Differential Expression of Immune Response Genes in Steller Sea Lions (\u3ci\u3eEumetopias jubatus\u3c/i\u3e): An Indicator of Ecosystem Health?

Characterization of the polygenic and polymorphic features of the Steller sea lion major histocompatibility complex (MHC) provides an ideal window for evaluating immunologic vigor of the population and identifying emergence of new genotypes that reflect ecosystem pressures. MHC genotyping can be used to measure the potential immunologic vigor of a population. However, since ecosystem-induced changes to MHC genotype can be slow to emerge, measurement of differential expression of these genes can potentially provide real-time evidence of immunologic perturbations. MHC DRB genes were cloned and sequenced using peripheral blood mononuclear leukocytes derived from 10 Steller sea lions from southeast Alaska, Prince William Sound, and the Aleutian Islands. Nine unique DRB gene sequences were represented in each of ten animals. MHC DRB gene expression was measured in a subset of six sea lions. Although DRB in genomic DNA was identical in all individuals, relative levels of expressed DRB mRNA was highly variable. Selective suppression of MHC DRB genes could be indicative of geographically disparate environmental pressures, thereby serving as an immediate and sensitive indicator of population and ecosystem health

Dryad data file.xls

Datafile containing AFLP, microsatellite and mtDNA datafiles

GOCC - Steller sea lion data

Genetic data for Steller sea lions; genotypes at 16 microsatellite loci and haplotypes at mtDNA, spatial data, and allelic and haplotypic frequencie

Environmental drivers of demography and potential factors limiting the recovery of an endangered marine top predator

Abstract Understanding what drives changes in wildlife demography is fundamental to the conservation and management of depleted or declining populations, though making inference about the intrinsic and extrinsic factors that influence survival and reproduction remains challenging. Here we use mark–resight data from 2000 to 2018 to examine the effects of environmental variability on age‐specific survival and natality for the endangered western distinct population segment (wDPS) of Steller sea lions (Eumetopias jubatus) in Alaska, USA. Though this population has been studied extensively over the last four decades, the causes of divergent abundance trends that have been observed across the wDPS range remain unknown. We developed a Bayesian multievent mark–resight model that accounts for female reproductive state uncertainty. Annual survival probabilities for male pups (0.44; 0.36–0.53), female yearlings (0.63; 0.49–0.73), and male yearlings (0.62; 0.51–0.71) born in the western portion of the wDPS range, estimated here for the first time, were lower than those in the eastern portion of the wDPS range, estimated as: male pups (0.69; 0.65–0.74), female yearlings (0.76; 0.71–0.81), and male yearlings (0.71; 0.65–0.78). There was a higher proportion of young female breeders in the western portion of the range, but overall natality was lower (0.69; 0.47–0.96) than in the eastern portion of the range (0.80; 0.74–0.84). Additionally, pup mass had a positive effect on pup survival in the eastern portion of the range and a negative effect in the western portion of the range, potentially due to earlier weaning of heavier pups. Local‐ and basin‐scale oceanographic features such as the Aleutian Low, the Arctic Oscillation Index, the North Pacific Gyre Oscillation, chlorophyll concentration, upwelling, and wind in certain seasons were correlated with vital rates. However, drawing strong inferences from these correlations is challenging given that relationships between ocean conditions and an adaptive top predator in a dynamic ecosystem are exceedingly complex. This study provides the first demographic rate estimates for the western portion of the range where abundance estimates continue to decline. These results will advance efforts to identify factors driving regionally divergent abundance trends, with implications for population‐level responses to future climate variability

