Data from: Genome-wide patterns of divergence and gene flow across a butterfly radiation

The Heliconius butterflies are a diverse recent radiation comprising
multiple levels of divergence with on-going gene flow between species. The
recently sequenced genome of Heliconius melpomene allowed us to
investigate the genomic evolution of this group using dense RAD marker
sequencing. Phylogenetic analysis of 54 individuals robustly supported
reciprocal monophyly of H. melpomene and H. cydno and refuted previous
phylogenetic hypotheses that H. melpomene may be paraphylectic with
respect to H. cydno. H. timareta also formed a monophyletic clade closely
related but distinct from H. cydno with H. heurippa falling within this
clade. We find evidence for pervasive gene flow between sympatric
populations of the sister clades H. melpomene and H. cydno/timareta,
particularly between H. cydno and H. melpomene from Central America and
between H. timareta and H. melpomene from the eastern slopes of the Andes.
Between races, divergence is primarily explained by isolation-by-distance;
and there is little, if any, genetic population structure between
parapatric races, suggesting that hybrid zones between races are not zones
of secondary contact. Our results support previous findings that colour
pattern loci are shared between populations and species with similar
colour pattern elements. Further this pattern is almost unique to these
genomic regions with only a very small number of other loci showing
significant similarity between populations and species with similar colour
patterns.