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.
edelman2019_lepidopteraAlignment
This is the full multi-species whole genome alignment generated by ProgressiveCactus.
fasta alignments and newick trees of loci used for species tree reconstruction
A 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.gz
eratoClade_HeraRef_5KB_all.tar
These 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.tar
fasta files from which samples were extracted to run phyloNet for the erato clade
melpomene_phyloNetFastas.tar
fasta files from which samples were extracted to run phyloNet for the melpomene clade
Progressive Cactus Files
This archive contains the configuration files used to generate the full lepidoptera progressiveCactus alignment.
progressiveCactusFiles.zip
eratoClade.50KBSliding.toHeraGenome
tree 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.toHmelGenome
trees of erato clade genomes in 50KB sliding windows made from the H. melpomene v2.5 reference coordinates.
melpomeneClade.50KBSliding.allTrees.nwk
trees of melpomene clade genomes in 50KB sliding windows made from the H. melpomene v2.5 reference coordinates.
repeats
repeatMasker output for all genomes in hal alignment
eratoGenomeInfo
This archive contains information on local recombination rate (for specified 10 kb windows) as well as general positional information for the locations of scaffolds on chromosomes
eratoClade_10KBAbutting_HeraRef.ge2kb.trees
erato 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.
