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...,