Phylogeographic study of Chinese seabuckthorn (Hippophae rhamnoides subsp. sinensis Rousi) reveals two distinct haplotype groups and multiple microrefugia on the Qinghai-Tibet Plateau

Abstract

Historical climate change can shape the genetic pattern of a species. Studies on this phenomenon provide great advantage in predicting the response of species to current and future global climate change. Chinese seabuckthorn (Hippophae rhamnoides subsp. sinensis) is one of the most important cultivated plants in Northwest China. However, the subspecies history and the potential genetic resources within the subspecies range remain unclear. In this study, we utilized two intergenic chloroplast regions to characterize the spatial genetic distribution of the species. We found 19 haplotypes in total, 12 of which were unique to the Chinese seabuckthorn. The populations observed on the Qinghai-Tibet Plateau (QTP) consisted of most of the haplotypes, while in the northeast of the range of the subspecies, an area not on the QTP, only four haplotypes were detected. Our study also revealed two distinct haplotype groups of the subspecies with a sharp transition region located in the south of the Zoige Basin. 89.96% of the genetic variation located between the regions. Mismatch analysis indicated old expansions of these two haplotype groups, approximately around the early stage of Pleistocene. Additional morphological proofs from existing studies and habitat differentiation supported a long independent colonization history among the two regions. Potential adaptation probably occurred but needs more genome and morphology data in future. Chinese seabuckthorn have an older population expansion compared with subspecies in Europe. The lack of large land ice sheets and the heterogeneous landscape of the QTP could have provided extensive microrefugia for Chinese seabuckthorn during the glaciation period. Multiple localities sustaining high-frequency private haplotypes support this hypothesis. Our study gives clear insight into the distribution of genetic resources and the evolutionary history of Chinese seabuckthorn.

Keywords: Analyses of molecular variance; Hippophae rhamnoides subsp. sinensis; beast; chloroplast intergenic fragments; demographic analysis; historical climate change.

Figure 1

(A) A median joining network of 19 haplotypes found in our study. The circle size is proportional to the haplotype frequency. The number on the connection lines indicates the mutation steps between haplotypes, while for unmarked lines, the default number of mutation steps is one. (B) The subspecies range distribution over the study area. (C) The spatial distribution of haplotypes for Chinese seabuckthorn. The haplotype colors are identical in (A and C). The shaded area is the range distribution of the subspecies according to Lian and Chen (1991). The black dashed line indicates the transition area where the haplotype group changes from the North type (above the line) to the Southwest type (below the line). (D) A detail map around the transition region in (C).

Figure 2

The maximum-likelihood tree topology of the cpDNA haplotypes detected from the TrnS-TrnG and TrnT-TrnY region of Chinese seabuckthorn; numbers above the branches indicate Bayesian posterior probabilities (left) and the bootstrap values for ML(right) analyses, respectively; inferred dates in Ma before present (95% confidence interval) are given in the rectangular boxes. NS, nonsupported.

Figure 3

Comparison of TrnS-TrnG results in this study with published data of Hippophae rhamnoides subsp. yunnanensis (Cheng et al. 2009). ML tree was constructed in Mega5. The values adjacent to the branches indicate the support value based on 2000 bootstrap replications. Only bootstrap values larger than 50% are shown. The node marked with a star indicates the haplotypes of Chinese seabuckthorn that are shared with H. rhamnoides subsp. yunnanensis. NS, nonsupported.