Data from: Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation

Many studies use genetic markers to explore population structure and variability within species. However, only a minority use more than one type of marker and, despite increasing evidence of a strong link between heterozygosity and individual fitness, few ask whether diversity correlates with population trajectory. To address these issues, we analysed data from the Steller's sea lion, Eumetiopias jubatus, where three stocks are distributed over a vast geographic range and where both genetic samples and detailed demographic data have been collected from many diverse breeding colonies. To previously published mtDNA and microsatellite datasets we have added new data for Amplified Fragment Length Polymorphism (AFLP) markers, comprising 238 loci scored in 285 sea lions sampled from 23 natal rookeries. Genotypic diversity was low relative to most vertebrates, with only 37 loci (15.5%) being polymorphic. Moreover, contrasting geographic patterns of genetic diversity were found at the three markers, with Nei's gene diversity tending to be higher for AFLPs and microsatellites in rookeries of the western and Asian stocks, while the highest mtDNA values were found in the eastern stock. Overall, and despite strongly contrasting demographic histories, after applying phylogenetic correction we found little correlation between genetic diversity and either colony size or demography. In contrast, we were able to show a highly significant positive relationship between AFLP diversity and current population size across diverse pinniped species, even though equivalent analyses did not reveal significant trends for either microsatellites or mtDN

Data from: Crossing to safety: Dispersal, colonization and mate choice in evolutionarily distinct populations of Steller sea lions, Eumetopias jubatus.

Population growth typically involves range expansion and establishment of new breeding sites, while the opposite occurs during declines. Although density-dependence is widely invoked in theoretical studies of emigration and colonization in expanding populations, few empirical studies have documented the mechanisms. Still fewer have documented the direction and mechanisms of individual transfer in declining populations. Here we screen large numbers of pups sampled on their natal rookeries for variation in mtDNA (n=1,106) and 16 microsatellite loci (n=588) and show that new Steller sea lion breeding sites did not follow the typical paradigm and were instead colonized by sea lions from both a declining (Endangered) population and an increasing population. Dispersing individuals colonized rookeries in the distributional hiatus between two evolutionarily distinct (st = 0.222, st = 0.053, K=2) metapopulations recently described as separate subspecies. Hardy-Weinberg, mixed-stock and relatedness analysis revealed levels of interbreeding on the new rookeries that exclude (1) assortative mating among eastern and western forms, and (2) inbreeding avoidance as primary motivations for dispersal. Positive and negative density-dependence is implicated in both cases of individual transfer. Migration distance limits, and conspecific attraction and performance likely influenced the sequence of rookery colonizations. This study demonstrates that resource limitation may trigger an exodus of breeding animals from declining populations, with substantial impacts on distribution and patterns of genetic variation. It also revealed that this event is rare because colonists dispersed across an evolutionary boundary suggesting that the causative factors behind recent declines are unusual or of larger magnitude than normally occur

GOCC - stellers 130 uni haps - FASTA

Provides text sequences in FASTA format of all 130 unique Steller sea lion mtDNA haplotypes and lists their GenBank accession numbers

