Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation

A species’ genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here we investigate selection in pink salmon (Oncorhynchus gorbuscha) using genome scans coupled with inference from a haploid-assisted linkage map. Pink salmon have a strict two-year semelparous life-history which has resulted in temporally isolated (allochronic) lineages that remain sympatric through sharing of spawning habitats in alternate years. The lineages differ in a range of adaptive traits, suggesting different genetic backgrounds. We used genotyping by sequencing of haploids to generate a high-density linkage map with 7,035 loci and screened an existing panel of 8,036 loci for signatures of selection. The linkage map enabled identification of novel genomic regions displaying signatures of parallel selection shared between lineages. Furthermore, 24 loci demonstrated divergent selection and differences in genetic diversity between lineages, suggesting that adaptation in the two lineages has arisen from different pools of standing genetic variation. Findings have implications for understanding asynchronous population abundances as well as predicting future ecosystem impacts from lineage-specific responses to climate change.

物种的遗传多样性承载着其整个演化历程中各类进化过程的印记。然而，对野生种群的选择作用进行稳健检测颇具难度，且常因缺乏重复检验而受阻。本研究借助基因组扫描结合单倍体辅助连锁图谱（haploid-assisted linkage map）的推断分析，对粉红鲑（Oncorhynchus gorbuscha）的选择作用展开探究。粉红鲑具有严格的两年生终生一胎生活史，这造就了时间隔离（生殖时序错位）的谱系——这些谱系会在不同年份共享产卵场，从而维持同域分布状态。这些谱系在一系列适应性性状上存在差异，暗示其遗传背景各不相同。我们通过单倍体测序基因分型技术构建了包含7035个基因座的高密度连锁图谱，并对已有的8036个基因座的选择信号进行了筛选。该连锁图谱帮助我们鉴定出了谱系间共享平行选择信号的全新基因组区域。此外，有24个基因座表现出歧化选择特征，且在不同谱系间存在遗传多样性差异，这表明两个谱系的适应性演化源自不同的现存遗传变异库。本研究结果对于理解种群数量的异步波动，以及预测谱系特异性响应气候变化所带来的未来生态系统影响均具有重要启示意义。