Data from: Conservation genomics of the threatened Trispot Darter (Etheostoma trisella)

# Etheostoma\_trisella\_population\_genomics\_2023 [https://doi.org/10.5061/dryad.jq2bvq8g6](https://doi.org/10.5061/dryad.jq2bvq8g6) This repository contains the data used to perform population genomic and phylogenetic analyses for *Etheostoma trisella* collected in the United States. The data are the result of DArTSeq: a combination of DArT complexity reduction with sequencing on the Next Generation Sequencing platforms. It represents combined marker discovery and genotyping for SNPs. Approximately 50,000 DNA fragments from DArT representations were assayed for polymorphism. We detect three distinct management units (i.e., genetic groups) which reflect isolated geographic localities (i.e., Little Canoe Creek, Ballplay Creek, and a system including the Conasauga and Coosawattee rivers). We also detected a recent bottleneck event in the Ballplay Creek population as well as a low effective population size. Tests of isolation by distance further suggest that populations are structured by riverine isolation rather than geographic distance. ## Description of the data and file structure The SNP report file in .csv format includes data for 93 *Etheostoma trisella* specimens. The file includes columns for AlleleID, CloneID, AlleleSequence, TrimmedSequence, SNP, SnpPosition, CallRate, OneRatioRef, OneRatioSnp, FreqHomRe, FreqHomSnp, FreqHets, PICRef, PICSnp, AvgPIC, AvgCountRef, AvgCountSnp, RepAvg. Binary states for loci are also indicated for each specimen. Specimens are named with a unique number identifier followed by collection locality. ## Sharing/Access information Not applicable. ## Code/Software Not applicable.

# 2023年三带镖鲈种群基因组学数据集 [https://doi.org/10.5061/dryad.jq2bvq8g6]
本仓库包含用于对美国采集的三带镖鲈（*Etheostoma trisella*）开展种群基因组学与系统发育分析的相关数据。该数据源自DArTSeq技术：即复杂度降低分型技术结合下一代测序（Next Generation Sequencing）平台的测序方案，整合了单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的标记发现与基因分型流程。研究对来自DArT文库的约50,000条DNA片段进行多态性检测，共鉴定出3个独立的管理单元（management unit），对应三个隔离的地理分布区域：小独木舟溪（Little Canoe Creek）、鲍尔普莱溪（Ballplay Creek），以及包含科诺萨加河与库萨蒂河的水系。此外，研究在鲍尔普莱溪种群中检测到近期瓶颈效应，且其有效种群大小（effective population size）较低。距离隔离分析进一步表明，种群结构受水系隔离而非地理距离驱动。
## 数据与文件结构说明
该数据集包含格式为.csv的SNP报告文件，涵盖93份三带镖鲈样本的相关数据。文件包含以下列：等位基因ID（AlleleID）、克隆ID（CloneID）、等位基因序列（AlleleSequence）、修剪后序列（TrimmedSequence）、SNP位点（SNP）、SNP位点位置（SnpPosition）、检出率（CallRate）、参考等位基因单态比例（OneRatioRef）、变异等位基因单态比例（OneRatioSnp）、参考等位基因纯合频率（FreqHomRe）、变异等位基因纯合频率（FreqHomSnp）、杂合频率（FreqHets）、参考等位基因多态信息含量（PICRef）、变异等位基因多态信息含量（PICSnp）、平均多态信息含量（AvgPIC）、参考等位基因平均计数（AvgCountRef）、变异等位基因平均计数（AvgCountSnp）、重复平均（RepAvg）。同时，文件中为每个样本标注了基因座的二元状态。样本命名规则为：唯一数字标识符后接采集地信息。
## 共享与访问说明
不适用。
## 代码与软件说明
不适用。

搜集汇总

背景与挑战

背景概述

该数据集包含93个濒危Trispot Darter（Etheostoma trisella）样本的单核苷酸多态性（SNP）数据，用于保护基因组学研究。通过分析揭示了三个遗传管理单元，对应不同的地理隔离种群，并检测到Ballplay Creek种群的近期瓶颈事件和低有效种群大小，为物种保护决策提供关键遗传信息。