DOI: 10.5061/dryad.00000003w
title: Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species

description: Contact zones between recently-diverged taxa provide opportunities to
 examine the causes of reproductive isolation and the processes that
 determine whether two species can coexist over a broad region. The Pacific
 Wren (Troglodytes pacificus) and Winter Wren (Troglodytes hiemalis) are
 two morphologically similar songbirds that started diverging about 4
 million years ago, older than most sister species pairs of temperate
 songbirds. The ranges of these species come into narrow contact in western
 Canada, where the two species remain distinct. To assess evidence for
 differentiation, hybridization, and introgression in this system, we
 examined variation in over 250,000 single nucleotide polymorphism markers
 distributed across the genome. The two species formed highly divergent
 genetic clusters, consistent with long-term differentiation. In a set of
 75 individuals, two first-generation hybrids (i.e., F1’s) were detected,
 indicating only moderate levels of assortative mating between these taxa.
 We found no recent backcrosses or other evidence of recent breeding
 success of F1’s, indicating very low or zero fitness of F1 hybrids.
 Examination of genomic variation shows evidence for only a single
 backcrossing event many generations ago. The moderate rate of
 hybridization combined with very low F1 hybrid fitness is expected to
 result in a population sink in the contact zone, largely explaining the
 narrow overlap of the two species. If such dynamics are common in nature,
 they could explain the narrow range overlap often observed between pairs
 of closely related species.
description: 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<br> Raw, unprocessed sequencing data is available through the
 NCBI SRA, Accession  (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<br> Sample metadata are provided in the
 folder `Sample_information`. ## Scripts<br>
 Instructions for running each step of the analysis is provided in text
 files in markdown format:  <br> 1) Instructions for processing the
 raw data is provided in `1_process_sequences.md`<br> 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`<br> 3) Instructions
 for the STRUCTURE analysis is provided in `3_STRUCTURE_analysis.md` and
 associated raw data are in the folder `3_STRUCTURE_data`<br> 4)
 Instructions for the phylogenetic network are provided in
 `4_Phylogenetic_network.md` and associated data are in the folder
 `4_SplitsTree`<br> 5) Instructions for performing the genome scans
 (Fst, pi_within, and pi_between) are in `5_GenomeScans.md`<br> 6)
 Instructions for computing the per-chromosome statistics (Fst, pi_within,
 and pi_between) are in '6_perChrom_stats.R'<br> 7) A
 description of how synteny with other taxa was checked in the translocated
 region is in `7_chr8_synteny.md`<br> 8) Instructions for calculating
 the observed heterozygosity of each sample is in
 `9_Heterozygosity.md`