Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

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 (Oncorhynchus mykiss) 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: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) 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 fre..., modified Nextera library preparation, dual-index sequencing on NextSeq 500, processed with PoolParty2, , # Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

## Description of the data and file structure

Sequence data were collected from modified Nextera library preparation, dual-index sequencing on NextSeq 500. Sequence data were then processed with PoolParty, and filtered to SNPs observed in at least one individual in each of 74 geographic samples. This file represents allele frequencies for those SNPs, mapped to the genome assembly of the Swanson line of rainbow trout (*Oncorhynchus mykiss*): GCF_002163495.1. Meta-data lines are preceded with '#', and spacing cells in meta-data lines contain 'NA' (not applicable).

The file is TEXT (txt) formatted and tab-delimited.

## Sharing/Access information

NCBI BioProject containing the sequence data

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## Code/Software

These data were processed with PoolParty2 (). See also Willis et al. 2022 Molecular Ecology Resources:

多种进化过程影响全基因组等位基因频率，而在自然种群中量化遗传漂变及多种选择模式的效应仍是一项挑战。本研究针对因人为活动影响而种群数量下降的大量硬头鳟（*Oncorhynchus mykiss*）种群，对比中性漂变模式，分析其主效基因座的变异情况。对74个硬头鳟种群开展全基因组重测序后，获得了约800万个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，其全基因组模式符合预期的中性种群结构特征。然而，与成体洄游时间（28号染色体：GREB1L/ROCK1）及成熟年龄（25号染色体：SIX6）相关的主效基因座的等位基因变异，则反映了选择对表型变异的作用模式，这与中性种群结构形成鲜明对比。主效基因座的变异受进化过程调控，在分化显著的沿海与内陆谱系间存在迥异的信号特征，而等位基因频率[原文内容截断]。# 硬头鳟种群序列变异的对比模式反映了独特的进化过程

## 数据与文件结构说明
序列数据采用改良的Nextera文库制备方案，通过NextSeq 500平台完成双索引测序。测序数据经PoolParty2软件处理后，过滤得到至少在74个地理样本中的任意一个个体中存在的SNP位点。本文件包含上述SNP位点的等位基因频率，已比对至虹鳟斯旺森品系的基因组组装版本GCF_002163495.1。元数据行以符号“#”开头，元数据行中的空值以“NA”（不可用）表示。
文件格式为纯文本（.txt），采用制表符分隔。

## 共享与获取信息
包含该序列数据的NCBI BioProject（原文未提供具体信息）

## 代码与软件
本数据经PoolParty2软件处理。另可参考Willis等人2022年发表于《分子生态学资源》的相关研究论文。