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Regional-scale differentiation and phylogeography of a desert plant Allium mongolicum (Liliaceae) inferred from chloroplast DNA sequence variation

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Abstract

Past geological and climatic changes have promoted regional-scale intraspecific differentiation and range contraction/expansion in many temperate plants. However, little is known about how the desert species in central Asia responded to past geological and climatic changes, especially for a few widespread desert plants. In the present study, we aimed to survey the population structure and phylogeographical history of Allium mongolicum, which is widely distributed in the deserts of northwestern China. We sequenced two chloroplast DNA fragments (accD-psaI and psbA-trnH) for 418 individuals from 38 populations across the whole range of the species. Fourteen chlorotypes were identified, and three out of them were dominant. All populations were divided into three larger distinct groups by SAMOVA, which was largely congruent with the geographical division based on the Monmonier’s maximum-difference algorithm. Each of the groups occupied a distinct geographical region with a specific dominant chlorotype. Analysis of molecular variance showed that a high proportion of the total genetic variation (70.05%) existed among the three regions. The demographic dynamic tests indicated that the desert species had experienced a sudden regional-scale range expansion/recolonization in the Quaternary glaciers, which was further identified by the ecological niche modeling. These results suggest that the species has a distinct regional-scale differentiation as well as multiple geographically isolated refugia. Our results further enforce the idea that the environmental changes since the late Miocene greatly promoted differentiation of desert plants in northwestern China, and the Quaternary climatic oscillations played an important role in structuring the current populations of these species.

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Acknowledgements

The authors thank Jianquan Liu (Lanzhou University) for his guidance and suggestions for this work, Huitao Liu (Cansas State University) for his English improvement in the manuscript, Li Feng (Northwest University) for his help in Ecological Niche modeling analysis and two anonymous reviewers for their constructive suggestions on revision. This research was supported by the National Natural Science Foundation of China (31360089, 31360098), the West Light Foundation of the Chinese Academy of Sciences and the Foundation for Innovation Research Groups of Gansu Province of China (145RJIA335).

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Authors and Affiliations

  1. State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, 730070, China

    Yinghua Zhang, Qiushi Yu, Xiaoke Hu, Jing Hu & Baoli Fan

  2. State Key Laboratory of Grassland Agro-Ecosystem, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China

    Qiushi Yu

  3. Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China

    Qian Zhang

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  1. Yinghua Zhang
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  2. Qiushi Yu
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  3. Qian Zhang
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  4. Xiaoke Hu
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  5. Jing Hu
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  6. Baoli Fan
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Correspondence to Qiushi Yu.

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Handling editor: Yunpeng Zhao.

Electronic supplementary material

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Information on Electronic Supplementary Materials

Online resource 1. Sequences of the 14 chlorotypes (H1-H14) identified in Allium mongolicum, which were used for producing phylogeny tree. The last one is the sequence of Allium anisopodium (outgroup). These sequences are the combined alignments of the two chloroplast DNA fragments (accD-psaI and psbA-trnH).

Online resource 2. Localities used for predicting the past and present distribution of Allium mongolicum under maximum entropy modeling with MAXENT version 3.3.3k. 1-38, field sampling sites; 39-85, specimen records from the Chinese Virtual Herbarium.

Online resource 3. Phylogenetic relationships of fourteen chlorotypes resolved in A. mongolicum using A. anisopodium as outgroup.

Online resource 4. Percentage of variance among populations and genetic diversity indices estimated by SAMOVA.

Online resource 5. Estimates of relative contributions of the environmental variables to the MAXENT model.

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Zhang, Y., Yu, Q., Zhang, Q. et al. Regional-scale differentiation and phylogeography of a desert plant Allium mongolicum (Liliaceae) inferred from chloroplast DNA sequence variation. Plant Syst Evol 303, 451–466 (2017). https://doi.org/10.1007/s00606-016-1383-6

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  • DOI: https://doi.org/10.1007/s00606-016-1383-6

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