Steller sea lion pup plasma metabolites

<p>Geographic differences in population growth trends are well-documented in Steller sea lions (<em>Eumetopias</em> <em>jubatus</em>), a species of North Pacific pinniped listed under the U.S. Endangered Species Act in 1990 following a marked decline in population abundance that began during the 1970s. As population growth is intrinsically linked to pup production and survival, examining factors related to pup physiological condition provides useful information to management authorities regarding potential drivers of regional differences.  During dam foraging trips, pups predictably transition among three fasting phases, distinguished by the changes in the predominant metabolic byproduct. We used standardized ranges of two plasma metabolites (blood urea nitrogen and β–hydroxybutyrate) to assign pups to fasting categories (n=1528, 1990–2016, 12 subpopulations): <em>Recently Fed–Phase I</em> (digestion/assimilation–expected hepatic/muscle glycogen usage), <em>Phase II</em> (expected lipid utilization), transitioning between <em>Phases II–III</em> (expected lipid utilization with increased protein reliance), or <em>Phase III</em> (expected protein catabolism). As anticipated, the majority of pups were classified as <em>Recently Fed–Phase I </em>(overall mean proportion=0.72) and few pups as <em>Phase III</em> (overall mean proportion=0.04). By further comparing pups in Short (<em>Recently Fed–Phase II</em>) and Long (all other pups) duration fasts, we identified three subpopulations with significantly (p<0.03) greater proportions of pups dependent upon endogenous sources of energy for extended periods, during a life stage of somatic growth and development: the 1) central (0.27 ± 0.09) and 2) western (0.36 ± 0.13) Aleutian Island (declining population trend) and 3) southern Southeast Alaska (0.32 ± 0.06; increasing population trend) subpopulations had greater Long fast proportions than the eastern Aleutian Islands (0.10 ± 0.05; stabilized population).  Due to contrasting population growth trends among these highlighted subpopulations over the past 50+ years, both density-independent and density-dependent factors likely influence the dam foraging trip duration, contributing to longer fasting durations for pups at some rookeries.</p><p>Funding provided by: National Oceanic and Atmospheric Administration<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000192<br>Award Number: NA17FX1079</p><p>Funding provided by: National Oceanic and Atmospheric Administration<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000192<br>Award Number: NA04NMF439017</p><p>Funding provided by: National Oceanic and Atmospheric Administration<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000192<br>Award Number: NA87FX0111</p><p>Funding provided by: National Oceanic and Atmospheric Administration<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000192<br>Award Number: NA08NMF4390544</p><p>Funding provided by: National Oceanic and Atmospheric Administration<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000192<br>Award Number: NA11NMFS43902000</p><p>Funding provided by: University of Alaska Fairbanks<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100012574<br>Award Number: 2016/2017Crawford</p><p>Funding provided by: University of Alaska Fairbanks<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100012574<br>Award Number: 2016Crawford</p><p>Funding provided by: Ocean Peace Research Partnership*<br>Crossref Funder Registry ID: <br>Award Number: FDN21386</p><p>Funding provided by: National Oceanic and Atmospheric Administration<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000192<br>Award Number: NA90AA-D-SG066 (project no. R/08-03)</p><ol> <li>Steller sea lion pups were captured live on their natal rookeries. They were restrained physically or chemically. Blood samples were drawn from the vein of the caudal gluteal plexus into blood tubes with anticoagulants (ethylenediaminetetraacetic acid or sodium heparin). During field physical examinations, morphometrics (mass, standard length, axillary girth) and sex were recorded for most pups, as well as any observed external abnormalities. Blood samples were kept chilled in the field until centrifuging (3000–3500 rpm for ten minutes), typically within four hours of collection. Plasma aliquots were stored at -20°C during the remainder of the field research trips (3–10 days) and at -80°C thereafter (months to years, maximal interval of 8 years) following return to the laboratory.</li> <li>Plasma-derived [BUN] and [β-HBA] were measured via spectrophotometer (SpectraMax 340PC384, Molecular Devices, San Jose, CA) using commercially-available endpoint assay kits: [BUN] via StanBio Kit #2050 and Sigma Aldrich Kit #66-20 and #MAK006; [β-HBA] via StanBio Kit #2440 and Sigma Aldrich Kits #310 and #MAK001 (StanBio, EKF Diagnostics USA, Boerne, TX; Sigma Aldrich, now Millipore Sigma, St. Louis, MO). Plasma samples with moderate to severe hemolysis were not included.  Technical replicates were ≤10% coefficient of variation. Calculations of metabolite concentrations were made using Softmax Pro (v. 4.8) software or the open-access interface MyAssays.com, applying a four-parameter logistic curve. A point-of-care ketometer (Precision Xtra™, Abbott Laboratories, Abbott Park, IL, ketometer precision=0.1 mmol/L [β-HBA]) was also used. Samples measuring between 0.2–0.4 mmol/L via ketometer were further analyzed via the biochemical assay to improve precision around that threshold important to fasting category assignment (threshold=0.3mmol/L; assay precision≈0.01 mmol/L [β-HBA]). Means of the technical replicates are reported in mmol/L for each metabolite.</li> </ol&gt