DOI: 10.5061/dryad.5n10d
title: Data from: Divergence with gene flow across a speciation continuum of Heliconius butterflies

description: 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.
description: Genotype calls for
 Heliconius erato clade (vcf format)Vcf files were generated
 by aligning to a reference using BWA. Genotypes were called using GATK.
 File prefix is _. Files are standard vcf
 format.vcfs_heliconius.zipData and trees for BEAST analysis of Heliconius erato cladeInput sequences with run parameters (xml files) and resulting trees (annot files) for BEAST analysis. Analyzed the Heliconius erato clade across 350-kb unlinked to color pattern. Compared relaxed clock to strict clock.beast_heliconius.zipData and tree for MrBayes analysis of Heliconius erato clade color unlinked lociInput sequences and run parameters (.nex files) and resulting tree (.tre file) for MrBayes analysis. Analyzed the Heliconius erato clade across 350-kb unlinked to color pattern.mrbayes_unlinked_heliconius.zipData and tree for MrBayes analysis of Heliconius erato clade red color locusInput sequences and run parameters (.nex files) and resulting tree (.tre file) for MrBayes analysis. Analyzed the Heliconius erato clade across 65-kb red color pattern locus.mrbayes_D65peak_heliconius.zip