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Genotyping-by-sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes.
Evolutionary Applications ( IF 4.1 ) Pub Date : 2020-02-27 , DOI: 10.1111/eva.12919
Amanda S Ackiss 1 , Wesley A Larson 2 , Wendylee Stott 3
Affiliation  

Effective resource management depends on our ability to partition diversity into biologically meaningful units. Recent evolutionary divergence, however, can often lead to ambiguity in morphological and genetic differentiation, complicating the delineation of valid conservation units. Such is the case with the “coregonine problem,” where recent postglacial radiations of coregonines into lacustrine habitats resulted in the evolution of numerous species flocks, often with ambiguous taxonomy. The application of genomics methods is beginning to shed light on this problem and the evolutionary mechanisms underlying divergence in these ecologically and economically important fishes. Here, we used restriction site‐associated DNA (RAD) sequencing to examine genetic diversity and differentiation among sympatric forms in the Coregonus artedi complex in the Apostle Islands of Lake Superior, the largest lake in the Laurentian Great Lakes. Using 29,068 SNPs, we were able to clearly distinguish among the three most common forms for the first time, as well as identify putative hybrids and potentially misidentified specimens. Population assignment rates for these forms using our RAD data were 93%–100% with the only mis‐assignments arising from putative hybrids, an improvement from 62% to 77% using microsatellites. Estimates of pairwise differentiation (FST: 0.045–0.056) were large given the detection of hybrids, suggesting that reduced fitness of hybrid individuals may be a potential mechanism for the maintenance of differentiation. We also used a newly built C. artedi linkage map to look for islands of genetic divergence among forms and found widespread differentiation across the genome, a pattern indicative of long‐term drift, suggesting that these forms have been reproductively isolated for a substantial amount of time. The results of this study provide valuable information that can be applied to develop well‐informed management strategies and stress the importance of re‐evaluating conservation units with genomic tools to ensure they accurately reflect species diversity.

中文翻译:

通过测序进行基因分型说明了劳伦式五大湖中同形异形核苷之间的高度差异。

有效的资源管理取决于我们将多样性划分为具有生物学意义的单位的能力。然而,近来的进化分歧常常会导致形态和遗传分化的模棱两可,从而使有效保护单位的划分更加复杂。“可可因问题”就是这种情况,在最近的冰河期后,可可因的辐射进入湖泊栖息地后,导致了许多物种群的进化,通常具有不明确的分类法。基因组学方法的应用开始阐明这一问题以及这些具有重要生态和经济意义的鱼类之间差异的进化机制。在这里,我们使用限制性酶切位点相关DNA(RAD)测序来检查遗传多样性和不同同胞形式之间的分化。Coregonus artedi复合体位于苏必利尔湖的使徒群岛,是劳伦大湖中最大的湖泊。使用29,068个SNP,我们首次能够清楚地区分三种最常见的形式,并鉴定出假定的杂种和可能被误认的标本。使用我们的RAD数据,这些表格的人口分配率为93%–100%,唯一的错误分配是由推定的杂种引起的,使用微卫星从62%改善到77%。在检测到杂种的情况下,成对分化的估计值很大(F ST:0.045–0.056),这表明杂种个体适应性的降低可能是维持分化的潜在机制。我们还使用了新近建成的C. artedi连锁图寻找形式之间的遗传差异的岛,并发现了整个基因组的广泛分化,这是长期漂移的一种模式,表明这些形式已被生殖分离了相当长的时间。这项研究的结果提供了可用于制定明智的管理策略的有价值的信息,并强调了使用基因组学工具重新评估保护单位以确保其准确反映物种多样性的重要性。
更新日期:2020-02-27
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