Data from: Recombination rate variation shapes barriers to introgression across butterfly genomes

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.