Dryad DOI: 

Title of dataset: Extensive introgression despite Haldane’s rule: Insights from grasshopper hybrid zones

Submitting author name: Linda Hagberg

Description of files and contents: This Dryad contains the dataset used to assess the tempo and mode of the evolution of Haldane’s rule, whether it may restrict genetic introgression, and whether it is associated to repeatable patterns of genomic differentiation in Pseudochorthippus parallelus populations. It contains the input files for the demographic analyses (2D site frequency spectra), the Beagle haplotype imputation files for ANGSD analyses, the input for producing the BEAST mitochondrial time tree and the mitochondrial and nuclear IQ-TREE maximum likelihood tree, and the 1D site frequency spectra used to calculate pi, Tajima's D, and theta. It includes output files as well, such as the covariance table for the PCA, and the per gene estimates of Dxy, FST, Tajima's D, theta, and pi.

List of files, file size, and file counts.

- 2dsfs_*_fold0_genesum.sfs (2 files, 1.00 - 1.11 kB, The site frequency spectra used as input for the demographic analyses, where the * replaces the portion of the filename containing the hybrid zone abbreviation.)
- alignments_md10.tar.gz (5930 files, 23.00 MB, The alignment files of each gene used as input to IQ-TREE to produce the the gene trees and the script to create them. Must be unarchived to use.)
- Brower_XML_publication.xml (778.16 kB, The BEAST input file for the mitochondrial time tree.)
- FcC_smatrix.fa (781.88 kB, The mitochondrial alignment used as input for IQ-TREE.)
- newbeagle*.beagle.gz (119.26 - 163.95 MB, The Beagle haplotype imputation files used as input for several analyses in ANGSD, where the * replaces the number of samples, i.e. whether it includes the outgroup. Must be unarchived to use.)
- pca_50plink.clst (457 B, The cluster file assigning individuals to populations used to produce the pca)
- pca_50plink.covar (23.80 kB, The covariance table of all individuals used to produce the PCA.)
- per_gene_dxy_*.csv (2 files, 1.05 - 1.06 MB, The values calculated for Dxy for each gene, where the * replaces the hybrid zone abbreviation.)
- per_gene_fst_* (2 files, 1.08 - 1.17 MB, The values calculated for Fst for each gene, where the * replaces the hybrid zone abbreviation.)
- per_gene_* (3 files, 3.17 - 3.36 MB, The values calculated for pi, Tajima's D, and theta for each gene, where the * replaces the respective summary statistic.)
- SFS_*.sfs (10 files, 147 - 148 B, The site frequency spectra used as input for the calculation of pi, Tajima's D, and theta, where the * replaces the portion of the filename containing the population abbreviation.)

Software needed to open the files: File archiver, text editor, ANGSD, Microsoft Excel or equivalent, BEAST.

NOTE: Three files containing the P. parallelus reference transcriptome, coordinates of gene positions within the reference, and coordinates of positions classified as neutral within the reference can be found in the dryad depository by Nolen et al (2020; https://doi.org/10.5061/dryad.pzgmsbchj).

Citations:
Nolen, Zachary et al. (2020), Historical isolation facilitates species radiation by sexual selection: insights from Chorthippus grasshoppers, Dryad, Dataset, https://doi.org/10.5061/dryad.pzgmsbchj