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 mtDNA