DOI: 10.5061/dryad.s3060
title: Data from: Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau

description: A knowledge of intraspecific divergence and range dynamics of dominant
 forest trees in response to past geological and climate change is of major
 importance to an understanding of their recent evolution and demography.
 Such knowledge is informative of how forests were affected by
 environmental factors in the past and may provide pointers to their
 response to future environmental change. However, genetic signatures of
 such historical events are often weak at individual loci due to large
 effective population sizes and long generation times of forest trees. This
 problem can be overcome by analysing genetic variation across multiple
 loci. We used this approach to examine intraspecific divergence and past
 range dynamics in the conifer Picea likiangensis, a dominant tree of
 forests occurring in eastern and southern areas of the Qinghai-Tibet
 Plateau (QTP). We sequenced 13 nuclear loci, two mitochondrial DNA regions
 and three plastid (chloroplast) DNA regions in 177 individuals sampled
 from 22 natural populations of this species, and tested the hypothesis
 that its evolutionary history was markedly affected by Pliocene QTP
 uplifts and Quaternary climatic oscillations. Consistent with the
 taxonomic delimitation of the three morphologically divergent varieties
 examined, all individuals clustered into three genetic groups with
 inter-variety admixture detected in regions of geographical overlap.
 Divergence between varieties was estimated to have occurred within the
 Pliocene and ecological niche modeling based on 20 ecological variables
 suggested that niche differentiation was high. Furthermore, modeling of
 population genetic data indicated that two of the varieties (var.
 rubescens and var. linzhiensis) expanded their population sizes after the
 largest Quaternary glaciation in the QTP, while expansion of the third
 variety (var. likiangensis) began prior to this, probably following the
 Pliocene QTP uplift. These findings point to the importance of geological
 and climatic changes during the Pliocene and Pleistocene as causes of
 intraspecific diversification and range shifts of dominant tree species in
 the QTP biodiversity hotspot region.
description: Bioclimate data of Picea
 likiangensis, Intraspecific divergence and range expansion in the
 Qinghai-Tibet PlateauBioclimate
 data.xlsMaxEnt input file of
 Picea likiangensis, Intraspecific divergence and range expansion in the
 Qinghai-Tibet PlateauMaxEnt input
 file.txtGenebank accessions
 number of Picea likiangensis, Intraspecific divergence and range expansion
 in the Qinghai-Tibet PlateauDNA sequence alignments
 of P. likiangensis 4clDNA sequence alignments
 of P. likiangensis EbsDNA sequence alignments
 of P. likiangensis Ft3DNA sequence alignments
 of P. likiangensis GiDNA sequence alignments
 of P. likiangensis Moo2DNA sequence alignments
 of P. likiangensis Moo7d1DNA sequence alignments
 of P. likiangensis PchDNA sequence alignments
 of P. likiangensis Sb16DNA sequence alignments
 of P. likiangensis Sb29DNA sequence alignments
 of P. likiangensis Sb62DNA sequence alignments
 of P. likiangensis Sel1364DNA sequence alignments
 of P. likiangensis Sel1390DNA sequence alignments
 of P. likiangensis Xy1420DNA sequence alignments
 of P.likiangensis nad1DNA sequence alignments
 of P.likiangensis nad5DNA sequence alignments
 of P.likiangensis ndhKCDNA sequence alignments
 of P.likiangensis trnLFDNA sequence alignments
 of P.likiangensis trnSG