A panel of new microsatellite loci for genetic studies of antarctic fur seals and other otariids

Hoffman, Joseph I.

doi:10.1007/s10592-008-9669-z

Cited by 14 publications

(8 citation statements)

References 18 publications

(17 reference statements)

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“…online early). The proven ability of microsatellites isolated from fur seals and sea lions to cross‐amplify across the Pinnipedia (Hoffman 2007; Hoffman et al. 2007b) could also potentially be exploited to allow comparative analyses.…”

Section: Resultsmentioning

confidence: 99%

“…On the one hand, microsatellites tend to be more informative than SNPs, making them well suited to detecting further associations between genotype and fitness (Amos et al online early). The proven ability of microsatellites isolated from fur seals and sea lions to cross-amplify across the Pinnipedia (Hoffman 2007;Hoffman et al 2007b) could also potentially be exploited to allow comparative analyses. However, microsatellite genotyping is labour intensive and careful scrutiny is required to minimize the impact of (a) (b) Fig.…”

Section: Molecular Marker Discoverymentioning

confidence: 99%

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Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome

Hoffman

2011

Molecular Ecology Resources

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Next-generation sequencing provides a powerful new approach for developing functional genomic tools for nonmodel species, helping to narrow the gap between studies of model organisms and those of natural populations. Consequently, massively parallel 454 sequencing was used to characterize a normalized cDNA library derived from skin biopsy samples of twelve Antarctic fur seal (Arctocephalus gazella) individuals. Over 412 Mb of sequence data were generated, comprising 1.4 million reads of average length 286 bp. De novo assembly using Newbler 2.3 yielded 156 contigs plus 22 869 isotigs, which in turn clustered into 18,576 isogroups. Almost half of the assembled transcript sequences showed significant similarity to the nr database, revealing a functionally diverse array of genes. Moreover, 97.9% of these mapped to the dog (Canis lupis familiaris) genome, with a strong positive relationship between the number of sequences locating to a given chromosome and the length of that chromosome in the dog indicating a broad genomic distribution. Average depth of coverage was also almost 20-fold, sufficient to detect several thousand putative microsatellite loci and single nucleotide polymorphisms. This study constitutes an important step towards developing genomic resources with which to address consequential questions in pinniped ecology and evolution. It also supports an earlier but smaller study showing that skin tissue can be a rich source of expressed genes, with important implications for studying the genomics not only of marine mammals, but also more generally of species that cannot be destructively sampled.

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Section: Resultsmentioning

confidence: 99%

Section: Molecular Marker Discoverymentioning

confidence: 99%

Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome

Hoffman

2011

Molecular Ecology Resources

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“…(2003); 12, Hoffman et al . (2008); 13, Hoffman (online early); 14, Hoffman, unpublished data; 15, Campbell (2003); 16, Hernandez‐Velazquez et al . (2005); 17, Maldonado et al .…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2009

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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 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 geographical range and where both genetic samples and detailed demographic data have been collected from many diverse breeding colonies. To previously published mitochondrial DNA (mtDNA) and microsatellite data sets, 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 geographical 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 a range of pinniped species, even though equivalent analyses did not reveal significant trends for either microsatellites or mtDNA.

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“…None of these remained significant following table-wide FDR correction for multiple statistical tests. locus Mastermix reference N a A e H E H O null allele frequency HWE p -value Ag-7 3 [ 27 ] 6 2.40 0.59 0.56 0.00018 0.046 Ag-1 3 [ 27 ] 6 3.12 0.69 0.64 0.02267 0.196 Agaz-10 4 [ 28 ] 8 4.35 0.77 0.78 0.00003 0.411 Agaz-1 4 [ 28 ] 14 6.19 0.84 0.83 0.00669 0.233 Hg1.3 1 [ 29 ] 8 4.91 0.80 0.77 0.00827 0.547 Hg6.3 ...…”

Section: Methodsmentioning

confidence: 99%

Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

Hoffman

Kowalski

Klimova³

et al. 2016

R. Soc. open sci.

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Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.

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A panel of new microsatellite loci for genetic studies of antarctic fur seals and other otariids

Cited by 14 publications

References 18 publications

Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome

Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome

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

Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

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