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 in this area corresponds to 3% of its total abundance in the north Pacific Ocean. The species is considered relatively sedentary and highly philopatric, which makes 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. The levels of genetic diversity were estimated for five colonies, using a 572-base pair mitochondrial DNA control region fragment and seven microsatellite loci, as well as the population genetic structure and its phylogeographic patterns. Fifteen variable sites were found 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 = 0.558). Population structure was detected within the range of harbor seals in the Mexican Pacific based on both mitochondrial and nuclear markers. The present study identified higher levels of differentiation (ΦST = 0.043–0.471) among colonies of Mexican Pacific harbor seals located in a relatively small area than that identified by other studies carried out in colonies along the eastern Pacific coast. There were only four haplotypes in common with those observed (451) along the rest of the Pacific colonies, while 11 of the remaining 14 haplotypes in the Mexican Pacific are private of a colony. The Pacific harbor seal colonies found in Mexico may have their origins in California, USA, colonies, via a founder event.