Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor‐quality samples

due to both the difficulty of broad-s cale sampling of many marine In contrast, demographic independence means that the population species and the limited availability of relevant environmental pre- dynamics of the affected group is more a consequence of births dictors. [...] Since the targeted SNP loci had been geno- Amplicon libraries were prepared following the GT-s eq proto- typed using two different methods, we selected the genotype data col, including the optional Exo- SAP pretreatment of the samples for each locus from the method that provided the higher quality or (Campbell et al., 2015), and pooled libraries were sequenced on an quantity of genotypes for the t. [...] The two largest pop- ulation splits are between Morro and Monterey Bays in the south, and between the Strait of Georgia and San Juan Islands in the north, where multiple methods suggest divergence in both mtDNA and nu- clear markers. [...] The third haplo- type (CR03) was distributed across most of the range, but represents a common haplotype that is more similar to CR02 (3 bp different) than to the cluster including CR01 (7 bp different) and the major- ity of the other haplotypes distributed throughout the rest of the range (see haplotype network, Figure S5). [...] Populations in the et al., 2010) or the presence of a historical phylogeographical sep- northern half of the coastal range are associated with several en- aration that has more recently reconnected, as has been suggested vironmental variables (e.g., mean and SD of the mixed layer depth, for populations in the eastern Atlantic Ocean (Fontaine, Baird, et al., and high variation in both sst and ssh),.