Willis Stuart, Coykendall D Katharine, Campbell Matthew R, Narum Shawn
Hagerman Genetics Lab Columbia River Inter-Tribal Fish Commission Hagerman Idaho USA.
Eagle Fish Genetics Lab Pacific States Marine Fisheries Commission Eagle Idaho USA.
Evol Appl. 2023 Dec 11;17(1):e13623. doi: 10.1111/eva.13623. eCollection 2024 Jan.
Multiple evolutionary processes influence genome-wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead () populations that have declined in abundance due to anthropogenic impacts. Whole-genome resequencing of 74 populations of steelhead revealed genome-wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: /) and age at maturity (chromosome 25: ) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.
多种进化过程影响全基因组的等位基因频率，量化遗传漂变的影响以及多种形式的选择在自然种群中仍然具有挑战性。在这里，我们研究了主要效应位点的变异，对比了在因人为影响而数量减少的大量虹鳟（）种群中中性漂变的模式。对74个虹鳟种群进行全基因组重测序，揭示了全基因组模式（约800万个单核苷酸多态性）与预期的中性种群结构一致。然而，与成年洄游时间（28号染色体：/）和成熟年龄（25号染色体：）相关的主要效应位点的等位基因变异，反映了选择如何作用于表型变异，这与中性结构形成对比。主要效应位点的变异受到进化过程的影响，在高度分化的沿海和内陆谱系之间存在不同的信号，而内陆谱系内种群内部和种群之间的等位基因频率受到局部自然选择以及近期人为影响的驱动。近期的人为影响似乎已经影响了主要效应等位基因的频率，包括对孵化场种群特定性状的人工选择，随后基因流入自然种群。来自各种尺度环境因素的选择也可能影响了主要效应等位基因的变异。这些结果揭示了影响主要效应位点等位基因频率的进化机制，这些机制对于保护这个受保护物种的表型性状和生活史变异至关重要。
