The genetic diversity, phylogeography, and population structure of Pacific harbor seals reveal isolation at the southern end of their distribution

The Pacific harbor seal (Phoca vitulina richardii) occurs in the Mexican
Pacific region at the southernmost edge of the subspecies’ distribution,
along 700 km of coastline and on nine islands west of the Baja California
peninsula. Its abundance corresponds to 3% of its total abundance in the
north Pacific Ocean. The species is considered relatively sedentary and
highly philopatric, which make it vulnerable to stochastic processes;
thus, reproductive and genetic isolation of the Mexican Pacific colonies
is expected. This study aimed to genetically characterize the harbor seal
in the Mexican Pacific to inform conservation efforts.  We
estimated the levels of genetic diversity for five colonies, using a
572-base pair mitochondrial DNA control region fragment and nine
microsatellite loci. We examined the population genetic structure and its
phylogeographic patterns. We found 15 variable sites that defined 18
mitochondrial DNA haplotypes. Results show one of the lowest levels of
diversity reported for the species (overall haplotype diversity h = 0.626
± SD 0.041; overall nucleotide diversity π = 0.0018 ± SD 0.0013; mean
expected heterozygosity HE = 0.537). We found a stronger genetic structure
with both markers than in the larger regions of the north Pacific, from
Alaska to California. The Pacific harbor seal colonies found in Mexico may
have their origins in northern colonies, via a founder event. We found
only four haplotypes in common with those observed (451) along the rest of
the Pacific colonies, while nine of the 14 haplotypes exclusive to the
Mexican Pacific are private.