Data from: Divergence with gene flow across a speciation continuum of Heliconius butterflies

Background: A key to understanding the origins of species is determining
the evolutionary processes that drive the patterns of genomic divergence
during speciation. New genomic technologies enable the study of
high-resolution genomic patterns of divergence across natural speciation
continua, where taxa pairs with different levels of reproductive isolation
can be used as proxies for different stages of speciation. Empirical
studies of these speciation continua can provide valuable insights into
how genomes diverge during speciation. Methods: We examine variation
across a handful of genomic regions in parapatric and allopatric
populations of Heliconius butterflies with varying levels of reproductive
isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome,
including 1-Mb across the red color pattern locus and multiple regions
unlinked to color pattern variation. Results: Phylogenetic analyses reveal
a speciation continuum of pairs of hybridizing races and incipient species
in the Heliconius erato clade. Comparisons of hybridizing pairs of
divergently colored races and incipient species reveal that genomic
divergence increases with ecological and reproductive isolation, not only
across the locus responsible for adaptive variation in red wing
coloration, but also at genomic regions unlinked to color pattern.
Discussion: We observe high levels of divergence between the incipient
species H. erato and H. himera, suggesting that divergence may accumulate
early in the speciation process. Comparisons of genomic divergence between
the incipient species and allopatric races suggest that limited gene flow
cannot account for the observed high levels of divergence between the
incipient species. Conclusions: Our results provide a reconstruction of
the speciation continuum across the H. erato clade and provide insights
into the processes that drive genomic divergence during speciation,
establishing the H. erato clade as a powerful framework for the study of
speciation.