Population structure and genetic divergence in Firmiana danxiaensis
(2.Wildlife Conservation Office of Shaoguan, Guangdong, Shaoguan, Guangdong 512000)
【Abstract】 Firmiana danxiaensis is an endemic plant species which is narrowly distributed in the northern parts of Shaoguan, Guangdong, China. To devise appropriate conservation strategies for this rare species, we examined the population structure and estimated the demographic history of nine natural populations using 18 EST-SSR markers. The results revealed a moderate degree of total genetic diversity (Ht = 0.631) at the species level but high genetic diversity within populations (Hs = 0.546). Strong genetic differentiation existed between two groups of Danxiashan and Nanxiong (FST = 0.150). This current pattern might have arisen from prolonged geographical isolation and human disturbances. The STRUCTURE analysis demonstrated that the whole population could be divided into two distinct gene pools, closely related by their geographic location and having experienced independent evolutionary routes. The genetic background of Danxiashan was more complicated than that of Nanxiong. The approximate Bayesian Computation (ABC) analysis indicated that divergence time between the two groups could be 100,000 years BP, and their effective population sizes were 7,290 and 5,550 individuals, respectively. Combining the information of genetic variation with niche modeling, we inferred that F. danxiaensis might have been widely distributed around the Nanling Mountain in the Quaternary period. The populations located in the northern of Nanling Mountain likely became extinct due to climate change. Danxiashan and Nanxiong provided the main refuges for the species during the last ice age. Being a rare species with small population sizes, better ecological investigation of natural populations and in situ conservation and implementation of restoration strategy are important measures to conserve this species.
【Keywords】 population genetic structure; genetic divergence; genetic diversity; Approximate Bayesian Computation; EST-SSR marker; Firmiana danxiaensis;
(Translated by GAO C)
Chen L, Zhou H, Wang MQ, Wu XT, Lin XY, Zhang Y, Wen YF (2018) Community characteristics comparison of Firmiana danxiaensis species. Chinese Wild Plant Resources, 37 (2), 46–49 (in Chinese with English abstract).
Chen SF, Li MW, Hou RF, Liao WB, Zhou RC, Fan Q (2014) Low genetic diversity and weak population differentiation in Firmiana danxiaensis, a tree species endemic to Danxia landform in northern Guangdong, China. Biochemical Systematics & Ecology, 55, 66–72.
Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144, 2001–2014.
Cornuet JM, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois R, Marin JM, Estoup A (2014) DIYABC v2.0: A software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics, 30, 1187–1189.
Demesure B, Sodzi N, Petit RJ (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology, 4, 129–131.
Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359–361.
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564–567.
Frankham R, Ballou JD, Briscoe DA (2002) Introduction to Conservation Genetics. Cambridge University Press, Cambridge, UK.
Freeland JR, Petersen SD, Kirk H (2011) Molecular Ecology, 2nd Edn. Wiley-Blackwell, West Sussex.
Goudet J (1995) FSTAT (Version 1.2): A computer program to calculate F-Statistics. Journal of Heredity, 86, 485–486.
Hamrick JL, Godt MJW (1996) Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of the Royal Society B: Biological Sciences, 351, 1291–1298.
Hamrick JL, Godt MJW, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New Forests, 6, 95–124.
Harrison SP, Yu G, Takahara H, Prentice IC (2001) Palaeovegetation (communications arising): Diversity of temperate plants in East Asia. Nature, 413, 129–130.
Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society of London, 359, 183–195.
Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247–276.
Howard WR (1997) A warm future in the past. Nature, 388, 418–419.
Huang J, Chen ZJ, Qi DL (2015) Study on distribution of Danxia Landform in China (first). Mountain Research, 33, 385–396 (in Chinese with English abstract).
Jakobsson M, Rosenberg NA (2007) CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801–1806.
Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends in Ecology & Evolution, 11 (10), 424–429.
Jing CR (1963) On the Quaternary glacial period in China. Scientific Research Papers, (1963), 253–268 (in Chinese).
Kalinowski ST (2005) HP-RARE 1.0: A computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Resources, 5, 187–189.
Kou YX, Cheng SM, Tian S, Li B, Fan DM, Chen YJ, Soltis DE, Soltis PS, Zhang ZY (2016) The antiquity of Cyclocary apaliurus (Juglandaceae) provides new insights into the evolution of relict plants in subtropical China since the late early Miocene. Journal of Biogeography, 43, 351–360.
