The Liaodong Bay spotted seal (Phoca largha) population experienced several drastic declines in the last 80 years. Recent studies are contradictory regarding the level of genetic diversity and population structure of P. largha, possibly because of the use of non-species-specific nuclear markers. Here, we report on i) the first isolation and characterization of 10 species-specific polymorphic microsatellite loci for the spotted seal, ii) sequences of a 572 bp mtDNA fragment in 25 Liaodong Bay individuals that we analyzed together with all published haplotypes from Liaodong Bay and Japan. Intermediate genetic diversity in microsatellite loci was found in the Liaodong Bay population and the effective population size estimates were 41.8 to 86.8 individuals. Low mtDNA genetic variability, especially nucleotide diversity, in the Liaodong Bay population was detected, but Bayesian skyline plots did not show any evidence of recent bottleneck. Both F-statistics and the haplotypic network indicate a clear differentiation between the Liaodong Bay and Japanese populations separated by a fixed mutation. Analysis of mtDNA data indicates that Liaodong Bay female seals show fidelity to their breeding site, and breeding time data suggest that this population is reproductively isolated from populations in other breeding areas. The observed low genetic diversity in mtDNA and the intermediate levels of nuclear microsatellite diversity, combined with the potential genetic isolation, suggest that the Liaodong Bay population might be at risk and that further investigation of the population genetics of spotted seals across their whole range is warranted for proper management of the species.
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