defining recovery and population trend analysis regions that better reflect dispersion and population structure and provides valuable information to managers as critical habitat is re-evaluated and the location of the stock boundary reconsidered.

Project description:Two novel research approaches were developed to facilitate controlled access to, and long-term monitoring of, juvenile Steller sea lions for periods longer than typically afforded by traditional fieldwork. The Transient Juvenile Steller sea lion Project at the Alaska SeaLife Center facilitated nutritional, physiological, and behavioral studies on the platform of temporary captivity. Temporarily captive sea lions (TJs, n = 35) were studied, and were intraperitoneally implanted with Life History Transmitters (LHX tags) to determine causes of mortality post-release. Our goal was to evaluate the potential for long-term impacts of temporary captivity and telemetry implants on the survival of study individuals. A simple open-population Cormack-Jolly-Seber mark-recapture model was built in program MARK, incorporating resightings of uniquely branded study individuals gathered by several contributing institutions. A priori models were developed to weigh the evidence of effects of experimental treatment on survival with covariates of sex, age, capture age, cohort, and age class. We compared survival of experimental treatment to a control group of n = 27 free-ranging animals (FRs) that were sampled during capture events and immediately released. Sex has previously been show to differentially affect juvenile survival in Steller sea lions. Therefore, sex was included in all models to account for unbalanced sex ratios within the experimental group. Considerable support was identified for the effects of sex, accounting for over 71% of total weight for all a priori models with delta AICc <5, and over 91% of model weight after removal of pretending variables. Overall, most support was found for the most parsimonious model based on sex and excluding experimental treatment. Models including experimental treatment were not supported after post-hoc considerations of model selection criteria. However, given the limited sample size, alternate models including effects of experimental treatments remain possible and effects may yet become apparent in larger sample sizes.

Project description:Entanglements affect marine mammal species around the globe, and for some, those impacts are great enough to cause population declines. This study aimed to document rates and causes of entanglement and trends in local haulout abundance for Steller and California sea lions on the north coast of Washington from 2010-2018. We conducted small boat surveys to count sea lions and document entangled individuals. Rates of entanglement and entangling material occurrence were compared with records of stranded individuals on the Washington and Oregon coast and with packing bands recorded during beach debris surveys. The rate of entanglement for California sea lions was 2.13%, almost entirely composed of adult males, with a peak rate during June and July potentially due to some entangled individuals not migrating to their breeding grounds. For Steller sea lions, the rate of entanglement was 0.41%, composed of 77% adults (32.4% male, 63.3% female), 17.1% juveniles, 5.9% unknown age, and no pups. Steller sea lions exhibited a 7.9% ± 3.2 rate of increase in abundance at the study haulouts, which was similar to that seen in California sea lions (7.8% ± 4.2); both increases were greater than the population growth rates observed range-wide despite high rates of entanglement. Most entanglements for both species were classified as packing bands, followed by entanglement scars. Salmon flashers were also prevalent and only occurred from June-September during the local ocean salmon troll fishery. Packing band occurrence in beach debris surveys correlated with packing band entanglements observed on haulouts. However, no packing band entanglements were observed in the stranding record and the rate of stranded animals exhibiting evidence of entanglement was lower than expected, indicating that entanglement survival is higher than previously assumed. Future studies tracking individual entanglement outcomes are needed to develop effective, targeted management strategies.

Dataset Information

The Genome of the Steller Sea Lion (Eumetopias jubatus).

Publications

The Genome of the Steller Sea Lion (<i>Eumetopias jubatus</i>).

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