Luo XY, Chen QH, Cai CR, Zeng HN, Ren B, Zheng WL, Feng JY (2015) Analysis on geographical elements of the community of plant species with extremely small population Firmiana danxiaensis. Journal of Shaoguan University, 36 (12), 28–31 (in Chinese with English abstract).
Myers N, Mittermeier RA, Mittermeier CG, Da FG, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853–858.
Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology, 13, 1143–1155.
Ouyang J, Huang J (2011) Spatial distribution of Danxia landforms in China. Geospatial Information, 9 (6), 55–59 (in Chinese with English abstract).
Palumbi SR (2001) Humans as the World’s Greatest Evolutionary Force. Science, 293, 1786–1790.
Peakall R, Smouse PE (2006) GENALEX 6: Genetic analysis in Excel, population genetic software for teaching and research. Molecular Ecology Resources, 6, 288–295.
Peng H (2011) Danxia of China towards the world. Map, (6), 114–121 (in Chinese).
Peng SL (2011) Comprehensive Scientific Investigation for Animal and Plant Resources in Mount Danxia, Guangdong. Science Press, Beijing (in Chinese).
Pritchard JK, Stephens MJ, Donnelly PJ (2000) STRUCTURE, version 2.3.3, inference of population structure using multilocus genotype data. Genetics, 155, 945–959.
Qiu YX, Fu CX, Comes HP (2011) Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora. Molecular Phylogenetics and Evolution, 59, 225–244.
Qiu YX, Guan BC, Fu CX, Comes HP (2009) Did glacials and/or interglacials promote allopatric incipient speciation in East Asian temperate plants? Phylogeographic and coalescent analyses on refugial isolation and divergence in Dysosma versipellis. Molecular Phylogenetics and Evolution, 51, 281–293.
Rosenberg NA (2010) DISTRUCT: A program for the graphical display of population structure. Molecular Ecology Notes, 4, 137–138.
Selkoe KA, Toonen RJ (2006) Microsatellite for ecologists: A practical guide to using and evaluating microsatellite markers. Ecology Letters, 9, 615–629.
Takezaki N, Nei M, Tamura K (2010) POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Molecular Biology & Evolution, 27, 747–752.
Tao JR (1992) Study on the fossil flowers of angiosperm. Acta Botanica Sinica, 34, 240–242 (in Chinese).
Templeton AR, Robertson RJ, Brisson J, Strasburg J (2001) Disrupting evolutionary processes: The effect of the habitat fragmentation on collared lizards in the Missouri Ozarks. Proceedings of the National Academy of Sciences, USA, 98, 5426–5432.
Tilman D, Lehman C (2001) Human-caused environmental change: Impacts on plant diversity and evolution. Proceedings of the National Academy of Sciences, USA, 98, 5433–5440.
Tsumura Y, Yoshimura K, Tomaru N, Ohba K (1995) Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theoretical and Applied Genetics, 91, 1222–1236.
Wang S, Xie Y (2004) China Species Red List (Vol. 1). Higher Education Press, Beijing (in Chinese).
Wen YF, Han WJ, Wu S (2010) Plant genetic diversity and its influencing factors. Journal of Central South University of Forestry & Technology, 30 (12), 80–87 (in Chinese with English abstract).
Xie XM, Zhang SZ, Li Y, Wu H (2003) Review of taxonomic studies on Sterculiaceae. Guihaia, 23, 311–317 (in Chinese with English abstract).
Xu SJ (2002) The distribution of the Sterculiaceous plants in China. Guihaia, 22, 494–498 (in Chinese with English abstract).
Xu SJ, Xu XH (2001) Geographical distribution of Sterculiaceae. Journal of Tropical and Subtropical Botany, 9 (1), 19–30 (in Chinese with English abstract).
Xu XH, Qiu HX, Xu SJ (1987) New species and variety of Sterculiaceae from China. Journal of South China Agricultural University, 8 (3), 1–5 (in Chinese with English abstract).
Yao XH, Ye QG, Kang M, Huang HW (2007) Microsatellite analysis reveals interpopulation differentiation and gene flow in the endangered tree Changiostyrax dolichocarpa (Styracaceae) with fragmented distribution in central China. New Phytologist, 176, 472–480.
Ye JW, Zhang Y, Wang XJ (2017) Phylogeographic history of broad-leaved forest plants in subtropical China. Acta Ecologica Sinica, 37, 5894–5904 (in Chinese with English abstract).
Ying JS (2001) Species diversity and distribution pattern of seed plants in China. Biodiversity Science, 9, 393–398 (in Chinese with English abstract).