Phylogeography of Gymnadenia conopsea from the Qinghai-Tibet Plateau

Abstract

Abstract: Chloroplast DNA（rbcl and psbA-trnH）of Gymnadenia conopsea（G. conopsea）from the Qinghai-Tibet Plateau was used for phylogeography research，aiming at revealing the distribution pattern and evolutional process of genetic lineage of G. conopsea. Eleven haplotypes were identified in 199 samples of 10 G. conopsea populations. The analysis of molecular variance（AMOVA）showed 65.93% of the genetic variance was from inter-populations and FST value of 0.659（P<0.01）also indicated that there was significant genetic differentiation between different populations. The genetic differentiation coefficients NST（0.398）< GST（0.626）implied no significant phylogeographic structure for G. conopsea populations in the Qinghai-Tibet Plateau. Mismatch analysis of multi-peak and Tajima’s D neutral test（-1.455，P>0.1）demonstrated G. conopsea populations had not experienced abrupt expansion recently. Phylogenetic analysis and divergence time estimation showed that G. conopsea in the Qinghai-Tibet Plateau originated indigenously，haplotypes started to differentiate 19.08 million years ago（Mya）in Miocene，indicating that the genetic differentiation of G. conopsea was related to the uplift of the Qinghai-Tibetan Plateau，and the genetic distribution pattern of G. conopsea was mostly formed before the Quaternary glaciation.

Key words: Gymnadenia conopsea, phylogeography, genetic diversity, the Qinghai-Tibet Plateau

CLC Number:

10.13560/j.cnki.biotech.bull.1985.2016.12.016

BAO Wu-yin,ZHANG Yang,LIN Peng-cheng,NAN Peng,HUANG Yan-yan,JIN Hao-fei,ZHONG Yang. Phylogeography of Gymnadenia conopsea from the Qinghai-Tibet Plateau[J]. Biotechnology Bulletin, 2016, 32(12): 96-102.

References

[1] Campbell VV, Rowe G, Beebee TJ, et al. Genetic differentiation amongst fragrant orchids（Gymnadenia conopsea sl）in the British Isles[J] . Botanical Journal of the Linnean Society, 2007, 155（3）：349-360.
[2] 杨永昌. 藏药志[M] . 西宁：青海人民出版社, 1991.
[3] 金洪, 王俊杰. 手掌参的组织培养研究[J] . 内蒙古农牧学院学报, 1995, 16（2）：74-77.
[4] Liu JQ, Sun YS, Ge XJ, et al.[4] Liu JQ, Sun YS, Ge XJ, et al. Phylogeographic studies of plants in China：advances in the past and directions in the future[J] . Journal of Systematics and Evolution, 2012, 50（4）：267-275.
[5] Wen J, Zhang JQ, Nie ZL, et al. Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau[J] . Front Genet, 2014, 5（4）：1-16.
[6] Chen JM, Du ZY, Sun SS, et al. Chloroplast DNA phylogeography reveals repeated range expansion in a widespread aquatic herb Hippuris vulgaris in the Qinghai-Tibetan Plateau and adjacent areas[J] . PLoS One, 2013, 8（4）：60948-60948.
[7] Wei X, Wang R, Cao L, et al. Origin of Oryza sativa in China inferred by nucleotide polymorphisms of organelle DNA[J] . PLoS One, 2012, 7（11）：49546-49546.
[8] Zhao C, Wang CB, Ma XG, et al. Phylogeographic analysis of a temperate-deciduous forest restricted plant（Bupleurum longiradiatum Turcz.）reveals two refuge areas in China with subsequent refugial isolation promoting speciation[J] . Molecular Phylogenetics and Evolution, 2013, 68（3）：628-643.
[9] Gustafsson S, Lonn M. Genetic differentiation and habitat preference of flowering-time variants within Gymnadenia conopsea[J] . Heredity, 2003, 91（3）：284-292.
[10] Scacchi R, De Angelis G. Isoenzyme polymorphisms in Gymnaedenia conopsea and its inferences for systematics within this species[J] . Biochemical Systematics and Ecology, 1989, 17（1）：25-33.
[11] Gustafsson S, Thoren PA. Microsatellite loci in Gymnadenia conopsea, the fragrant orchid[J] . Molecular Ecology Notes, 2001, 1（1-2）：81-82.
[12] Stark C, Michalski SG, Babik W, et al. Strong genetic differentiation between Gymnadenia conopsea and G. densiflora despite morphological similarity[J] . Plant Systematics and Evolution, 2011, 293（1-4）：213-226.
[13] Little DP, Barrington DS. Major evolutionary events in the origin and diversification of the fern genus Polystichum（Dryopteridac-eae）[J] . American Journal of Botany, 2003, 90（3）：508-514.
[14] Taberlet P, Gielly L, Pautou G, et al. Universal primers for amplification of three non-coding regions of chloroplast DNA[J] . Plant Molecular Biology, 1991, 17（5）：1105-1109.
[15] Thompson JD, Gibson TJ, Plewniak F, et al. The CLUSTAL_X windows interface：flexible strategies for multiple sequence alignment aided by quality analysis tools[J] . Nucleic Acids Research, 1997, 25（24）：4876-4882.
[16] Tamura K, Stecher G, Peterson D, et al. MEGA6：molecular evolutionary genetics analysis version 6. 0[J] . Molecular Biology and Evolution, 2013, 30（12）：2725-2729.
[17] Nei M, Tajima F, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data[J] . Journal of Molecular Evolution, 1983, 19（2）：153-170.
[18] Nei M. Molecular evolutionary genetics[M] . New York：Colum-bia University Press, 1987.
[19] Rozas J, Sanchez-Delbarrio JC, Messeguer X, et al. DnaSP, DNA polymorphism analyses by the coalescent and other methods[J] . Bioinformatics, 2003, 19（18）：2496-2497.
[20] Clement M, Posada D, Crandall KA. TCS：a computer program to estimate gene genealogies[J] . Molecular Ecology, 2000, 9（10）：1657-1659.
[21] Yang ZH. PAML 4：phylogenetic analysis by maximum likelihood[J] . Molecular Biology and Evolution, 2007, 24（8）：1586-1591.
[22] Excoffier L, Lischer HE. Arlequin suite ver 3. 5：a new series of programs to perform population genetics analyses under Linux and Windows[J] . Molecular Ecology Resources, 2010, 10（3）：564-567.
[23] Pons O, Petit R. Measwring and testing genetic differentiation with ordered versus unordered alleles[J] . Genetics, 1996, 144（3）：1237-1245.
[24] 陈伟烈. 西藏植被[M] . 北京：科学出版社, 1988.