Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and nonparallel adaptation. All landlocked populations displayed an increased frequency of a large inversion on chromosome Omy05, while 3 of the 4 populations exhibited elevated frequencies of another inversion located on chromosome Omy20. In addition, we identified numerous regions outside these 2 inversions that also show significant shifts in allele frequencies consistent with adaptive evolution. However, there was little concordance among above-barrier populations in these specific genomic regions under selection. In part, the lack of concordance appears to arise from ancestral autopolyploidy in rainbow trout that provides duplicate genomic regions of similar functional composition for selection to act upon. Thus, while selection acting on landlocked populations universally favors the resident ecotype, outside of the major chromosomal inversions, the resulting genetic changes are largely distinct among populations. Our results indicate that selection on standing genetic variation is likely the primary mode of rapid adaptation, and that both supergene complexes and individual loci contribute to adaptive evolution, further highlighting the diversity of adaptive genomic variation involved in complex phenotypic evolution.

中文翻译：

---

多基因基础和基因组复制在适应类似选择性环境中的作用

适应的遗传变化在复杂性方面差异很大，并且在同一物种内，对类似选择压力的遗传反应可能相同，也可能不同。我们检查了独立于海洋通道分离的虹鳟鱼（Oncorhynchus mykiss）种群中发生的复杂（超基因）和简单（SNP）遗传变异，并将它们相互比较，并与代表其祖先来源的溯河下游种群进行比较并行和非并行适应的特征。所有内陆种群在染色体 Omy05 上的大倒位频率增加，而 4 个种群中的 3 个在染色体 Omy20 上的另一个倒位频率升高。此外，我们确定了这两个反转之外的许多区域，这些区域也显示出与自适应进化一致的等位基因频率的显着变化。然而，在这些被选择的特定基因组区域中，上述屏障种群之间几乎没有一致性。在某种程度上，缺乏一致性似乎是由于虹鳟鱼的祖先同源多倍体提供了具有相似功能组成的重复基因组区域供选择作用。因此，虽然作用于内陆种群的选择普遍有利于常驻生态型，但在主要的染色体倒位之外，由此产生的遗传变化在种群之间在很大程度上是不同的。我们的结果表明，对常备遗传变异的选择可能是快速适应的主要模式，