North Pacific harbor porpoise SNP and microhaplotype genotypes, mitochondrial control region haplotype sequences

Harbor porpoises in the North Pacific are found in coastal waters from
southern California to Japan, but population structure is poorly known
outside of a few local areas. We used multiplexed amplicon sequencing of
292 loci and genotyped clusters of SNPs as microhaplotypes (N=271 samples)
in addition to mtDNA sequence data (N=413 samples), to examine the genetic
structure from samples collected along the Pacific coast and inland
waterways from California to southern British Columbia. We confirmed an
overall pattern of strong isolation-by-distance, suggesting that
individual dispersal is restricted. We also found evidence of regions
where genetic differences are larger than expected based on geographic
distance alone, implying current or historical barriers to gene flow. In
particular, the southernmost population in California is genetically
distinct (FST = 0.02 (microhaplotypes); 0.31 (mtDNA)), with both reduced
genetic variability and high frequency of an otherwise rare mtDNA
haplotype. At the northern end of our study range, we found significant
genetic differentiation of samples from the Strait of Georgia, previously
identified as a potential biogeographic boundary or secondary contact zone
between harbor porpoise populations. Association of microhaplotypes with
remotely-sensed environmental variables indicated potential local
adaptation, especially at the southern end of the species’ range. These
results inform conservation and management for this nearshore species,
illustrate the value of genomic methods for detecting patterns of genetic
structure within a continuously distributed marine species, and highlight
the power of microhaplotype genotyping for detecting genetic structure in
harbor porpoises despite reliance on poor-quality samples.