Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure

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 data sets. 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 ...对离散且独特的个体类群或种群组合的识别，是受开发利用物种管理的核心内容。种群基因组学的发展为重新评估现有保护单元提供了全新契机，但不同研究方法间的对比分析仍较为少见。本研究针对纽芬兰南部一处受威胁的大西洋鲑（Salmo salar）种群，在可能存在跨大西洋次生接触的场景下，对比了限制性位点相关DNA测序（RAD-seq）、单核苷酸多态性（single nucleotide polymorphism, SNP）芯片以及微卫星标记组合这三种技术解析其空间遗传结构的效能。贝叶斯聚类分析识别出将现有保护单元划分为两个大型亚群的结构，多变量分析结果显示，三类数据集所揭示的空间遗传结构存在显著相似性。可作为欧洲血统判定标记的线粒体DNA（mtDNA）等位基因，在纽芬兰东南部的出现频率显著升高，且与所有标记类型对应的空间遗传结构均存在显著相关性。这两个类群间存在符合基因渐渗现象的相关证据……