A comparison of genetic diversity and differentiation in five Chinese pines using cpSSR and AFLP markers

Abstract

Gene diversity and genetic differentiation in five Chinese pines, Pinus henryi, P. tabulaeformis, P. yunnanensis, P. taiwanensis and P. massoniana, were compared using amplified fragment length polymorphism (AFLP) and simple chloroplast sequence repeat (cpSSR). High genetic differentiation and median gene diversity with cpSSR markers were found both at population and species level, while median differentiation and higher gene diversity in AFLP data. Measures of subdivision that consider similarity between haplotypes offered better information on the geographic structure of plants than the standard subdivisions. Among several methods analyzed in AFLPs, the square root method provided downwardly biased estimates of the genetic parameters, while the Lynch and Milligan method over-estimated genetic diversity due to a small sample size. The Bayesian statistic was the most accurate and popular method for these dominant species and its value of species differentiation (?^B = 0.1035) was close to the parameter given by analysis of molecular variance (AMOVA).

References

1. Avise J C (2000). Phylogeography. Cambridge: Harvard University Press 2. Boys J, Cherry M, Dayanandan S (2005). Microsatellite analysis reveals geneticallydistinct populations of red pine (Pinus resinosa, Pinaceae). Am J Bot, 92(5): 833–841. doi:10.3732/ajb.92.5.833 3. Bucci G, Anzidei M, Madaghiele A, Vendramin G G (1998). Detection of haplotypic variation and natural hybridizationin halepensis-complex pine speciesusing chloroplast simple sequence repeat (SSR) markers. Mol Ecol, 7(2): 1633–1643. doi:10.1046/j.1365-294x.1998.00466.x 4. Cornuet J M, Luikart G (1996). Descriptionand power analysis of two tests for detecting recent population bottlenecksfrom allele frequency data. Genetics, 144: 2001–2014 5. Di Rienzo A, Peterson A C, Garza J C, Valdes A M, Slatkin M, Freimer N B (1994). Mutational processes of sample-sequence repeat lociin human populations. Proc Natl Acad SciUSA, 91: 3166–3179. doi:10.1073/pnas.91.8.3166 6. Díaz V, Muńiz L M, Ferrer E (2001). Random amplified polymorphic DNAand amplified fragment length polymorphism assessment of genetic variationin Nicaraguan populations of Pinus oocarpa. Mol Ecol, 10(11): 2593–2603. doi:10.1046/j.0962-1083.2001.01390.x 7. Excoffier L, Laval G, Schneider S (2005). Arlequin ver. 3.0: An integratedsoftware package for population genetics data analysis.Evol Bioinform Online, 1: 47–50 8. Fan Y R, Mao Y C, Li L Y, Dai J L, Liu S F (1999). Study on the geneticvariation of enzyme genes in Pinus taiwanensis population. J Northeast For Univ, 27(3): 14–19 (in Chinese) 9. Frankham R, Ballou J D, Briscoe D A (2002). Introduction to Conservation Genetics. Cambridge: Cambridge University Press 10. Hamrick J L, Godt M J W (1997). Effectsof life history traits on genetic diversity in plant species. In: Silvertown J, Franco M, Harper J L eds. Plant Life Histories. Cambridge: Cambridge UniversityPress, 102–118 11. Holsinger K E, Lewis P O (2003). Hickory:A Package for Analysis of Population Genetic Data. Farmington, Connecticut: Departmentof Ecology and Evolutionary Biology, University of Connecticut, USA 12. Holsinger K E, Lewis P O, Dey D K (2002). A Bayesian method for analysis ofgenetic population structure with dominant marker data. Mol Ecol, 11(7): 1157–1164. doi:10.1046/j.1365-294X.2002.01512.x 13. Huang Q Q, Wang L H, Nobuhiro T, Kiha O (1995). The genetic variation of isozyme in natural populations of Massonpine. Acta Genet Sin, 22(2): 142–151 (in Chinese) 14. Li B, Gu W C (2003). Reviewon genetic diversity in Pinus. Hereditas (Beijing), 25(6): 740–748 (in Chinese) 