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Microsatellite markers reveal high allelic variation in natural populations of Cryptomeria japonica near refugial areas of the last glacial period

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Abstract

Using 11 microsatellite markers, we investigated the allelic variation and genetic structure of Cryptomeria japonica, across most of its natural distribution. The markers displayed high levels of polymorphism (average gene diversity=0.77, average number of alleles=24.0), in sharp contrast to the lower levels of polymorphism found in allozyme and cleaved amplified polymorphic sequence markers in previous studies. Little genetic differentiation was found among populations (FST=0.028, P<0.001), probably because the species is wind-pollinated and long-lived. No clear relationship between Nei’s genetic distances and geographical locations of the populations were found using the principal coordinate and unweighted pair-group method with arithmetic averaging analyses. The lack of such trends might be due partly to microsatellite homoplasy arising from mutation blurring the genealogical record. However, there was a trend towards high allelic diversity in five populations (Ashitaka, Ashiu, Oki-Island, Yakushima-Island-1 and -2), which are very close to, or in, refugial areas of the last glacial period as defined by Tsukada based on pollen analysis data and current climatic divisions. We postulate that these refugial populations might have been less affected by genetic drift than the other populations due to their relatively large size.

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References

  • Adams RI, Brown KM, Hamilton MB (2004) The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis). Mol Ecol 13:2579–2588

    Google Scholar 

  • Callen DF, Thompson AD, Shen Y, Phillips HA, Richards RI, Mulley JC, Sutherland GR (1993) Incidence and origin of “Null” alleles in the (AC)n microsatellite markers. Am J Hum Genet 52:922–927

    Google Scholar 

  • Chase M, Kessell R, Bawa K (1996) Microsatellite markers for population and conservation genetics of tropical trees. Am J Bot 83:51–57

    Google Scholar 

  • Cloutier D, Rioux D, Beaulieu J, Schoen DJ (2003) Somatic stability of microsatellite loci in Eastern white pine, Pinus strobus L. Heredity 90:247–252

    Google Scholar 

  • Comps B, Gömöry D, Letouzey J, Thiebaut B, Petit RJ (2001) Diverging trends between hetrozygosity and allelic richness during postglacial colonization in the European beech. Genetics 157:389–397

    Google Scholar 

  • El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theor Appl Genet 92:832–839

    Article  Google Scholar 

  • Estoup A, Cornuet JM (1999) Microsatellite evolution: inferences from population data. In: Goldstein DB, Schlötterer C (eds) Microsatellite: evolution and applications. Oxford University Press, Oxford, pp 49–65

    Google Scholar 

  • Estoup A, Jarne P, Cornuet JM (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol Ecol 11:1591–1604

    Article  CAS  PubMed  Google Scholar 

  • Goudet J (2000) FSTAT: a program to estimate and test gene diversities and fixation indices (version 2.9.1). Available at: http://www.unil.ch/izea/softwares/fstat.html

  • Hamrick JL, Godt MJW, Sherman-Broylers SL (1992) Factors influencing levels of genetic diversity in woody plant species. New For 6:95–124

    Google Scholar 

  • Hancock JM (1999) Microsatellites and other simple sequences: genomic context and mutational mechanisms. In: Goldstein DB, Schlötterer C (eds) Microsatellite: evolution and applications. Oxford University Press, Oxford, pp 1–9

    Google Scholar 

  • Hayashi Y (1960) Taxonomical and phytogeographical study of Japanese conifers (in Japanese). Norin-Shuppan, Tokyo

    Google Scholar 

  • Hedrick PW (1999) Highly variable loci and their interpretation in evolution and conservation. Evolution 53:313–318

    Google Scholar 

  • Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linn Soc 58:247–276

    Article  Google Scholar 

  • Hurlbert SH (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology 52:577–586

    Google Scholar 

  • Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends Ecol Evol 11:424–429

    Article  Google Scholar 

  • Kimura M, Crow J (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725–738

    CAS  PubMed  Google Scholar 

  • Kimura M, Ohta T (1978) Stepwise mutation model and distribution of allelic frequencies in a finite population. Proc Natl Acad Sci USA 75:2868–2872

    Google Scholar 

  • Michalakis Y, Excoffier L (1996) A genetic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142:1061–1064

    Google Scholar 

  • Moriguchi Y, Iwata H, Ujino-Ihara T, Yoshimura K, Taira H, Tsumura Y (2003) Development and characterization of microsatellite markers for Cryptomeria japonica D. Don. Theor Appl Genet 106:751–758

    Google Scholar 

  • Mukai T, Cockerham CC (1977) Spontaneous mutation rate at enzyme loci in Drosophila melanogaster. Proc Natl Acad Sci USA 74:2514–2517

    Google Scholar 

  • Murai S (1947) Major forestry tree species in the Tohoku region and their varietal problems (in Japanese). In: Kokudo Saiken Zourin Gijutsu Kouenshu, Aomori-rinyukai, Aomori

    Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    Google Scholar 

  • Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10

    Google Scholar 

  • Ohba K (1993) Clonal forestry with sugi (Cryptomeria japonica). In: Ahuja MR, Libby WJ (eds) Clonal forestry 2. Conservation and application. Springer, Berlin Heidelberg New York, pp 66–89

    Google Scholar 

  • Ohta T, Kimura M(1973) The model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a genetic population. Genet Res 22:201–204

    Google Scholar 

  • Schneider S, Kueffer JM, Roessli D, Excoffier L (1997) ARLEQUIN, version 2.0: software for population genetic data analysis. Genetic and Biometry Laboratory, University of Geneva, Switzerland. Available at: http://lgb.unige.ch/arlequin/

  • Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462

    CAS  PubMed  Google Scholar 

  • Sokal RR, Seneath PHA (1963) Principals of numerical taxonomy. Freeman, San Francisco

    Google Scholar 

  • Takahara H (1998) Sugi-rin no hensen. (in Japanese) In: Yasuda Y, Miyoushi N (eds) Nippon Rettou Syokusei-si. Asakura-Shoten, Tokyo, pp 207–223

    Google Scholar 

  • Takahara H, Tanida K, Miyoshi N (2001) The full-glacial refuge of Cryptomeria japonica in the Oki Islands, western Japan. Jpn J Palynol 47:21–33

    Google Scholar 

  • Takeda H (1931) Series of Japanese geography vol. 5 Mt. Fuji (in Japanese). Kaizo-sha, Tokyo

    Google Scholar 

  • Tani N, Takahashi T, Iwata H, Mukai Y, Ujino-Ihara T, Matumoto A, Yoshimura K, Yoshimaru H, Murai M, Nagasaka K, Tsumura Y (2003) A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed tags. Genetics 165:1551–1568

    CAS  PubMed  Google Scholar 

  • Tani N, Takahashi T, Ujino-Ihara T, Iwata H, Yoshimura K, Tsumura Y (2004) Development and characteristics of microsatellite markers for sugi (Cryptomeria japonica D. Don) derived from microsatellite-enriched libraries. Ann Forensic Sci 61:569–575

    Google Scholar 

  • Tomaru N, Tsumura Y, Ohba K (1994) Genetic variation and population differentiation in natural populations of Cryptomeria japonica. Plant Species Biol 9:191–199

    Google Scholar 

  • Tomaru N, Mitsutsuji T, Takahashi M, Tsumura Y, Uchida K, Ohba K (1997) Genetic diversity in Fagus crenata (Japanese beech): influence of the distributional shift during the last-Quaternary. Heredity 78:241–251

    Article  Google Scholar 

  • Tsukada M (1982) Cryptomeria japonica: glacial refugia and late-glacial and postglacial migration. Ecology 63:1091–1105

    Google Scholar 

  • Tsumura Y, Ohba K (1992) Allozyme variation of five natural populations of Cryptomeria japonica in western Japan. Jpn J Genet 67:299–308

    Google Scholar 

  • Tsumura Y, Ohba K (1993) Genetic structure of geographical marginal populations of Cryptomeria japonica. Can J For Res 23:859–863

    Google Scholar 

  • Tsumura Y, Tomaru N (1999) Genetic diversity of Cryptomeria japonica using co-dominant DNA markers based on sequenced-tagged sites. Theor Appl Genet 98:396–404

    Article  CAS  Google Scholar 

  • Tsumura Y, Yoshimura K, Tomaru N, Ohba K (1995) Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theor Appl Genet 91:1222–1236

    CAS  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Google Scholar 

  • Wright S (1951) The genetic structure of populations. Ann Eugen 15:323–354

    Google Scholar 

  • Yasue M, Ogiyama K, Suto S, Tsukahara H, Miyahara F, Ohba K (1987) Geographical differentiation of natural Cryptomeria stands analyzed by diterpene hydrocarbon constituents of individual trees. J Jpn For Soc 69:152–156

    Google Scholar 

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Acknowledgements

The authors are grateful to H. Iwata, S. Ueno, S. Kanetani and T. Kado for valuable suggestions and technical support. We also thank M. Sakimoto, K. Hirayama, A. Matsumoto, T. Ihara, K. Yoshimura, K. Nagasaka, and Y. Moriguchi for their help in sample collection. The study was partly supported by a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (no. 16380112) and a grant for Research on Conservation of Endemic Tree Species and Genetic Diversity in the Ecosystem of the Yakushima Islands from the Ministry of Environment, Japan.

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Correspondence to Yoshihiko Tsumura.

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Takahashi, T., Tani, N., Taira, H. et al. Microsatellite markers reveal high allelic variation in natural populations of Cryptomeria japonica near refugial areas of the last glacial period. J Plant Res 118, 83–90 (2005). https://doi.org/10.1007/s10265-005-0198-2

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