SNP dataset for cape race brook trout

Many studies have investigated the loss of adaptive potential in endangered or exploited species experiencing recent population declines. Less research has studied adaptive genomic variation in small populations known to have persisted for long periods, despite the unique contribution that such populations provide for determining mechanisms underlying population persistence in evolutionary and conservation modeling. Small populations of Brook trout (Salvelinus fontinalis) have persisted in Cape Race, Newfoundland for >12,000 years. We used genotyping-by-sequencing data to investigate the demographic history and adaptive genomic variation of 26 populations with effective population sizes (Ne) ranging from 11 to 442, and to explore mechanisms underlying long-term persistence. We show that all populations experienced demographic declines following postglacial colonization but have remained in their current, small Ne state for thousands of years. We also reveal greater homozygosity in ad..., , , # SNP dataset for cape race brook trout ### Description of the Data and file structure There are datasets that were used to perform the analyses for this paper: 1\. CapeRace_NeutralSNPs.vcf Neutral SNPs from Cape Race Brook trout populations. 2.CapeRace_annotatedSNPs.vcf Annotated SNPs from Cape Race Brook trout populations. 3\. CapeRace_OutlierSNPs.vcf PCAdapt outlier SNPs from Cape Race Brook trout populations. All .vcf files can be viewed in a standard text editor. 诸多研究已针对近期种群数量下降的濒危或开发利用物种展开调查，剖析其适应性潜力的丧失机制。然而，尽管此类长期存续的小种群对于解析进化与保护建模中种群存续的核心机制具有独特价值，针对这类种群的适应性基因组变异研究却相对匮乏。纽芬兰开普雷斯（Cape Race）的溪红点鲑（Brook trout, *Salvelinus fontinalis*）小种群已存续超12000年。本研究通过测序分型（genotyping-by-sequencing, GBS）数据，对26个有效种群规模（effective population size, *N_e*）介于11至442之间的溪红点鲑种群进行种群历史动态与适应性基因组变异分析，并探究其长期存续的内在机制。研究结果显示，所有种群均在冰期后拓殖过程中经历了种群数量下降，并在此后数千年间维持当前的小有效种群规模状态。我们还发现...中的纯合性更高（原文此处内容未完整展示） # 开普雷斯溪红点鲑SNP数据集 ## 数据集与文件结构说明 本研究用于论文分析的数据集如下： 1. CapeRace_NeutralSNPs.vcf：开普雷斯溪红点鲑种群的中性SNP位点数据 2. CapeRace_annotatedSNPs.vcf：开普雷斯溪红点鲑种群的注释型SNP位点数据 3. CapeRace_OutlierSNPs.vcf：开普雷斯溪红点鲑种群的PCAdapt离群SNP位点数据 所有.vcf格式文件均可通过标准文本编辑器打开查看。