Genetic diversity and population structure of Garcinia paucinervis, an endangered species using microsatellite markers

  • Jun-Jie Zhang
  • Xiao Wei
  • Sheng-Feng Chai
  • Zheng-Feng Wang
  • Theophine Akunne
  • Shao-Hua Wu
  • Jun-Hong Yi
  • Ji-Qing WeiEmail author
  • Zong-You ChenEmail author
Research Article


Genetic diversity influences the fitness of species and provides variation for adaptation. Garcinia paucinervis Chun et How (Clusiaceae) is an endangered species with important ecological, medicinal and ornamental values endemic to Southwest China and Northern Vietnam, whose populations were severely fragmented in island habitats and population sizes were influenced by human. The assessment of genetic variation of G. paucinervis is anticipated to provide essential information for efficient conservation strategies. In this study, a suite of population genetics tests and analyses were used to investigate genetic diversity and structure of the 11 natural populations (a total of 360 individuals) of G. paucinervis in Guangxi and Yunnan Provinces, China, based on genotypes at 14 loci. Our results revealed a low to moderate genetic diversity in G. paucinervis remnants (HE = 0.487, I = 0.924, AR = 3.420). The global inbreeding coefficient (FIS = 0.004) showed significant deviation from Hardy–Weinberg equilibrium, implying that the risk of inbreeding depression accompanied by heterozygote deficiency was probably due to severe habitat fragmentation and decreasing population sizes. Significant bottlenecks were detected in two populations. There has been little recent exchange of genes between most of the population pairs. Mantel test revealed that the genetic distance was not related to the geographical distance, suggesting a limitation of gene flow. A population from Yunnan Province could be classified as an independent cluster separated from the other populations, which should be considered as a prior conservation unit.


Garcinia paucinervis Microsatellite Genetic diversity Genetic differentiation Population structure Conservation strategies 



We would like to express our sincere thanks to Mr. Shi-hong Lü, Dr. Yan-cai Shi, Mr. Yun-sheng Jiang and Mr. Jian-min Tang for the field observation and collecting samples, as well as Dr. Ming Kang for comments on this manuscript. This project was supported by Natural Science Foundation of Guangxi (2015GXNSFDA13915), Guangxi Science and Technology Base and Special Fund for Talents (AD17129022), and National Natural Science Foundation of China (31600306).


