School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.
Environmental Research Institute, University College Cork, Cork, Ireland.
Mol Ecol. 2024 Dec;33(23):e17538. doi: 10.1111/mec.17538. Epub 2024 Nov 4.
Migration in animals and associated adaptations to contrasting environments are underpinned by complex genetic architecture. Here, we explore the genomic basis of facultative anadromy in brown trout (Salmo trutta), wherein some individuals migrate to sea while others remain resident in natal rivers, to better understand how alternative migratory tactics (AMTs) are maintained evolutionarily. To identify genomic variants associated with AMTs, we sequenced whole genomes for 194 individual trout from five anadromous-resident population pairs, situated above and below waterfalls, in five different Irish rivers. These waterfalls act as natural barriers to upstream migration and hence we predicted that loci underpinning AMTs should be under similar divergent selection across these replicate pairs. A sliding windows based analysis revealed a highly polygenic adaptive divergence between anadromous and resident populations, encompassing 329 differentiated genomic regions. These regions were associated with 292 genes involved in various processes crucial for AMTs, including energy homeostasis, reproduction, osmoregulation, immunity, circadian rhythm and neural function. Furthermore, examining patterns of diversity we were able to link specific genes and biological processes to putative AMT trait classes: migratory-propensity, migratory-lifestyle and residency. Importantly, AMT outlier regions possessed higher genetic diversity than the background genome, particularly in the anadromous group, suggesting balancing selection may play a role in maintaining genetic variation. Overall, the results from this study provide important insights into the genetic architecture of migration and the evolutionary mechanisms shaping genomic diversity within and across populations.
动物的迁徙和与之相关的对不同环境的适应是由复杂的遗传结构支撑的。在这里，我们探索了褐鳟（Salmo trutta）兼性洄游的基因组基础，其中一些个体洄游到海洋，而另一些则留在出生地的河流中，以更好地理解替代迁徙策略（AMTs）是如何在进化中得以维持的。为了确定与 AMTs 相关的基因组变异，我们对来自五个爱尔兰河流的 194 个个体的全基因组进行了测序，这些个体来自五个具有瀑布的洄游-定居种群对，瀑布是向上游迁徙的天然屏障，因此我们预测，支持 AMTs 的基因座应该在这些重复种群对之间受到相似的分歧选择。基于滑动窗口的分析揭示了洄游和定居种群之间高度多基因的适应性分歧，包括 329 个分化的基因组区域。这些区域与 292 个参与各种关键洄游策略的基因有关，包括能量平衡、繁殖、渗透压调节、免疫、昼夜节律和神经功能。此外，通过研究多样性模式，我们能够将特定的基因和生物学过程与假设的 AMT 性状类型联系起来：迁徙倾向、迁徙生活方式和定居。重要的是，AMT 异常区域的遗传多样性高于背景基因组，特别是在洄游群体中，这表明平衡选择可能在维持遗传变异方面发挥作用。总的来说，这项研究的结果为迁徙的遗传结构以及塑造种群内和种群间基因组多样性的进化机制提供了重要的见解。
