Using serially collected specimens to investigate the potential population genetic consequences of reported declines in eastern woodland salamanders

This dataset includes all data and scripts used to investigate demographic shifts in Plethodon salamanders. We designed exonic target loci using custom scripts, generated sequence data via exon-based target capture, and called SNPs using SECAPR v.1.1.15. Here, we provide VCF files from our variant calling pipeline. We calculated summary statistics using the populations module in STACKS and estimated Tajima's D using Python libraries. We provide all scripts used to design exonic capture probes, process genomic data, and calculate summary statistics.  , , # Data from: Using serially collected specimens to investigate the potential population genetic consequences of reported declines in eastern woodland salamanders This repository contains data and analysis files for a comprehensive genetic diversity study of six *Plethodon* salamander species across multiple temporal and geographic sampling strategies. ## Project Overview This study examines genetic diversity patterns in *Plethodon* salamanders using targeted sequence capture data. The research compares genetic diversity estimates across: * **6 species**: *P. cinereus*, *P. cylindraceus*, *P. glutinosus*, *P. montanus*, *P. welleri*, *P. yonahlossee* * **2 localities**: IGG (Indian Grave Gap) and SG (Skull's Gap) * **3 sample types/timepoints**: FFS (formalin-fixed specimens from the 1960s and 1970s), frozen blood (1980s), and fresh liver (2018/2019) * **141 total samples** across all combinations ## Directory Structure ### `/Final_Baits/` Contains bait design files and coverage s...,本数据集包含用于探究无肺螈属（*Plethodon*）蝾螈种群动态变化的全部数据与配套脚本。本研究通过自定义脚本设计外显子靶位点，采用外显子靶向捕获技术生成测序数据，并使用SECAPR v.1.1.15软件调用单核苷酸多态性（SNPs）。本研究提供了变体调用流程产出的VCF（变体调用格式，Variant Call Format）文件。本研究通过STACKS软件的populations模块计算汇总统计量，并借助Python库估算塔伊马D（Tajima's D）统计量。同时，本数据集还提供了用于设计外显子捕获探针、处理基因组数据以及计算汇总统计量的全部脚本。 数据来源：利用连续采集的标本探究东部林栖无肺螈种群数量下降的潜在种群遗传后果 本数据集包含针对6种无肺螈属（*Plethodon*）蝾螈开展的全面遗传多样性研究所需的全部数据与分析文件，该研究采用多时间维度与地理维度的采样方案。 ## 项目概述 本研究利用靶向序列捕获数据，探究无肺螈属（*Plethodon*）蝾螈的遗传多样性模式。本研究针对以下维度对比遗传多样性评估结果： * **6个物种**：灰无肺螈（*P. cinereus*）、圆柱无肺螈（*P. cylindraceus*）、黏滑无肺螈（*P. glutinosus*）、山地无肺螈（*P. montanus*）、韦勒无肺螈（*P. welleri*）以及约纳洛斯无肺螈（*P. yonahlossee*） * **2个采样点**：IGG（印第安墓谷，Indian Grave Gap）与SG（头骨谷，Skull's Gap） * **3种样本类型/时间节点**：FFS（20世纪60、70年代的甲醛固定标本）、冷冻血液样本（1980年代）以及新鲜肝脏组织样本（2018/2019年） * **所有组合合计共141个样本** ## 目录结构 ### `/Final_Baits/` 包含诱饵设计文件与覆盖度相关数据（原文内容截断）