  1. Ávila-Díaz I, Oyama K (2007) Conservation genetics of an endemic and endangered epiphytic Laelia speciosa (Orchidaceae). Am J Bot 94:184–193CrossRefGoogle Scholar
  2. Botstein D (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–331Google Scholar
  3. Brookfield JF (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol 5:453CrossRefGoogle Scholar
  4. Cao PJ, Yao QF, Ding BY, Zeng HY, Zhong YX, Fu CX, Jin XF (2006) Genetic diversity of Sinojackia dolichocarpa (Styracaceae), a species endangered and endemic to China, detected by inter-simple sequence repeat (ISSR). Biochem Syst Ecol 34:231–239CrossRefGoogle Scholar
  5. Carvajal-Rodriguez A (2018) Myriads: p-value-based multiple testing correction. Bioinformatics 34:1043–1104CrossRefGoogle Scholar
  6. Carvajal-Rodríguez A, de Uña-Alvarez J, Rolán-Alvarez E (2009) A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests. BMC Bioinformatics 10:209CrossRefGoogle Scholar
  7. Carvalho DC, Oliveira DAA, Sampaio I, Beheregaray LB (2014) Analysis of propagule pressure and genetic diversity in the invasibility of a freshwater apex predator: the peacock bass (genus Cichla). Neotrop Ichthyol 12:105–116CrossRefGoogle Scholar
  8. Chan CH, Robertson HA, Saul EK, Nia LV, Phuong LV, Kong XC, Zhao Y, Chambers GK (2011) Genetic variation in the kakerori (Pomarea dimidiata), an endangered endemic bird successfully recovering in the Cook Islands. Conserv Genet 12:441–447CrossRefGoogle Scholar
  9. Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631CrossRefGoogle Scholar
  10. Chung MY, Nason JD, López-Pujol J, Yamashiro T, Yang BY, Luo YB, Chung MG (2014) Genetic consequences of fragmentation on populations of the terrestrial orchid Cymbidium goeringii. Biol Conserv 170:222–231CrossRefGoogle Scholar
  11. Cullingham CI, James PMA, Cooke JEK, Coltman DW (2012) Characterizing the physical and genetic structure of the lodgepole pine × jack pine hybrid zone: mosaic structure and differential introgression. Evol Appl 5:879–891CrossRefGoogle Scholar
  12. Dardengo JFE, Rossi AAB, Varella TL (2018) The effects of fragmentation on the genetic structure of Theobroma speciosum (Malvaceae) populations in Mato Grosso, Brazil. Rev Biol Trop 66:218–226CrossRefGoogle Scholar
  13. Deacon NJ, Cavender-Bares J (2015) Limited pollen dispersal contributes to population genetic structure but not local adaptation in Quercus oleoides forests of Costa Rica. PLoS ONE 10:e0138783CrossRefGoogle Scholar
  14. Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  15. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefGoogle Scholar
  16. Fagen LI, Xia N (2005) Population structure and genetic diversity of an endangered species, Glyptostrobus pensilis (Cupressaceae). Bot Bull Acad Sin 46:155–162Google Scholar
  17. Francisco-Ortega J, Santos-Guerra A, Kim SC, Crawford DJ (2000) Plant genetic diversity in the Canary Islands: a conservation perspective. Am J Bot 87:909–919CrossRefGoogle Scholar
  18. Frankham R (2005) Genetics and extinction. Biol Conserv 126:131–140CrossRefGoogle Scholar
  19. Fu LG (1991) China plant red data book. Science Press, Beijing, pp 736–737 (in Chinese) Google Scholar
  20. Funk WC, McKay JC, Hohenlohe PA, Allendorf FW (2012) Harnessing genomics for delineating conservation units. Trends Ecol Evol 9:489–496CrossRefGoogle Scholar
  21. Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ (2011) Current trends in microsatellite genotyping. Mol Ecol Resour 11:591–611CrossRefGoogle Scholar
  22. Honjo M, Ueno S, Tsumura Y, Washitami I, Ohsawa R (2004) Phylogeographic study based on intraspecific sequence variation of chloroplast DNA for the conservation of genetic diversity in the Japanese endangered species Primula sieboldii. Biol Conserv 120:211–220CrossRefGoogle Scholar
  23. Hu G, Zhang ZH, Yang P, Zhang QW, Yuan CA (2017) Development of microsatellite markers in Garcinia paucinervis (Clusiaceae), an endangered species of karst habitats. Appl Plant Sci 5:1600131CrossRefGoogle Scholar
  24. Jost LOU (2008) Gst and its relatives do not measure differentiation. Mol Ecol 17:4015–4026CrossRefGoogle Scholar
  25. Jump AS, Peñuelas J (2006) Genetic effects of chronic habitat fragmentation in a wind-pollinated tree. Proc Natl Acad Sci USA 103:8096–8100CrossRefGoogle Scholar
  26. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106CrossRefGoogle Scholar
  27. Kang M, Jiang M, Huang H (2005) Genetic diversity in fragmented populations of Berchemiella wilsonii var. pubipetiolata (Rhamnaceae). Ann Bot 95:1145–1151CrossRefGoogle Scholar
  28. Karron JD (1997) Genetic consequences of different patterns of distribution and abundance. In: Kunin WE, Gaston KJ (eds) The biology of rarity: causes and consequences of rare-common differences. Chapman Hall, London, pp 174–189CrossRefGoogle Scholar
  29. Kramer AT, Ison JL, Ashley MV, Howe HF (2008) The paradox of forest fragmentation genetics. Conserv Biol 22:878–885CrossRefGoogle Scholar
  30. Lande R (1999) Extinction risks from anthropogenic, ecological, and genetic factors. In: Landweber LF, Dobson AP (eds) Genetics and the extinction of species: DNA and the conservation of biodiversity. Princeton University Press, Princeton, pp 1–22Google Scholar
  31. Liang RL (2015) Garcinia paucinervis: Guangxi ironwood. Forestry Guangxi 32:24–25 (in Chinese) Google Scholar
