Waples R K, Seeb J E, Seeb L W
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA.
Mol Ecol. 2017 Aug;26(16):4131-4144. doi: 10.1111/mec.14163. Epub 2017 Jun 6.
Whole-genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently, paralogs are often excluded from studies. The effects of an ancient whole-genome duplication (approximately 88 MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site-associated DNA sequencing on 10 collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and rediploidized regions of the genome. We use a pedigree and high-density linkage map to identify paralogous loci and to investigate genetic variation across the genome. By applying multivariate statistical methods, we show that it is possible to characterize paralogous loci and that they display similar patterns of population structure as the diploidized portion of the genome. We find genetic associations with the adaptively important trait of run-timing in both sets of loci. By including paralogous loci in genome scans, we can observe evolutionary signals in genomic regions that have routinely been excluded from population genetic studies in other polyploid-derived species.
全基因组复制是具有持久影响基因组结构的重大进化事件。复制事件使遗传分析变得复杂，因为旁系同源序列难以区分；因此，旁系同源物在研究中常常被排除。通过众多旁系同源基因序列的持续存在和部分四体遗传，古代全基因组复制（约8800万年前）的影响在鲑科鱼类中仍然明显。我们对来自美国和加拿大萨利希海的10个秋鲑群体进行了限制性位点相关DNA测序，以研究基因组四体区域和重新二倍体化区域的遗传多样性和种群结构。我们使用一个谱系和高密度连锁图谱来识别旁系同源位点，并研究全基因组的遗传变异。通过应用多变量统计方法，我们表明有可能对旁系同源位点进行表征，并且它们显示出与基因组二倍体化部分相似的种群结构模式。我们在两组位点中都发现了与洄游时间这一具有适应性重要性的性状的遗传关联。通过在基因组扫描中纳入旁系同源位点，我们能够在其他多倍体衍生物种的种群遗传研究中通常被排除的基因组区域观察到进化信号。
