Data from: Congruent population structure across paralogous and non-paralogous loci in Salish Sea chum salmon (Oncorhynchus keta)

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 88MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site-associated DNA sequencing (RADseq) on ten collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and re-diploidized 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 genetic 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（Whole genome duplications）是对基因组结构具有持久影响的重要进化事件。复制事件会使遗传分析变得复杂，因为旁系同源序列（paralogous sequences）难以区分，因此旁系同源序列常被排除在研究之外。一次发生于约8800万年前的古全基因组复制事件，其影响至今仍可在鲑科鱼类中观测到——大量旁系同源基因序列得以保留，且仍存在部分四体遗传（tetrasomic inheritance）现象。本研究针对美国与加拿大萨利希海（Salish Sea）的10个大麻哈鱼（chum salmon）样本组，采用限制性酶切位点相关DNA测序（restriction site-associated DNA sequencing, RADseq）技术，旨在探究基因组四体遗传区与重新二倍体化区域的遗传多样性及种群结构。我们借助家系谱系与高密度连锁图谱，识别旁系同源基因座，并对全基因组范围内的遗传变异展开分析。通过应用多变量统计方法，本研究证实可对旁系同源遗传基因座进行鉴定，且这类基因座与基因组二倍体化区域展现出相似的种群结构模式。我们在两类基因座中均发现了与洄游时间这一适应性关键性状相关的遗传关联。将旁系同源基因座纳入基因组扫描后，我们可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内，观测到进化信号。