DOI: 10.5061/dryad.88r69
title: Data from: Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): inference from transcriptome-wide coalescence analyses

description: Ancient origins, profound ecological divergence, and extensive
 hybridization make the fire-bellied toads Bombina bombina and B. variegata
 (Anura: Bombinatoridae) an intriguing test case of ecological speciation.
 Previous modeling has proposed that the narrow Bombina hybrid zones
 represent strong barriers to neutral introgression. We test this
 prediction by inferring the rate of gene exchange between pure populations
 on either side of the intensively studied Kraków transect. We developed a
 method to extract high confidence sets of orthologous genes from de novo
 transcriptome assemblies, fitted a range of divergence models to these
 data and assessed their relative support with analytic likelihood
 calculations. There was clear evidence for postdivergence gene flow, but,
 as expected, no perceptible signal of recent introgression via the nearby
 hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and
 B. orientalis) validated our parameter estimates against a larger set of
 prior expectations. Despite substantial cumulative introgression over
 millions of years, adaptive divergence of the hybridizing taxa is
 essentially unaffected by their lack of reproductive isolation. Extended
 distribution ranges also buffer them against small-scale environmental
 perturbations that have been shown to reverse the speciation process in
 other, more recent ecotypes.
description: ReadMeDescription of the data
 package, associated submissions, and contents of filesreference_contigs_BboList of contig names in the Bombina bombina reference transcriptomereference_contigs_BvvList of contig names in the Bombina variegata variegata reference transcriptomereference_contigs_BvsList of contig names in the Bombina variegata scabra reference transcriptomereference_contigs_BorList of contig names in the Bombina orientalis reference transcriptomeOrthoMCL_orfs_BboPredicted peptide sequences from the Bombina bombina reference transcriptomeOrthoMCL_orfs_BvvPredicted peptide sequences from the Bombina variegata variegata reference transcriptomeOrthoMCL_orfs_BvsPredicted peptide sequences from the Bombina variegata scabra reference transcriptomeOrthoMCL_orfs_BorPredicted peptide sequences from the Bombina orientalis reference transcriptomeOrthoMCL_peptides_XtrPeptide sequences from the Silurana (Xenopus) tropicalis proteomeOrthoMCL_groups_1.5Unfiltered OrthoMCL clusters (inflation value = 1.5)RobustGroups_4taxRobust orthogroupsRobustGroups_4tax_no_multiorf_indexRobust orthogroups, after removal of clusters that contain contigs with more than one ORF preditionorthogroup_alignments_Bvv_BboCross-taxon nucleotide alignments within robust orthogroups (B. v. variegata/B. bombina)orthogroup_alignments_Bvv_BorCross-taxon nucleotide alignments within robust orthogroups (B. v. variegata/B. orientalis)orthogroup_alignments_Bvv_BvsCross-taxon nucleotide alignments within robust orthogroups (B. v. variegata/B. v. scabra)site_counts_Bvv_BboCounts of variable sites in blocks of 150 fourfold degenerate sites (B. v. varieagta/B. bombina)site_counts_Bvv_BorCounts of variable sites in blocks of 150 fourfold degenerate sites (B. v. varieagta/B. orientalis)site_counts_Bvv_BvsCounts of variable sites in blocks of 150 fourfold degenerate sites (B. v. varieagta/B. v. scabra)Roche454_paralogue_names_BboList of alternate contig names for B. bombina Roche 454 paraloguesRoche454_paralogue_names_BvvList of alternate contig names for B. v. variegata Roche 454 paralogues