Abstract
Taxus mairei (Lemée & Lév.) S.Y. Hu ex T. S. Liu is a vulnerable tree species, and it is also a precious timber species in China. We used 13 microsatellites to assess the genetic diversity and differentiation of 665 T. mairei samples from 18 natural populations. A total of 291 alleles were detected. The average number of alleles (Na = 22.39), expected heterozygosity (He = 0.74), polymorphic information content (PIC = 0.86) and Shannon diversity index (I = 1.66) of the loci indicated a high level of genetic diversity in natural T. mairei populations. Moreover, gene flow was more active among populations (Nm = 1.62) than within populations. Among the 18 populations, the Xinfeng population in Jiangxi Province has the highest genetic diversity. Although each of the studied populations should be protected from further deforestation and agricultural expansion, the Xinfeng population deserves the highest conservation priority. The results based on analysis of molecular variance showed that genetic variation occurred mainly within populations (84.90%; P < 0.001), which indicated that the degree of genetic differentiation of the natural populations of T. mairei was low. Based on UPGMA, the 18 populations were categorized into two groups. A Mantel test showed that there was no significant correlation between standard genetic distance and geographical distance or altitude differences among the populations. The genetic clustering results also indicated that there are varying degrees of gene penetration among natural populations of T. mairei. The information presented here forms the basis for the development of genetic guidelines for appropriate conservation programs.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Aguilar R, Ashworth L, Galetto L, Aizen MA (2006) Plant reproductive susceptibility to habitat fragmentation: review and synthesis through a meta-analysis. Ecol Lett 9:968–980. https://doi.org/10.1111/j.1461-0248.2006.00927.x
Bertiller MB, Sain CL, Carrera AL (2002) Effect of fine-scale spatial variation of soil nitrogen on the performance of the sexes of Poa ligularis in patchy ecosystems of Northern Patagonia. Int J Plant Sci 163:419–425. https://doi.org/10.1086/339515
Chen WW (2016) Mating system and dispersal patterns of the natural populations of Metasequoia glyptostroboides. Mphil Thesis, East China Narmal University (in Chinese)
Cheng BB (2016) Molecular phylogeographic and genetic of Taxus L.(Taxaceae) in China. PhD Thesis, Chinese Academy of Forestry (in Chinese)
Cruzan MB (2001) Population size and fragmentation thresholds for the maintenance of genetic diversity in the herbaceous endemic scutellaria montana (lamiaceae). Evolution 55(8):1569–1580. https://doi.org/10.1111/j.0014-3820.2001.tb00676.x
Dawson TE, Ehleringer JR (1993) Gender-specific physiology, carbon isotope discrimination, and habitat distribution in boxelder, Acer Negundo. Ecology 74(3):798–815. https://doi.org/10.2307/1940807
Deng YT, Liu XS, Xiao YF, Guo XD, Zhang D, Xu GB (2016) The endangered causes and conversation for Chinese Yew. Guangxi for Sci 45(4):442–446. https://doi.org/10.19692/j.cnki.gfs.2016.04.019 (in Chinese)
Diniz-Filho JAF, Soares TN, Lima JS, Dobrovolski R, Landeiro VL, Telles MPDC, Rangel TF, Bini LM (2013) Mantel test in population genetics. Genet Mol Biol 36(4):475–485. https://doi.org/10.1590/S1415-47572013000400002
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.3): an integrated software package for population genetic data analysis. Evol Bioinform 1:47–50
Freeman DC, Klikoff LG, Harper KT (1976) Differential resource utilization by the sexes of dioecious plants. Science 193:597–599. https://doi.org/10.1126/science.193.4253.597
Goudet J (1995) FSTAT (Version-1.2): a computer program to calculate F-statistics. J Hered 86(6):485–486. https://doi.org/10.1093/oxfordjournals.jhered.a111627
Hamrick JL, Godt NJW (1989) Allozyme diversity in plant species. Plant population genetic, breeding and genetic resources pp 43–63
Hamrick JL, Godt NJW (1996) Effects of life history traits on genetic diversity in plant species. Philos Trans R Soc B Biol Sci 351:1291–1298. https://doi.org/10.1098/rstb.1996.0112
Harlizius B, Lopes MS, Duijvesteijn N, Goor LHPVD, Haeringen WAV, Pannenian H, Guiniaräes SEF, Merks JWM, Knol EF (2011) A single nucleotide polymorphism set for paternal identification to reduce the costs of trait recording in commercial pig breeding. J Anim Sci 89:1661–1668. https://doi.org/10.2527/jas.2010-3347
Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59(8):1633–1638. https://doi.org/10.2307/3449070
Holsinger KE, Weir BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting FST. Nat Rev Genet 10:639–650. https://doi.org/10.1038/nrg2611
Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9(5):1322–1332. https://doi.org/10.1111/j.1755-0998.2009.02591.x
Iszkuło G, Jasińska AK, Giertych MJ, Boratyński A (2009) Do secondary sexual dimorphism and female intolerance to drought influence the sex ratio and extinction risk of Taxus baccata? Plant Ecol 200:229–240. https://doi.org/10.1007/s11258-008-9447-5
Kalinowski ST (2004) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5(1):187–189. https://doi.org/10.1111/j.1471-8286.2004.00845.x
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106. https://doi.org/10.1111/j.1365-294x.2007.03089.x
Kopelman NM, Mayzel J, Jakobsson M et al (2015) CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 15(5):1179–1191. https://doi.org/10.1111/1755-0998.12387
Li YL, Liu JX (2018) StructureSelector: a web-based software to select and visualize the optimal number of clusters using multiple methods. Mol Ecol Resour 18:176–177. https://doi.org/10.1111/1755-0998.12719
Li XK, Xiang WS, Ou ZL, Su ZM (2003) Clonal growth Spatial attern and dynamics of the endangered plant Taxus mairei population. Acta Bot Yunnanica 25(6):625–632 (in Chinese)
Li N, Wang Z, Lu CH, Xiong TS, Fu WY, Wu JP (2014) Seed foraging and dispersal of Chinese yew (Taxus chinensis var. mairei) by frugivorous birds within patchy habitats. Acta Ecol Sin 34(7):1681–1689. https://doi.org/10.5846/xtxb201303220485 (in Chinese)
Lin XY (2018) Development of EST-SSR markers and population genetic variation in Glyptostrobus pensilis. Mphil Thesis, Central South University of Forestry&Technology (in Chinese)
Liu LH, Wang LX, Zhao CP, Yao J, Zhang FT, Zhang H, Ye ZJ, Qin ZL, Zheng YL (2009) Genetic diversity and alterations of population structure in restorers of dual cross-line hybrid wheat with thermo-photoperiod sensitive male sterile. Chin J Biochem Mol Biol 25(9):867–875. https://doi.org/10.13865/j.cnki.cjbmb.2009.09.013 (in Chinese)
Lu DW, Zhou YQ, Li SB, Yu XS, Li SH, Zhang CH, Yang C, Yang S, Yang ZY (2014) Biological characteristics, ecological characteristics and cultivation techniques in Taxus chinensis var. mairei. Non Wood for Res 32(4):159–164 (in Chinese)
Mcneely JA, Miller KR, Reid WV, et al (1990) Conserving the world's biological diversity. Prepared and published by the International Union for Conservation of Nature and Natural Resources
Mullen SP (2007) Conservation and the genetics of populations. Blackwell, London
Nei M (1972) Genetic distance between populations. Am Nat 106(949):283–292. https://doi.org/10.1086/282771
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci 70(12):3321–3323. https://doi.org/10.2307/62835
Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol 19:153–170. https://doi.org/10.1007/bf02300753
Oosterhout CV, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x
Ortiz PL, Arista M, Talavera S (2002) Sex ratio and reproductive effort in the dioecious Juniperus communis subsp. Alpina (Suter) Čelak. (Cupressaceae) along an altitudinal gradient. Ann Bot 89:205–211. https://doi.org/10.1093/aob/mcf028
Peakall R, Smouse PE (2006) GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539. https://doi.org/10.1093/bioinformatics/bts460
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959
Pucholt P, Hallingbäck HR, Berlin S (2017) Allelic incompatibility can explain female biased sex ratios in dioecious plants. BMC Genomics 18:251. https://doi.org/10.1186/s12864-017-3634-5
Qi M, Zhou Q, Ni ZX, Wu YQ, Han X, Xu LA (2019) Genetic structure analysis of ancient Ginkgo biloba L. populations based on SSR markers. Chin J Ecol 38(9):2902–2910. https://doi.org/10.13292/j.1000-4890.201909.017 (in Chinese)
Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86(3):248–249. https://doi.org/10.1093/oxfordjournals.jhered.a111573
Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conserv Biol 17(1):230–237. https://doi.org/10.1046/j.1523-1739.2003.01236.x
Rousset F (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106. https://doi.org/10.1111/j.1471-8286.2007.01931.x
Somanothan H, Borges RM (2000) Influence of exploitation on population structure, spatial distribution and reproductive success of dioecious species in a fragmented cloud forest in India. Biol Conserv 94:243–256. https://doi.org/10.1016/s0006-3207(99)00170-6