  32. Lowe AJ, Boshier D, Ward M, Bacles CFE, Navarro C (2005) Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees. Heredity 95:255–273CrossRefGoogle Scholar
  33. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Can Res 27:209–220Google Scholar
  34. Neel MC, Commings MP (2003) Effectiveness of conservation targets in capturing genetic diversity. Conserv Biol 17:219–229. CrossRefGoogle Scholar
  35. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590Google Scholar
  36. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143–1155CrossRefGoogle Scholar
  37. Peakall ROD, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Resour 6:288–295CrossRefGoogle Scholar
  38. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959Google Scholar
  39. Reisch C, Poschlod P, Wingender R (2003) Genetic variation of Saxifraga paniculata Mill. (Saxifragaceae): molecular evidence for glacial relict endemism in central Europe. Biol J Lin Soc 80:11–21CrossRefGoogle Scholar
  40. Rousset F (2008) Genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106CrossRefGoogle Scholar
  41. Segarra-Moragues JG, Palop-Esteban M, González-Candelas F, Catalán P (2005) On the verge of extinction: genetics of the critically endangered Iberian plant species, Borderea chouardii (Dioscoreaceae) and implications for conservation management. Mol Ecol 14:969–982CrossRefGoogle Scholar
  42. Slatkin M (1994) Gene Flow and Population Structure. In: Real LA (ed) Ecological genetics. Princeton University Press, Princeton, pp 3–17Google Scholar
  43. Spencer CC, Neigel JE, Leberg PL (2000) Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Mol Ecol 9:1517–1528CrossRefGoogle Scholar
  44. Szpiech ZA, Jakobsson M, Rosenberg NA (2008) ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24:2498–2504CrossRefGoogle Scholar
  45. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471CrossRefGoogle Scholar
  46. Templeton AR (2010) Introduction to conservation genetics. Cambridge University Press, Cambridge, p 56Google Scholar
  47. Toure D, Burnet JE, Jianwei Z (2010) Rare plants protection importance and implementation of measures to avoid, minimize or mitigate impacts on their survival in Longhushan Nature Reserve, Guangxi Autonomous Region, China. J Am Sci 6:221–238Google Scholar
  48. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Resour 4:535–538CrossRefGoogle Scholar
  49. Wang ZF, Cao HL, Wu LF, Guo Y, Mei QM, Li M, Wang Y, Wang ZM (2017) A set of novel microsatellite markers developed for an economically important tree, Dracontomelon duperreanum, in China. Genet Mol Res 16:gmr16029578Google Scholar
  50. Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multi-locus genotypes. Genetics 163:1177–1191Google Scholar
  51. Yang L, Liu ZL, Li J, Dyer RJ (2015) Genetic structure of Pinus henryi and Pinus tabuliformis: natural landscapes as significant barriers to gene flow among populations. Biochem Syst Ecol 61:124–132CrossRefGoogle Scholar
  52. 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 Phytol 176:472–480CrossRefGoogle Scholar
  53. Yu XM, Zhou Q, Qian ZQ, Li S, Zhao GF (2006) Analysis of genetic diversity and population differentiation of Larix potaninii var. chinensis using microsatellite DNA. Biochem Genet 44:483–493CrossRefGoogle Scholar
  54. Zhai SH, Yin GS, Yang XH (2018) Population genetics of the endangered and wild edible plant Ottelia acuminata in southwestern China using novel SSR markers. Biochem Genet 56:1–20CrossRefGoogle Scholar
  55. Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol 12:563–584CrossRefGoogle Scholar
  56. Zhang X, Liu B, Zhou Y, Liu ZZ, Li P, Long CL (2015) Potential ornamental plants in Clusiaceae from China. Acta Hort 28:233–238CrossRefGoogle Scholar
  57. Zhang JJ, Chai SF, Lü SH, Shi YC, Jiang YS, Wei X (2017) The habitat characteristics and analysis on endangering factors of rare and endangered plant Garcinia paucinervis. Ecol Environ Sci 26:582–589 (in Chinese) Google Scholar
  58. Zhang JJ, Wei X, Wu SH, Chai SF, Lü SH, Han Y (2018a) Morphological differentiation of Garcinia paucinervis fruits and seeds and effects of exogenous substances on its seed germination and seedling growth. Guihaia 38:509–520 (in Chinese) Google Scholar
  59. Zhang YY, Shi E, Yang ZP, Geng QF, Qiu YX, Wang ZS (2018b) Development and application of genomic resources in an endangered palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China. Front Plant Sci 9:246CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Jun-Jie Zhang
    • 1
    • 2
    • 3
  • Xiao Wei
    • 2
  • Sheng-Feng Chai
    • 2
  • Zheng-Feng Wang
    • 4
  • Theophine Akunne
    • 2
    • 5
  • Shao-Hua Wu
    • 3
  • Jun-Hong Yi
    • 6
  • Ji-Qing Wei
    • 2
    Email author
  • Zong-You Chen
    • 2
    Email author
  1. 1.College of Tourism and Landscape ArchitectureGuilin University of TechnologyGuilinChina
  2. 2.Guangxi Institute of BotanyGuangxi Zhuangzu Autonomous Region and Chinese Academy of SciencesGuilinChina
  3. 3.College of HorticultureFujian Agriculture and Forestry UniversityFuzhouChina
  4. 4.Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
  5. 5.Department of Pharmacology and Toxicology, Faculty of Pharmaceutical SciencesUniversity of NigeriaNsukkaNigeria
  6. 6.Jiangxi Agricultural UniversityNanchangChina

Personalised recommendations