DOI: 10.5061/dryad.104g3d0
title: Data from: The genomic landscape at a late stage of stickleback speciation: high genomic divergence interspersed by small localized regions of introgression

description: Speciation is a continuous process and analysis of species pairs at
 different stages of divergence provides insight into how it unfolds.
 Previous genomic studies on young species pairs have revealed peaks of
 divergence and heterogeneous genomic differentiation. Yet less known is
 how localised peaks of differentiation progress to genome-wide divergence
 during the later stages of speciation in the presence of persistent gene
 flow. Spanning the speciation continuum, stickleback species pairs are
 ideal for investigating how genomic divergence builds up during
 speciation. However, attention has largely focused on young postglacial
 species pairs, with little knowledge of the genomic signatures of
 divergence and introgression in older stickleback systems. The Japanese
 stickleback species pair, composed of the Pacific Ocean three-spined
 stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G.
 nipponicus), which co-occur in the Japanese islands, is at a late stage of
 speciation. Divergence likely started well before the end of the last
 glacial period and crosses between Japan Sea females and Pacific Ocean
 males result in hybrid male sterility. Here we use coalescent analyses and
 Approximate Bayesian Computation to show that the two species split
 approximately 0.68-1 million years ago but that they have continued to
 exchange genes at a low rate throughout divergence. Population genomic
 data revealed that, despite gene flow, a high level of genomic
 differentiation is maintained across the majority of the genome. However,
 we identified multiple, small regions of introgression, occurring mainly
 in areas of low recombination rate. Our results demonstrate that a high
 level of genome-wide divergence can establish in the face of persistent
 introgression and that gene flow can be localized to small genomic regions
 at the later stages of speciation with gene flow.
description: ms_controller_v1.7R wrapper script to run msABC and generate simulations. Use '--help' to see available options. Requires GNU Parallel to run properly.abc_processor_v1.5Rscript using abc package to postprocess output from msABC simulations. See '--help' for more information.model_selector_v1.1Rscript wrapper for performing model selection using abc R package. Use '--help' for additional information.calc_gsiR script for calculating gsi (genealogical sorting index) on phylogenetic treestree_classifcation_cleanR script for classifying phylogenetic trees based on geography/species.autosomal_phylogenetic_treesAutosomal phylogenetic trees for Japan Sea, Pacific Ocean and Atlantic Ocean individuals. Estimated for 10, 50 and 100 KB windows.female_only_phylogenetic_trees_whole_genomePhylogenetic trees for females only for the entire stickleback genome. Includes estimates for 10, 50 and 100 Kb windowsabc_sampled_loci.fastaObserved loci sampled from the stickleback genome used for ABC analysis. Stored as a fasta file (gzip compressed)genome_sampling_RscriptsSet of R scripts to randomly sample the genome using a fasta index file. See Readme file for more details.fastsimcoal_data_and_modelsJoint SFS from RAD data and models used in fastsimcoal analysis of site-frequency spectrum.final_rad_lift.vcfRAD-seq variant call format for Japan Sea, Pacific Ocean and Atlantic Ocean individuals.genome_10kb_windows_data10Kb genome window estimates of Fst, dxy, gmin, pi and tajima's D.Gmin_fd_dxy_sliding_windows_scriptA python script for estimating dxy, fd and Gmin. Modified version of script available here: https://github.com/johnomics/Martin_Davey_Jiggins_evaluating_introgression_statistics/blob/master/egglib_sliding_windows.pyegglib_sliding_windows_mr3.pygmin_bias_10kSliding window 10Kb Gmin analysis with minimimum haplotype pairs identified in each window. This was done to check that there is no bias (i.e. valleys are not caused by introgressed haplotypes in the same window).