DOI: 10.5061/dryad.dr19s
title: Data from: Cryptic phylogeographic history sheds light on the generation of species diversity in sky-island mountains

description: Biodiversity hotspots should be given high priority for conservation under
 the situation of global climate change. The sky islands in southwestern
 China are characterized by extraordinarily high species diversity and are
 among one of the world’s top biodiversity hotspots. However, neither the
 actual species diversity in this region or mechanisms generating this
 diversity are well explored. Here, we report on the phylogeographic
 analysis of the long-tailed mole (Scaptonyx fusicaudus), a semi-fossorial
 mammal that inhabits the montane cool forests across the Chinese sky
 islands and is considered to represent one species divided into two
 subspecies. Analyses using DNA sequence data from one mitochondrial and
 six nuclear genes revealed that populations inhabiting different mountains
 exhibited exceptionally strong geographic structure. The lowlands and
 large rivers act as “soft” and “hard” barriers to dispersal, respectively,
 isolating evolutionary lineages for up to 11 million years. Our results
 suggest that the mountain ranges act as interglacial refugia buffering
 populations from climate fluctuations, further facilitating allopatric
 diversification. Strikingly, species delimitation analyses suggests that
 the long-tailed mole may comprise 18 operational taxonomic units and 17
 putative species. Our results suggest that for low-vagility species, the
 complex topography of the Chinese sky islands has shaped genetic diversity
 and structure and promoted exceptional diversification through a
 combination of eco-environmental stability as well as geographic
 fragmentation. The patterns observed in S. fusicaudus may be
 representative for other cold-adapted species, reflecting the generation
 of mammalian faunal diversity in the sky-island mountains of southwestern
 China.
description: 01-CYTBingroup cytb02-BRCA1ingroup BRCA103-ATP7ingroup ATP704-AD-noncodingingroup ADORA305-AP-noncodingingroup APP06-BCHEingroup BCHE07-RAG1ingroup RAG102-BRCA1-phasedingroup BRCA1-phased03-ATP7-phasedingroup ATP7-phased04-AD-noncoding-phasedingroup ADROA3-phased05-AP-noncoding-phasedingroup APP-phased06-BCHE-phasedingroup BCHE-phased07-RAG1-phasedingroup RAG1-phasedConcatenated alignments-1-beastnexus file for concatenated analyses using BEASTconcatenated-02-07-phased-complete201-17putative-6p-bygeneconcatenated NUCLEAR sequences used for *BEAST coalescent tree estimation01-cytb-raxmlCYTB gene tree conducted using RAXML01-CYTB-3p-1RL-BD-2cali-10M.(subst).outCYT B gene tree conducted using BEAST02-R-GMYCdata and results from GMYC species delimitation analyses03-bPTPdata and results of the bPTP species delimitation analyses04-usearchdata and result of the OTU analyses using USEARCH05-BPP-zipdata for BPP species delimitation analyses06-Partitionfinderresults of Partition analyses to determine the best-fit evolutionary models for each gene as well for the concatenated nuclear genes07-structure-zipinput files for structure analysesScaptonyx-DIYABCinput file for DIYABC analyses from run1 to run4species distribution modeling and PCAdata for MAXENT analyses as well as the results of the PCA analysesconcatenated-nDNA-phased-complete-PSSSDivergence time estimation and comparison using PS/SS as implemented in BEAST1.8 (input & output)11-species tree delimitation-staceyspecies tree estimation using the STACEY algorithm as implemented in BEAST2.4scaptonyx-diyabc2.1.0-run1-4Datasets used in four runs of DIYABC analyses.