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Chloroplast DNA-based genetic diversity and phylogeography of Pyrus betulaefolia (Rosaceae) in Northern China

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Abstract

Pyrus betulaefolia Bunge, considered as an intermediate between oriental and occidental pear groups, is one of the most important wild pear species. The number of its populations is decreasing because of habitat destruction, fragmentation, and continuous exploitation, so protection and conservation measures are urgently needed. Assessment of its genetic diversity and phylogeography are imperative for its efficient conservation. Two chloroplast DNA intergenic fragments were used to detect genetic diversity and phylogeography of 320 individuals from 18 wild P. betulaefolia populations. Haplotype variation, genetic differentiation, and historical events of the populations were estimated. The results showed that P. betulaefolia populations sampled in northern China contained a high level of genetic diversity (H T = 0.826). A significant isolation-by-distance value (r = 0.587, P < 0.001, 1,000 permutations) among all 18 populations indicated a correlation between genetic divergence and geographic distance. Four population groups were identified in a neighbor-joining tree based on the genetic distance. Analyses of molecular variation showed that the genetic variation mainly existed among population groups, representing 64.61 % of the total variation. Phylogeographic analyses indicated that the populations of P. betulaefolia experienced a scenario of rapid range expansion, which probably occurred between 608,000 and 204,580 years ago. Meanwhile, both the restricted gene flow with isolation by distance and allopatric fragmentation were crucial processes responsible for shaping the genetic patterns of P. betulaefolia. The occurrence of specific haplotypes might be ascribed to an ancestral introgression or joint retention of an ancestral polymorphism with other Pyrus species at the northern edge of the distribution of P. betulaefolia. Three populations displaying a high level of haplotype diversity and unique haplotypes were assumed to be relict populations of Quaternary glaciation and should have conservation priority. Three additional large populations should also be preferentially protected by building natural preservation zones.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 30871690), Specialized Research Fund for the Doctoral Program of Higher Education of China (No. 20110101110091), and Specialized Research Fund for Major Science and Technique of Zhejiang Province of China (No. 2012C12904-2).

Data archiving statement

The accD–psaI and trnL–trnF sequences have been submitted to GeneBank and the accession numbers were from KF771383 to KF771402.

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Authors and Affiliations

  1. Department of Horticulture, The State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development of Quality Improvement, Zhejiang University, Hangzhou, Zhejiang, 310058, China

    Yu Zong, Ping Sun, Jing Liu, Xiaoyan Yue, Qingfeng Niu & Yuanwen Teng

  2. Jinhua Academy of Agricultural Science, Jinhua, Zhejiang, 321000, China

    Ping Sun

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  1. Yu Zong
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Correspondence to Yuanwen Teng.

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Communicated by D. Chagné

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Fig. S1

Mismatch distribution analysis for 18 populations of Pyrus betulaefolia. The observed number of differences between pairs of haplotypes is plotted with a dashed line. The solid line indicates the expected distribution under a sudden expansion model. (JPEG 1262 kb)

Fig. S2

Haplotype networks of Pyrus betulaefolia constructed in TCS under the 95% statistical parsimony criterion. The nineteen haplotypes H1–H19 are represented by different colors. Small, open circles represent missing haplotypes. Both solid and dot lines represent single mutant events, dot lines showed the resolved loops in the nested clade analysis. Numbers labeled on the branches indicate the locations of mutant nucleotides. (JPEG 2180 kb)

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Zong, Y., Sun, P., Liu, J. et al. Chloroplast DNA-based genetic diversity and phylogeography of Pyrus betulaefolia (Rosaceae) in Northern China. Tree Genetics & Genomes 10, 739–749 (2014). https://doi.org/10.1007/s11295-014-0718-0

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