Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure
Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure
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DOI：
10.1111/mec.13395
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发表时间：
2015-10-01
影响因子：
4.9
通讯作者：
Verspoor, Eric
中科院分区：
文献类型：
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作者：
Bradbury, Ian R.;Hamilton, Lorraine C.;Verspoor, Eric
识别个体或种群的离散和独特组合是管理被开发物种的核心。人口基因组学的进步提供了新的机会，重新评估现有的保护单位，但方法之间的比较仍然很少。我们比较了实用的RAD-seq，单核苷酸多态性（SNP）阵列和微卫星面板，以解决空间结构的情况下，可能跨大西洋的第二次接触在受威胁的大西洋鲑鱼，萨尔莫萨拉，人口在纽芬兰南部。贝叶斯聚类确定了两个大组细分现有的保护单位和多变量分析表明，三个数据集之间的空间结构显着相似。欧洲血统的mtDNA等位基因诊断显示在纽芬兰东南部的频率增加，并在所有标记类型的空间结构相关。在这两个SNP数据集中都存在与这两个组之间的渐渗一致的证据，但在微卫星数据中不存在。不对称程度的渗入也是明显的SNP数据集的证据，基因流向东方或欧洲型。这项工作突出了基于RAD-seq的方法用于解决复杂空间模式的实用性，解决了纽芬兰大西洋鲑鱼中跨大西洋二级接触的区域，并展示了多个标记比较在识别基因渗入动态中的实用性。
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 present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets 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 in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.