DOI: 10.5061/dryad.t1g1jwtc9
title: Data from: Species diversification in the sky islands of southwestern China revealed by genomic, introgression and demographic analyses of Asian shrew moles

description: The mountains of Southwest China, a global biodiversity hotspot, have a
 unique “sky island” landscape with high diversity of both ancient and
 recently formed species. While their distribution patterns offer
 significant insights into diversification processes, the complex
 geological and climatic history, combined with dynamic histories of gene
 flow in endemic taxa, makes unravelling this history challenging. This
 study focuses on Asian shrew moles (genus Uropsilus), an ancient group
 endemic to this region with an unresolved taxonomic system. By combining
 phylogenomic, introgression, and demographic history analyses, we
 investigated the historical patterns of species diversification in this
 genus. We detected phylogenetic discordances among rapidly diverged
 lineages, driven by incomplete lineage sorting, both recent and ancient
 gene flow, and ghost introgression. The gene flow patterns revealed strong
 genetic isolation in the Hengduan Mountains region, contrasted by more
 extensive dispersal or connectivity in areas to its east, while suggesting
 potential ring-like diversification around the Sichuan Basin. Demographic
 history indicated that rapidly diverged lineages south of the Yangtze
 River exhibited significantly different responses to climatic fluctuations
 compared to other lineages, with the East Asian monsoon likely driving
 their radiative differentiation and dispersal. Our study demonstrates the
 impacts of mountain uplift, climatic changes, and the connectivity of sky
 island refugia in shaping the diverse patterns of species differentiation
 and their distribution.
description: # Data from: Phylogenomic and Biogeographic Study of Asian shrew moles The
 data includes the input files used in the analysis of the study. #### The
 following is the file structure and data description:
 "Uropsilus_filtered_SNP.vcf.gz" The whole-genome high-quality
 biallelic single-nucleotide polymorphisms (SNPs) of 39 samples.
 "raxml_input_SNPs.phy" The SNPs file used for constructing the
 maximum likelihood (ML) tree, converted to .phy format for input into
 RAxML 8.2.12. "NJ_IBS.txt" Pairwise estimates of
 identity-by-state (IBS) scores for all samples obtained by PLINK 1.90,
 used for constructing a neighbor-joining (NJ) tree with Phylip 3.698.
 "iqtree_input_CDS_4dtv.fas" The four-fold degenerate sites
 obtained from single-copy orthologous genes (CDS-4dtv) of 16 Uropsilus
 cryptic species and an outgroup Talpa occidentalis, used for constructing
 a ML tree with IQ-TREE 2.1.4.
 "15_mitochondria_genes_concatenation.phy" A concatenated dataset
 comprising 13 protein-coding genes and two ribosomal RNA (rRNA) genes from
 mitogenomes of all 39 samples, used for constructing a ML tree with RAxML
 8.2.12. "SNAPP_input.xml" The file used for input into SNAPP of
 BEAST 2.6.6. "mcmc_input_CDS_4dtv.phy" The CDS-4dtv dataset same
 as "iqtree_input_CDS_4dtv.fas", but converted to .phy format for
 input into PAML-MCMCTree. "mcmctree_input_cali.tree" The ML tree
 constructed by CDS-4dtv dataset, used as input tree for PAML-MCMCTree.
 "SNPs2CF_input_SNP_thin1000.phy" The pruned SNPs used for
 calculating the Concordance Factors (CFs). "SNPs2CF.csv" The CFs
 data, input for SNaQ. "astral_input_gene_trees.treefile" The
 gene trees for sliding windows constructed by IQTREE v2.4.0, which are
 prepared as input for species tree and concordance factors analyses in
 IQTREE v2.4.0 and ASTRAL v5.7.8. "consensus_seq_for_dfoil.zip"
 The genomic concordance sequences files used for DFOIL analysis.
 "psmc_fq_files.zip" The fastq files used for PSMC analysis.
 "BPP_input_loci.phy" 1000 loci used for BPP analysis.
 "BPP_control_files.zip" control files for each introgression
 model's analysis in BPP.