Supporting material: Orogeny of Ethiopian sky islands and Pliocene climate shifts promoted budding speciation and complex admixture in flightless Calosoma ground beetles

Supporting material for "Orogeny of Ethiopian sky islands and Pliocene climate shifts promoted budding speciation and complex admixture in flightless Calosoma ground beetles" alignments_partitions.zip all_loci.* contains all loci generated, 50p_loci_nofilter.* contains the 50% locus occupancy analysis and partitions, and arrowi_ref_SNP_processed.phy contains the SNP's used in the phylogenetic analysis 50p_loci_nofilter.fasta 50p_loci_nofilter.nex all_loci.fasta all_loci.nex arrowi_ref_SNP_processed.phy Both cluster.zip and localities.zip contain input BEAST anaysis files and resultswithin each are the colaescent constant and yule process analyses and results for each replicate; e.g.,: coal_localities.log coal_localities.ops coal_localities.trees popgen.zip contains the population genetic R analysis script in R markdown format and input data popgen_Ethiopia_haplotypes_arrowi_ref_maxmiss0.5_thin1000_keeps.vcf.recode.vcf popgen.Rmd supporting_data.ods structure.zip contains the generated structure file and structure analysis files gestroi.str "extraparams" "mainparams" seed.txt 10 replicates for K1-6 treefiles.zip contains all treefiles used in the analyses: 50p_nofilter_sansCBX0213_50runs.treefile 50p_nofilter_sansCBX0213_asteroid_r100_b1000.bestTree.newick 50p_nofilter_sansCBX0213_gCF.cf.tree 50p_nofilter_sansCBX0213_MFP_BB1000_locustrees.treefile 50p_nofilter_sansCBX0213_sCF.iqtree 50p_nofilter_wASTRAL_R.treefile clusters_dating_loci.treefile coal_cluster.combined.treeanntator.trees preliminary_ML.treefile species_dating_loci.treefile