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...

北太平洋港湾鼠海豚（Harbor porpoises）分布于从南加州至日本的近岸海域，但除少数局部区域外，学界对其种群遗传结构的认知仍较为有限。本研究采用292个基因座的多重扩增子测序技术，将单核苷酸多态性（Single Nucleotide Polymorphism, SNP）聚类分型为微单倍型（microhaplotypes，共检测271份样本），并辅以线粒体DNA（mitochondrial DNA, mtDNA）序列数据（共检测413份样本），对采集自加州至不列颠哥伦比亚省南部的太平洋沿岸及内陆水道的样本开展遗传结构分析。研究证实整体存在显著的距离隔离模式，表明个体扩散受到限制。本研究同时发现部分区域的遗传差异远超仅基于地理距离的预期水平，暗示存在当前或历史遗留的基因流障碍。尤为值得关注的是，加州境内最南端的种群具有显著的遗传分化（微单倍型的FST值为0.02；线粒体DNA的FST值为0.31），其遗传多样性水平降低，且携带一种在其他群体中极为罕见的线粒体DNA单倍型……