Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

Dongmei Chen,Washington Gapare,Harry X Wu,Shan Yin,Chunjiang Liu,Hongmei Du,Norikazu Yamanaka,Xiao Sun,Hongzhang Kang,Xianxian Zhang

doi:10.1371/journal.pone.0047268

Abstract

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N ST = 0.751> G ST = 0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s FS indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.

Highlights

The climatic changes of the Quaternary have exerted a profound influence on the patterns of modern plant distribution and evolution at the global scale [1,2]
Thirty-four populations were from Mainland China, three from Zhoushan Archipelago which located in East China Seas, four from Taiwan Island, three from Korea Peninsula and the remained six from Japanese Archipelago (Fig. 1; Table 1)
A total of 26 haplotypes were detected in the 50 Q. variabilis populations across eastern Asia (Information S1, Fig. 1)

Summary

Introduction

The climatic changes of the Quaternary (i.e., over the past 2.6 million years) have exerted a profound influence on the patterns of modern plant distribution and evolution at the global scale [1,2]. East Asia experienced strong climate oscillations during the glacial and interglacial periods no massive glaciers occurred since the Quaternary [7,8]. A general view is that during the LGM period, the temperature declined by about 5– 11uC relative to the current climate across the Asian Continent. After the LGM, the climate became warmer with several smaller glaciers occurring in an interval manner, resulting in decrease in temperature across the Asian continent [8].

Methods

Results

Conclusion