DOI: 10.5061/dryad.182dv
title: Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation

description: Speciation events often occur in rapid bursts of diversification, but the
 ecological and genetic factors that promote these radiations are still
 much debated. Using whole transcriptomes from all 13 species in the
 ecologically and reproductively diverse wild tomato clade (Solanum sect.
 Lycopersicon), we infer the species phylogeny and patterns of genetic
 diversity in this group. Despite widespread phylogenetic discordance due
 to the sorting of ancestral variation, we date the origin of this
 radiation to approximately 2.5 million years ago and find evidence for at
 least three sources of adaptive genetic variation that fuel
 diversification. First, we detect introgression both historically between
 early-branching lineages and recently between individual populations, at
 specific loci whose functions indicate likely adaptive benefits. Second,
 we find evidence of lineage-specific de novo evolution for many genes,
 including loci involved in the production of red fruit color. Finally,
 using a “PhyloGWAS” approach, we detect environment-specific sorting of
 ancestral variation among populations that come from different species but
 share common environmental conditions. Estimated across the whole clade,
 small but substantial and approximately equal fractions of the euchromatic
 portion of the genome are inferred to contribute to each of these three
 sources of adaptive genetic variation. These results indicate that
 multiple genetic sources can promote rapid diversification and speciation
 in response to new ecological opportunity, in agreement with our emerging
 phylogenomic understanding of the complexity of both ancient and recent
 species radiations.
description: Combined VCF for all 29
 accessions for chromosome 0Pease_etal_SL2.50ch00.vcf.gzCombined VCF for all 29 accessions for chromosome 1Pease_etal_SL2.50ch01.vcf.gzCombined VCF for all 29 accessions for chromosome 2Pease_etal_SL2.50ch02.vcf.gzCombined VCF for all 29 accessions for chromosome 3Pease_etal_SL2.50ch03.vcf.gzCombined VCF for all 29 accessions for chromosome 4Pease_etal_SL2.50ch04.vcf.gzCombined VCF for all 29 accessions for chromosome 5Pease_etal_SL2.50ch05.vcf.gzCombined VCF for all 29 accessions for chromosome 6Pease_etal_SL2.50ch06.vcf.gzCombined VCF for all 29 accessions for chromosome 7Pease_etal_SL2.50ch07.vcf.gzCombined VCF for all 29 accessions for chromosome 8Pease_etal_SL2.50ch08.vcf.gzCombined VCF for all 29 accessions for chromosome 9Pease_etal_SL2.50ch09.vcf.gzCombined VCF for all 29 accessions for chromosome 10Pease_etal_SL2.50ch10.vcf.gzCombined VCF for all 29 accessions for chromosome 11Pease_etal_SL2.50ch11.vcf.gzCombined VCF for all 29 accessions for chromosome 12Pease_etal_SL2.50ch12.vcf.gzRaw Reads located at NCBI BioProject PRJNA305880http://www.ncbi.nlm.nih.gov/bioproject/305880HQ Alignment in Multisample Variant FormatPease_etal_Tomato29acc_HQ.mvf.gzHD Alignment in Multisample Variant FormatPease_etal_Tomato29acc_HD.mvf.gzLQ Alignment in Multisample Variant FormatPease_etal_Tomato29acc_LQ.mvf.gzHQ Coding Sequence Alignment in Multisample Variant FormatPease_etal_Tomato29acc_HQ_prot.mvf.gzGenome-wide all sample phylogenies from gene regions, 100kb and 1Mb regionsPease_etal_TomatoPhylo_GeneTrees.tar.gzGenome-Wide Concatenated/Coalescent/Consensus PhylogeniesPease_etal_TomatoPhylo_GenomeWideTrees.tar.gzQuartet Gene Trees, D-statistics, and DFOIL results for Figs S4/5Pease_etal_TomatoPhylo_QuartetTreeDstatsDFOIL.tar.gz