Data from: Hidden histories of gene flow in highland birds revealed with genomic markers

Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these 'hidden histories' using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation-with-bouts-of-gene-flow will turn out to be a common mode of speciation.Structure Input FileData matrix for Structure runsSTRUCTURE_input.txtSNAPP Input FileInput file for SNAPP species tree runs in BEASTSNAPP_input.xmlSNP_callsVarious files associated with calling SNPs from UCE loci for use with SNAPP and StructureUCE Data MatrixConcatenated UCE data matrix for phylogenetic analysisS_File_2_UCE_incomplete_matrix_alignment_labeled.phylipmtDNA alignmentAlignment of 13 mtDNA protein coding gene for phylogenetic analysisS_File_3_mtDNA_prot_cod_reg_alignment_labeled.phylipmtDNA partitionsPartition file for mtDNA alignmentS_File_4_mtDNA_partitions_for_RAxML.txtDNA Data Statistics TableExtended table with statistics on sequenced DNA data for individual specimensS1_Statistics_table.xlsxScripts for SNP CallingVarious custom scripts used to call SNPs for Structure and SNAPPScripts.zipFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-125778