15. Li C, Chai B F, Wang M B (2006). Genetic diversity of Pinus tabulaeformis populations in NorthChina. Bull Bot Res, 1: 98–102 (in Chinese) 16. Lynch M, Milligan B G (1994). Analysisof population genetic structure with RAPD markers. Mol Ecol, 3: 91–99. doi:10.1111/j.1365-294X.1994.tb00109.x 17. Miller M P (1997). Tools for population genetic analyses (TFPGA)1.3 A Windows(r)program for the analysis of allozyme and molecular population geneticdata 18. Navascués M, Emerson B C (2005). Chloroplastmicrosatellites: measures of genetic diversity and the effect of homoplasy. Mol Ecol, 14: 1333–1341. doi:10.1111/j.1365-294X.2005.02504.x 19. Naydenov K D, Tremblay F M, Fenton J J, Alexandrov A (2006). Structure of Pinus nigra Arn. populations in Bulgaria revealed by chloroplast microsatellitesand terpenes analysis: Provenance test. Biochem Syst Ecol, 34(7): 562–574. doi:10.1016/j.bse.2006.01.011 20. Petit R J, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin G G (2005). Comparative organization of chloroplast, mitochondrialand nuclear diversity in plant populations. Mol Ecol, 14(3): 689–701. doi:10.1111/j.1365-294X.2004.02410.x 21. Ribeiro M M, Mariette S, Vendramin G G, Szmidt A E, Plomion C, Kremer A (2002). Comparison of genetic diversity estimates within andamong populations of maritime pine using chloroplast simple-sequencerepeat and amplified fragment length polymorphism data. Mol Ecol, 11(5): 869–877. doi:10.1046/j.1365-294X.2002.01490.x 22. Richardson B A, Brunsfeld J, Klopfenstein N B (2002). DNA from bird-dispersed seed andwind-disseminated pollen provides insights into postglacial colonizationand population genetic structure of whitebark pine (Pinus albicaulis). Mol Ecol, 11(2): 215–227. doi:10.1046/j.1365-294X.2002.01435.x 23. Steward C N, Excoffier L (1996). Assessingpopulation genetic structure and variability with RAPD data: applicationto Vaccinium macrocarpon (Americancranberry). J Evol Biol, 9(2): 153–171. doi:10.1046/j.1420-9101.1996.9020153.x 24. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002). Data from amplified fragment length polymorphism (AFLP)markers show indication of size homoplasy and of a relationship betweendegree of homoplasy and fragment size. Mol Ecol, 11(1): 139–151. doi:10.1046/j.0962-1083.2001.01415.x 25. Vendramin G G, Lelli L, Ross P, Morgante M (1996). A set of primers for the amplification of 20 chloroplastmicrosatellites in Pinaceae. Mol Ecol, 5(4): 595–598. doi:10.1111/j.1365-294X.1996.tb00353.x 26. Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995). AFLP: a new techniquefor DNA fingerprinting. Nucleic Acids Res, 23(21): 4407–4414. doi:10.1093/nar/23.21.4407 27. Wu J, Krutovshii K, Strauss S H (1999). Nuclear DNA diversity, populationdifferentiation and phylogenetic relationships in the California closed-conepines based on RAPD and allozyme markers. Genome, 42: 893–908. doi:10.1139/gen-42-5-893 28. Yang J, Li S, Cao D W, Liu Z L, Zhao G F (2005). Establishment andanalysis of dipteronia Oliv.’s AFLP reaction system.Acta Bot Boreal-OccidentSin, 11: 35–39 (in Chinese) 29. Yang X, Zhao G F, Zhou T H, Liu Z L (2007). Sampling strategy for genetic diversity and genetic relationshipof relative species. Acta Bot Boreal-OccidentSin, 27: 1121–1126 (in Chinese) 30. Yeh F C, Yang R, Boyle T (1999). POPGENE version 1.31: Microsoft Window-basedfreeware for population genetic analysis. 31. Yu H (1999). A study on ecogenetics and evolution of Pinus yunnanensis and close relative species.Postdoctoral thesis.Beijing: Institute of Botany,Chinese Academy of Sciences (in Chinese) 32. Zhivotovsky L A (1999). Estimating population structure in diploids with multilocusdominant DNA markers. Mol Ecol, 8(6): 907–913. doi:10.1046/j.1365-294x.1999.00620.x