DOI: 10.5061/dryad.sk2pd88
title: Data from: Recombination rate variation shapes barriers to introgression across butterfly genomes

description: Hybridisation and introgression can dramatically alter the relationships
 among groups of species, leading to phylogenetic discordance across the
 genome and between populations. Introgression can also erode species
 differences over time, but selection against introgression at certain loci
 acts to maintain post-mating species barriers. Theory predicts that
 species barriers made up of many loci throughout the genome should lead to
 a broad correlation between introgression and recombination rate, which
 determines the extent to which selection on deleterious foreign alleles
 will affect neutral alleles at physically linked loci. Here we describe
 the variation in genealogical relationships across the genome among three
 species of Heliconius butterflies: H. melpomene, H. cydno and H. timareta,
 using whole genomes of 92 individuals, and ask whether this variation can
 be explained by heterogeneous barriers to introgression. We find that
 species relationships vary predictably at the chromosomal scale. By
 quantifying recombination rate and admixture proportions, we then show
 that rates of introgression are predicted by variation in recombination
 rate. This implies that species barriers are highly polygenic, with
 selection acting against introgressed alleles across most of the genome.
 In addition, long chromosomes, which have lower recombination rates,
 produce stronger barriers on average than short chromosomes. Finally, we
 find a consistent difference between two species pairs on either side of
 the Andes, which suggests differences in the architecture of the species
 barriers. Our findings illustrate how the combined effects of
 hybridisation, recombination and natural selection, acting at multitudes
 of loci over long periods, can dramatically sculpt the phylogenetic
 relationships among species.
description: VCF: SNP Set 1 (92
 individuals) VCF file for SNP Set 1
 described in the paper. Although reads were mapped to the Hmel2 scaffolds,
 the coordinate system has been converted to chromosomes according to the
 Hmel2.5 scaffolding. Genotypes of females on chromosome 21 are given as
 haploid. This version was updated in May 2020 to correct a misordering of
 the sample labels. bar92.DP8MP4BIMAC2HET75.hapFem.minimal.corrected.vcf.gz VCF: SNP Set 2 (92 individuals) VCF file for SNP Set 2 described in the paper. Although reads were mapped to the Hmel2 scaffolds, the coordinate system has been converted to chromosomes according to the Hmel2.5 scaffolding. Genotypes of females on chromosome 21 are given as haploid. This version was updated in May 2020 to correct a misordering of the sample labels. bar92.DP8MP9BIMAC2HET75.hapFem.minimal.corrected.vcf.gz Whole genome distance matrix for 92 Heliconius individuals Pairwise absolute genetic distances among the 92 individuals computed using SNP Set 1, further filtered to retain only SNPs separated by at least 1 kb. This file was used as input for SplitsTree to generate the network in Figure 1B. bar92.DP8MP4BIMAC2HET75dist1K.dist PCA results (90 Heliconius individuals) Eigenstrat SmartPCA results for 90 individuals (outgroups excluded), presented in Figure 1B. bar90.DP8MP9BIMAC2HET75.hapFem.eigenstrat.PCA.evec Topology weightings from Twisst (42 files) Twisst data underlying figures 2 & 3 and supplementary figures S1-S4. 42 files are provided, two for each chromosome. Files ending in ".weights.tsv.gz" give the topology weightings for the fifteen possible topologies (see Figure 2). Each line represents a different 50 SNP window. Files ending in ".data.tsv" give the chromosome and coordinates of each window. twisst_data.tar.gz Population recombination rates from LDhelmet (84 files) Maximum likelihood estimates of the population recombination rate for each 100 kb window. 84 files are provided: one for each chromosome for four separate populations of Heliconius cydno, timareta, melpomene (west) and melpomene (east) LDhelmet_data.tar.gz Admixture proportion data (fd) (14 files) Estimated admixture proportions (fd) along with related estimates, used to generate figures 3 and 4 and supplementary figures S7, S8 and S11-S13. 14 files are provided, covering different population sets as described in supplementary figure S6. File names indicate the populations used in the order P1, P2, P3 and Outgroup (always "num"). Files of two different window sizes are provided: 100 kb windows, sliding in increments of 20 kb, with a minimum of 1000 genotyped sites per window required ("w100m1s20"); and 20 kb windows, sliding in increments of 5 kb, with a minimum of 300 genotyped sites per window required ("w20m300s5"). Two files are also provided giving estimates for whole-chromosomes. ABBA_BABA_data.tar.gz Simulation results (3 files) Simulated topology weighting results presented in S2 Fig. are provided in the files "sim_weights_means_S2_Fig.tsv" (mean values) and "sim_weights_fixed_S2_Fig.tsv" (fixed values). The three lines in each file represent the three scenarios shown in S2 Fig. Simulated values for divergence and admixture statistics presented in S5 Fig. are provided in the file "div_admix_stats_polarized.50k_100_inst.mean.tsv". The "Scenario" column refers to the three scenarios shown on the left in S5 Fig. sim_data.tar.gz Crossover recombination rate Crossover recombination rate estimated for 100 kb windows based on the linkage maps of Davey et al. (Evol. Lett. 1, 138–154, 2017). crossover_rec_rates_Davey2017.tsv Proportion CDS Proportion of CDS per 100 kb window based on the Hmel2 genome annotation. Coordinates are converted to chromosomes based on the Hmel2.5 scaffolding. prop_CDS.tsv