Whole-Genome Resequencing Reveals Polygenic Signatures of Directional and Balancing Selection on Alternative Migratory Life Histories.

IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Ecology Pub Date : 2024-11-04 DOI:10.1111/mec.17538
Peter A Moran, Thomas J Colgan, Karl P Phillips, Jamie Coughlan, Philip McGinnity, Thomas E Reed
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Abstract

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.

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全基因组重测序揭示了另类迁徙生活史上定向和平衡选择的多基因特征。
动物的洄游以及对不同环境的相关适应性是由复杂的遗传结构支撑的。在这里,我们探索了褐鳟(Salmo trutta)的溯河洄游基因组学基础,即一些个体洄游到海洋,而另一些个体则留在出生地的河流中,从而更好地了解替代性洄游策略(AMTs)是如何在进化过程中得以维持的。为了确定与AMTs相关的基因组变异,我们对来自爱尔兰五条不同河流中瀑布上方和下方的五个溯河而居种群对的194条鳟鱼个体进行了全基因组测序。这些瀑布是鳟鱼向上游迁徙的天然屏障,因此我们预测,在这些重复的鳟鱼种群对中,支撑AMT的基因位点应该受到类似的分化选择。基于滑动窗口的分析表明,溯河洄游种群和常住种群之间存在高度多基因适应性差异,包括 329 个差异基因组区域。这些区域与 292 个基因有关,这些基因参与了对溯河生态系统至关重要的各种过程,包括能量平衡、繁殖、渗透调节、免疫、昼夜节律和神经功能。此外,通过研究多样性模式,我们能够将特定基因和生物过程与推定的 AMT 特征类别联系起来:迁徙倾向、迁徙生活方式和居住地。重要的是,AMT离群区域的遗传多样性高于背景基因组,尤其是在溯河群中,这表明平衡选择可能在维持遗传变异方面发挥了作用。总之,这项研究的结果为我们了解迁徙的遗传结构以及形成种群内和种群间基因组多样性的进化机制提供了重要的启示。
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来源期刊
Molecular Ecology
Molecular Ecology 生物-进化生物学
CiteScore
8.40
自引率
10.20%
发文量
472
审稿时长
1 months
期刊介绍: Molecular Ecology publishes papers that utilize molecular genetic techniques to address consequential questions in ecology, evolution, behaviour and conservation. Studies may employ neutral markers for inference about ecological and evolutionary processes or examine ecologically important genes and their products directly. We discourage papers that are primarily descriptive and are relevant only to the taxon being studied. Papers reporting on molecular marker development, molecular diagnostics, barcoding, or DNA taxonomy, or technical methods should be re-directed to our sister journal, Molecular Ecology Resources. Likewise, papers with a strongly applied focus should be submitted to Evolutionary Applications. Research areas of interest to Molecular Ecology include: * population structure and phylogeography * reproductive strategies * relatedness and kin selection * sex allocation * population genetic theory * analytical methods development * conservation genetics * speciation genetics * microbial biodiversity * evolutionary dynamics of QTLs * ecological interactions * molecular adaptation and environmental genomics * impact of genetically modified organisms
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