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We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of single nucleotide polymoirphisms as microhaplotypes (<jats:italic>N<\/jats:italic>\u00a0=\u00a0271 samples) in addition to mitochondrial (mtDNA) sequence data (<jats:italic>N<\/jats:italic>\u00a0=\u00a0413 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\u2010by\u2010distance, suggesting that individual dispersal is restricted. We also found evidence of regions where genetic differences are larger than expected based on geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct (<jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub>\u00a0=\u00a00.02 [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 biogeographical 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\u2019 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\u2010quality samples.<\/jats:p>","DOI":"10.1111\/mec.15827","type":"journal-article","created":{"date-parts":[[2021,2,8]],"date-time":"2021-02-08T07:11:22Z","timestamp":1612768282000},"page":"1457-1476","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor\u2010quality samples"],"prefix":"10.1111","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3279-1519","authenticated-orcid":false,"given":"Phillip A.","family":"Morin","sequence":"first","affiliation":[{"name":"Southwest Fisheries Science Center National Marine Fisheries Service NOAA La Jolla CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1608-1904","authenticated-orcid":false,"given":"Brenna R.","family":"Forester","sequence":"additional","affiliation":[{"name":"Department of Biology Colorado State University Fort Collins CO USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9195-4701","authenticated-orcid":false,"given":"Karin A.","family":"Forney","sequence":"additional","affiliation":[{"name":"Southwest Fisheries Science Center National Marine Fisheries Service NOAA Moss Landing CA USA"},{"name":"Moss Landing Marine Laboratories San Jose State University Moss Landing CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carla A.","family":"Crossman","sequence":"additional","affiliation":[{"name":"Biology Department Saint Mary\u2019s University Halifax NS Canada"},{"name":"Cetacean Research Program Vancouver Aquarium Vancouver BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8532-2329","authenticated-orcid":false,"given":"Brittany L.","family":"Hancock\u2010Hanser","sequence":"additional","affiliation":[{"name":"Southwest Fisheries Science Center National Marine Fisheries Service NOAA La Jolla CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0090-8604","authenticated-orcid":false,"given":"Kelly M.","family":"Robertson","sequence":"additional","affiliation":[{"name":"Southwest Fisheries Science Center National Marine Fisheries Service NOAA La Jolla CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lance G.","family":"Barrett\u2010Lennard","sequence":"additional","affiliation":[{"name":"Cetacean Research Program Vancouver Aquarium Vancouver BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9419-6336","authenticated-orcid":false,"given":"Robin W.","family":"Baird","sequence":"additional","affiliation":[{"name":"Cascadia Research Collective Olympia WA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Calambokidis","sequence":"additional","affiliation":[{"name":"Cascadia Research Collective Olympia WA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pat","family":"Gearin","sequence":"additional","affiliation":[{"name":"Marine Mammal Laboratory Alaska Fisheries Science Center National Marine Fisheries Service NOAA Seattle WA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. 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