Song YB, Xu L, Duan JP, Zhang WJ, Shentu XL, Li TX, Zang RG, Ming Dong M (2020) Sex ratio and spatial pattern of Taxus fuana, a wild plant with extremely small populations in Tibet. Biodivers Sci 28(3):269–276. https://doi.org/10.17520/biods.2019102 (in Chinese)
Sun QW, Wang L, Zhang XP, Hao CY, Tian SN (2009) Study on the population dynamics of Taxus chinensis var. mairei in the mountain area of Southern Anhui province. For Res 22(4):579–585 (in Chinese)
Takezaki N, Nei M (2008) Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA. Genetics 178:385–392. https://doi.org/10.1534/genetics.107.081505
Takezaki N, Nei M, Tamura K (2010) POPTREE 2: software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol 27:747–752. https://doi.org/10.1093/molbev/msp312
Vu DD, Bui TTX, Nguyen MT, Vu DG, Nguyen MD, Bui VT, Huang XH, Zhang Y (2014) Genetic diversity in two threatened species in Vietnam: Taxus chinensis and Taxus wallichiana. J for Res 28:265–272. https://doi.org/10.1007/s11676-016-0323-1
Wang HX, Hu ZA (1996) Plant breeding system, genetic structure and conservation of genetic diversity. Chin Biodivers 4(2):92–96 (in Chinese)
Wang ZS, Sun HQ, Wang HW, Ge S (2010) Isolation and characterization of 50 nuclear microsatellite markers for Cathaya argyrophylla, a Chinese endemic conifer. Am J Bot 97(11):e117–e120. https://doi.org/10.3732/ajb.1000270
Wang MQ, Wu XT, Wang LB, Wen YF (2019) Comparison of gene flow for Taxus chinensis var. mairei. Mol Plant Breed 17(19):6269–6275. https://doi.org/10.13271/j.mpb.017.006269 (in Chinese)
Wang XG (2003) The research on population quantiative characteristics of precious and endangering plant-form Taxus chinensis var. mairei. Mphil Thesis, Fujian Agriculture and Forestry University (in Chinese)
Wang X (2014) Comparative analysis of population genetic structure in Abies chensiensis and A.fargesii inferred from microsatellite markers. Mphil Thesis, Guangxi Normal University (in Chinese)
Wen YF, Han WJ, Wu S (2010) Plant genetic diversity and its influencing factors. J Cent South Univ for Technol 30(12):80–87 (in Chinese)
Xie WD (2017) Research on the correlation of genetics of Taxus chinensis var. Mairei in Nanling Mountain. PhD Thesis, Central South Universityof Forestry and Technology (in Chinese)
Xu GB (2015) Endangered mechanism and conversation for Taxus wallichiana var. Mairei. Science Press, Beijing
Yang Y, Christian T, Li N (2013) Taxus mairei. The IUCN Red List of Threatened Species 2013:e.T191659A1991533. https://doi.org/10.2305/IUCN.UK.2013-1.RLTS.T191659A1991533.en
Yi GM, Li JH, Wang DM, Tong ZK, Lu YQ (2013) SSR Distribution characteristic analysis and molecular marker development in Taxus wallichiana var. mairei. Acta Hortic Sin 40(3):571–578. https://doi.org/10.16420/j.issn.0513-353x.2013.03.031 (in Chinese)
Zhang DQ, Zhou N (2013) Genetic diversity and population structure of the endangered conifer Taxus wallichiana var. mairei (Taxaceae) revealed by simple sequence repeat (SSR) markers. Biochem Syst Ecol 49:107–114. https://doi.org/10.1016/j.bse.2013.03.030
Zhou ZC, Yu NJ, Jin GQ (2009) Selection of medicinal germplasm and efficient cultivation of Taxus wallichiana var. mairei and Cephalotaxus fortunei. China Forestry Publishing House, Beijing
Zhou SR, Zhou CC, Pannell JR (2010) Genetic load, inbreeding depression and heterosis in an age-structured metapopulation. J Evol Biol 23(11):2324–2332. https://doi.org/10.1111/j.1420-9101,2010.02091.x
Zhou H, Zhu Q, Yang YF, Liu HW, Yu FX, Qiu DY (2015) Cloning and sequence analysis of bHLH gene from Taxus chinensis var. mairei. Bull Bot Res 35(1):52–59 (in Chinese)
Acknowledgements
We thank Professor Zhichun Zhou for helpful suggestions and arrangements for the experiments performed at Zhejiang Provincial Key Laboratory of Tree Breeding, Hangzhou, P. R. China. This research was funded by fundamental Research Funds of the Central Public Welfare Research Institutes, Chinese Academy of Forestry (No.CAFYBB2018ZB010). Samples were collected by Longhua Yu, Liyun Wang, and Fengqing Li.
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Luo, Q., Li, F., Yu, L. et al. Genetic diversity of natural populations of Taxus mairei. Conserv Genet 23, 63–74 (2022). https://doi.org/10.1007/s10592-021-01403-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10592-021-01403-9