![](https://static.inaturalist.org/photos/64272938/original.jpg?1584917392) # Usage Notes This repository contains scripts and data required to replicate the analyses from the paper "Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species". The repository is organized into a series of markdown files that provide instructions for running analyses, and folders that contain raw data or intermediate files produced during analyses. ## Raw Data Raw, unprocessed sequencing data is available through the NCBI SRA (these files are too large to be hosted in the repostory). The processed data (012NA genotype files) are in the folder `PAWR_WIWR_012NA_files`. These data include the genotype files with the suffix `.012NA` (contain genotypes for each sample at each position), position files with the suffix `.pos` (listing chromosome name and position for each SNP), and individual files with the suffix `.indv` (listing the sample order of each individual in the dataset). ## Sample metadata Sample metadata are provided in the folder `Sample_information`. ## Scripts Instructions for running each step of the analysis is provided in text files in markdown format: 1) Instructions for processing the raw data is provided in `1_process_sequences.md` 2) Instructions for performing PCA on the data is provided in `2_PCA_plotting.md` and associated data are in the folder `2_PCA_data` 3) Instructions for the STRUCTURE analysis is provided in `3_STRUCTURE_analysis.md` and associated raw data are in the folder `3_STRUCTURE_data` 4) Instructions for the phylogenetic network are provided in `4_Phylogenetic_network.md` and associated data are in the folder `4_SplitsTree` 5) Instructions for performing the genome scans (Fst, pi_within, and pi_between) are in `5_GenomeScans.md` 6) Instructions for computing the per-chromosome statistics (Fst, pi_within, and pi_between) are in '6_perChrom_stats.R' 7) A description of how synteny with other taxa was checked in the translocated region is in `7_chr8_synteny.md` 8) Instructions for calculating the observed heterozygosity of each sample is in `9_Heterozygosity.md`