The demographic response of a deciduous shrub (the Indigofera bungeana complex, Fabaceae) to the Pleistocene climate changes in East Asia

Xue-Li Zhao,Yun-Dong Gao,Zhang-Ming Zhu,Bo Xu,Xin-Fen Gao

doi:10.1038/s41598-017-00613-x

Abstract

East Asia harbors the highest level of floristic diversity among the world’s temperate regions. Despite the increase in phylogeographic studies of temperate plants in East Asia, far less attention has been paid to widely distributed deciduous shrubs that widespread across several floral regions. We sequenced two chloroplast DNA (cpDNA) fragments (ndhJ-trnF and trnD-trnT) and one nuclear DNA (Pgk1) of 472 individuals from 51 populations of such a group, the Indigofera bungeana complex. We used population genetic data as well as ecological niche modelling to examine the evolutionary history and glacial refugia during the Last Glacial Maximum (LGM) of this group. We recovered 133 cpDNA and 68 nuclear haplotypes. The star-phylogeny of the recovered cpDNA and nuclear haplotypes and demographic analyses suggested distinct range expansion of I. bungeana complex have occurred during the early and middle Pleistocene. The climate change of the LGM might have affected little on the distribution of this complex based on the niche modelling. However, these climate changes and geographic isolation probably resulted in fixtures of the private haplotypes and genetic differentiations between regions. Our results suggested that this arid-tolerant species complex may have different responses to the Quaternary climate changes with those climate-sensitive species.

Highlights

It is well appreciated that climate oscillations during the Quaternary have profoundly shaped the geographic distributions and current genetic diversity of many temperate species in the Northern Hemisphere[1]
We focused on the phylogeographic patterns of the Indigofera bungeana complex (Fabaceae), a complex of deciduous shrubs widespread in temperate East Asia, with a continuous geographic distribution covering southern China, northern China and the Hengduan Mountains region (HMR)
We aimed to address the following questions: (1) Are phylogeographic inferences from chloroplast DNA (cpDNA) data consistent with those from nuclear DNA data? (2) When and how did this complex obtain its widespread distribution in East Asia? (3) Did the I. bungeana complex retreat southward or survive in situ during the Last Glacial Maximum (LGM)?

Summary

Introduction

It is well appreciated that climate oscillations during the Quaternary have profoundly shaped the geographic distributions and current genetic diversity of many temperate species in the Northern Hemisphere[1]. Have examined the phylogeographic structure of a single species/species complex or monophyletic group whose current distributions cover all of these regions in East Asia. Members of this complex grow in sunny, arid habitats at elevations between 100‒2700 m17 Their widespread distribution provides a unique opportunity to examine how plants responded to past climate changes over a large region in East Asia. Two maternally inherited chloroplast DNAs (cpDNAs) were used, as in most phylogeographic studies[16, 18], due to the merits of rare recombinations and smaller effective population size[19] This type of population genetic data allows an inference of historical range shifts and recolonization routes[20,21,22].

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