Harbor porpoise 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 single nucleotide polymoirphisms as microhaplotypes (N = 271 samples) in addition to mitochondrial (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 geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct (F_ST = 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 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’ 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.

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基于源自劣质样品的微单倍型的连续分布的沿海海洋物种港口海豚的种群结构

北太平洋的海豚在从加利福尼亚南部到日本的沿海水域中都可以发现，但是在一些当地地区以外的人口结构却鲜为人知。我们使用多路复用扩增子292位点测序和基因分型单核苷酸polymoirphisms的簇microhaplotypes（Ñ 除了线粒体（线粒体DNA）序列数据= 271个样本）（Ñ = 413个样本）以检查从沿太平洋海岸和加利福尼亚至不列颠哥伦比亚省南部的内陆水道收集的样本的遗传结构。我们确认了强距离隔离的总体模式，这表明个人分散受到限制。我们还发现仅基于地理距离就存在遗传差异大于预期的区域的证据，这暗示了当前或历史上阻碍基因流动的障碍。特别是，加利福尼亚州最南端的人口在基因上是独特的（F _ST = 0.02 [微单倍型]；0.31 [mtDNA]），同时具有较低的遗传变异性和原本罕见的mtDNA单倍型的高频率。在研究范围的最北端，我们发现了乔治亚海峡样品的显着遗传分化，该样品先前被确定为海豚鼠种群之间的潜在生物地理边界或次生接触带。微单倍型与遥感环境变量的关联表明潜在的局部适应性，特别是在物种范围的南端。这些结果为该近海物种的保护和管理提供了依据，说明了基因组学方法对于检测连续分布的海洋物种内遗传结构模式的价值，