Genetic structure of an endemic japanese conifer, sciadopitys verticillata (sciadopityaceae), by using microsatellite markers

Journal of Heredity

Volumn 101, Issue 3, 2010, Pages 292-297

  Kawase, Daiju ^a   Tsumura, Yoshihiko ^b   Tomaru, Nobuhiro ^c   Seo, Akihiro ^a   Yumoto, Takakazu ^a  

^a RESEARCH INSTITUTE FOR HUMANITY AND NATURE   (Japan)

^b FORESTRY AND FOREST PRODUCTS RESEARCH INSTITUTE   (Japan)

^c NAGOYA UNIVERSITY   (Japan)

Author keywords

Coffin; Genetic variation; Microsatellite analysis; Population structure; Sciadopitys verticillata

Indexed keywords

ALLELE; ARTICLE; BAYES THEOREM; BOTTLENECK POPULATION; CLUSTER ANALYSIS; CONIFER; GENETIC VARIABILITY; MICROSATELLITE MARKER; POPULATION GENETIC PARAMETERS; PRIORITY JOURNAL; SCIADOPITYS VERTICILLATA;

CONIFEROPHYTA; GENETIC MARKERS; GENETIC STRUCTURES; GENETIC VARIATION; HETEROZYGOTE; JAPAN; MICROSATELLITE REPEATS; MODELS, GENETIC; POPULATION DYNAMICS;

CONIFEROPHYTA; SCIADOPITYACEAE; SCIADOPITYS VERTICILLATA;

EID: 77951683414     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esp128     Document Type: Article

References (39)

1. Baba S. 1991. Karyological study of identification and relationship between species of the family Taxodiaceae (Department of Environmental Sciences and Technology). Sci Bull Coll Agric Univ Ryukyus. 38:77-174.
2. Carstens BC, Richards CL. 2007. Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution. 61:1439-1454.
3. Dieringer D, Schlötterer C. 2003. MICROSATELLITE ANALYSER (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes. 3:167-169.
4. Demesure B, Comps B, Petit RJ. 1996. Chloroplast DNA phylogeography of common beech (Fagus sylvatica L.) in Europe. Evolution. 50:2515-2520.
5. 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.
6. Estoup A, Cornuet JM. 2000. Microsatellite evolution: inferences from population data. In: Goldstein DB, Schlö tterer C, editors. Microsatellites: Evolution and Applications. Oxford: Oxford University Press. p. 49-65.
7. 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.
8. Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 164:1567-1587.
9. Felsenstein J. 2004. PHYLIP (phylogenetic inference package) version 3.6, distributed by the author. Seattle (WA): Department of Genome Sciences, University of Washington.
10. Goudet J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). [Internet]. Lausanne, Switzerland: Lausanne University; [cited 2008 Nov 18]. Available from: URL http://www2 .unil.ch/popgen/softwares/fstat.htm.
11. Hamrick JL, Godt MJW, Sherman-Broyles SL. 1992. Factors influencing levels of genetic diversity in woody plant species. New For. 6:95-124.
12. Hayashi Y. 1960. Taxonomical and phytogeographical study of Japanese conifers. Tokyo: Nourin Shuppan Japanese.
13. Hayata B. 1931. The Sciadopityaceae represented by Sciadopitys verticillata Sieb. et Zucc., an endemic species of Japan. Bot Mag Tokyo. 45:567-569.
14. Igarashia Y, Oba T. 2006. Fluctuations in the East Asian monsoon over the last 144 ka in the northwest Pacific based on a high-resolution pollen analysis of IMAGES core MD01-2421. Quat Sci Rev. 25: 1447-1459.
15. Itoh T, Shimaji K. 1996. Wood species of excavated pillars used for ancient buildings. Wood Res Rev. 14:49-76.
16. Kanauchi A. 2005. Pollen analysis of the Jaishi oike Moordeposit, in the southern part of the Izu Peninsula. Sundai Shigaku. 125:119-130.
17. Katoh T. 1948. Studies on the distribution of "Koyamaki" (5Sciadopitys verticillata Sieb. et. Zucc.) natural forest and a few factors of its climatic environment. Bull Kyushu Univ For. 16:55-115.
18. Kawase D, Saneyoshi U, Yoshihiko T, Nobuhiro T, Akihiro S, Takakazu Y. Forthcoming. Development and characterization of EST-SSR markers for Sciadopitys verticillata (Sciadopityaceae). Conserv Genet. doi:10.1007/s10592-009-9877-1
19. Luikart G, Cornuet JM. 1998. Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv Biol. 12:228-237.
20. Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA. 70:3321-3323.
21. Nei M, Tajima F, Tateno Y. 1983. Accuracy of estimated phylogenic trees from molecular data. J Mol Evol. 19:153-170.
22. Okabayashi K. 2006. Kohunjidai mokkan no Youzaisentaku ni kansuru Kenkyu. Kashihara (Nara Prefecture): Kashihara Archaeological Institute Japanese.
23. Peakall R, Smouse PE. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes. 6:288-295.
24. Petit RJ, Aguinagalde I, De Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, et al. 2003. Glacial refugia: hotspots but not melting pots of genetic diversity. Science. 300: 1563-1565.
25. Petit RJ, Kremer A, Wagner DB. 1993. Geographic structure of chloroplast DNA polymorphisms in European oaks. Theor Appl Genet. 87:122-128.
26. Piry SG, Luikart G, Cornuet JM. 1999. BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered. 90:502-503.
27. Primmer CR, Saino N, Moller AP, Ellegren H. 1998. Unraveling the processes of microsatellite evolution through analysis of germ line mutations in barn swallows (Hirundorustica). Mol Biol Evol. 15:1047-1054.
28. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945-959.
29. Stewart CN, Via LE. 1993. A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. Biotechniques. 14:748-750.
30. Suyama Y, Tsumura Y, Ohba K. 1997. A cline of allozyme variation in Abies mariesii. J Plant Res. 110:219-226.
31. Suzuki M. 2002. Nihonjin to Ki no Bunka. Tokyo: Yasaka Shobou Japanese.
32. Takahashi T, Tani N, Taira H, Tsumura Y. 2005. 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.
33. Tani N, Tomaru N, Araki M, Ohba K. 1996. Genetic diversity and differentiation in populations of Japanese stone pine (Pinus pumila) in Japan. Can J For Res. 26:1454-1462.
34. Tomaru N, Tsumura Y, Ohba K. 1994. Genetic variation and population differentiation in natural populations of Cryptomeria japonica. Pl Spec Biol. 9:191-199.
35. Tsukada M. 1963. Umbrella Pine, Sciadopitys verticillata: past and present distribution in Japan. Science. 142:1680-1681.
36. Tsukada M. 1982. Cryptomeria japonica: glacial refugia and late-glacial postglacial migration. Ecology. 63:1091-1105.
37. Tsukada M. 1985. Map of vegetation during the last glacial maximum in Japan. Quat Res. 23:369-381.
38. Tsumura Y, Kado T, Takahashi T, Tani N, Ujino-Ihara T, Iwata H. 2007. Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics. 176:2393-2403.
39. Uchida K, Tomaru N, Tomaru C, Yamamoto C, Ohba K. 1997. Allozyme variation in natural populations of hinoki, Chamaecyparis obtusa (Sieb. et Zucc.) Endl., and its comparison with the plus-trees selected from artificial stands. Breed Sci. 47:7-14