Atlantic salmon RAD-seq raw sequence reads. Salmo salar

Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array, and a microsatellite panel, to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three datasets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland, and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was evident in both SNP datasets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP datasets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact Atlantic salmon in Newfoundland, and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.

对离散且独特的个体集群或种群进行识别，是受开发利用物种管理的核心内容。种群基因组学（population genomics）的发展为重新评估现有保护单元提供了新契机，但不同研究方法间的对比研究仍较为匮乏。本研究对比了限制性位点关联测序（RAD-seq）、单核苷酸多态性（single nucleotide polymorphism, SNP）芯片以及微卫星检测组合的应用效能，旨在解析纽芬兰南部受威胁的大西洋鲑（Salmo salar）种群在跨大西洋二次接触情景下的空间遗传结构。贝叶斯聚类分析识别出两个大类群，将现有保护单元划分为两部分；多变量分析显示，三种数据集所揭示的空间遗传结构具有显著一致性。携带欧洲血统特异性标记的线粒体DNA（mitochondrial DNA, mtDNA）等位基因在纽芬兰东南部的出现频率更高，且在所有标记类型中均与空间遗传结构显著相关。两种SNP数据集均检测到与这两个类群间基因渐渗相符的证据，但微卫星数据集未发现此类信号。SNP数据集还显示出基因渐渗程度的不对称性，存在向东（即向欧洲型类群）的基因流证据。本研究凸显了基于RAD-seq的研究方法在解析复杂空间遗传模式中的应用价值，明确了纽芬兰地区大西洋鲑跨大西洋二次接触的区域，并证实了多标记对比在解析基因渐渗动态过程中的有效性。