DOI: 10.5061/dryad.b7bj832
title: Data from: Genomic architecture and introgression shape a butterfly radiation

description: We probe the history of rapidly radiating Heliconius butterflies by means
 of 20 new genome assemblies and employ them to investigate the genomic
 architecture of gene flow among lineages. By developing a test to
 distinguish incomplete lineage sorting from introgression, we demonstrate
 that histories of loci that differ from the species tree arose mostly
 through introgression. Moreover, these loci are underrepresented in low
 recombination and gene-rich regions, consistent with the purging of
 introgressed alleles tightly linked with incompatibility loci.
 Additionally, our analysis identifies an inversion that captures a color
 pattern switch locus which was transferred between lineages via
 introgression and is convergent with a similar rearrangement in another
 part of the genus. This analysis of multiple de novo genome sequences
 enables an improved understanding of the importance of introgression and
 selective processes in adaptive radiation.
description: edelman2019_lepidopteraAlignmentThis is the full multi-species whole genome alignment generated by ProgressiveCactus.fasta alignments and newick trees of loci used for species tree reconstructionA number of different datasets were used to generate species tree estimates in this paper. This file includes alignments (in fasta format) and locus-by-locus gene trees (in newick format). The datasets include fully-aligned coding and non-coding blocks among all heliconiini species included here (Agraulis vanillae, Eueides tales, Heliconius melpomene, H. cydno, H. timareta, H. pardalinus, H. numata, H. besckei, H. doris, H. erato, H. himera, H. erato x H. himera F1 hybrid, H. hecalesia, H. telesiphe, H. demeter, and H. sara), as well as blocks among the Heliconiini species + lepidopteran outgroups (Plutella xytostella, Bombyx mori, Melitea cinxia, Danaus plexippus, Larema accius, Papilio polytes, and Bicyclus anynana). In addition to these blocks, we have alignments and trees for genes extracted based on the H. melpomene reference annotation.phylogeny_trees_fastas_2.tar.gzeratoClade_HeraRef_5KB_all.tarThese fasta files were used to calculate fd and to generate trees for our branch length test. This is the full dataset, which was subset in various ways for testing as detailed in the paper.eratoClade.phyloNetFastas.tarfasta files from which samples were extracted to run phyloNet for the erato clademelpomene_phyloNetFastas.tarfasta files from which samples were extracted to run phyloNet for the melpomene cladeProgressive Cactus FilesThis archive contains the configuration files used to generate the full lepidoptera progressiveCactus alignment.progressiveCactusFiles.ziperatoClade.50KBSliding.toHeraGenometree file used for figure 2A - trees of erato clade genomes in 50KB sliding windows made from the H. erato demophoon reference coordinates.eratoClade_50KBSliding.allTrees.toHmelGenometrees of erato clade genomes in 50KB sliding windows made from the H. melpomene v2.5 reference coordinates.melpomeneClade.50KBSliding.allTrees.nwktrees of melpomene clade genomes in 50KB sliding windows made from the H. melpomene v2.5 reference coordinates.repeatsrepeatMasker output for all genomes in hal alignmenteratoGenomeInfoThis archive contains information on local recombination rate (for specified 10 kb windows) as well as general positional information for the locations of scaffolds on chromosomeseratoClade_10KBAbutting_HeraRef.ge2kb.treeserato clade trees made from 10 kb abutting windows constructed from the H. erato demophoon reference coordinates. These trees were used for the recombination rate analyses in the paper.