Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica

Genetics

Volumn 176, Issue 4, 2007, Pages 2393-2403

  Tsumura, Yoshihiko ^a   Kado, Tomoyuki ^a   Takahashi, Tomokazu ^b   Tani, Naoki ^a   Ujino Ihara, Tokuko ^a   Iwata, Hiroyoshi ^c  

^a FORESTRY AND FOREST PRODUCTS RESEARCH INSTITUTE   (Japan)

^b NIIGATA UNIVERSITY   (Japan)

^c NATIONAL AGRICULTURAL RESEARCH CENTER   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONFIDENCE INTERVAL; GENE IDENTIFICATION; GENE LOCUS; GENETIC VARIABILITY; GENOME; JAPANESE CEDAR; NATURAL POPULATION; NONHUMAN; PHYLOGENY; POPULATION GENETIC PARAMETERS; PRIORITY JOURNAL; SIMULATION;

ADAPTATION, PHYSIOLOGICAL; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; CRYPTOMERIA; DNA, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; GENETIC MARKERS; GENETICS, POPULATION; GENOMICS; JAPAN; MODELS, GENETIC; PHYLOGENY; VARIATION (GENETICS);

CRYPTOMERIA JAPONICA;

EID: 34548456864     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.072652     Document Type: Article

References (58)

1. BEAUMONT, M. A., and R. A. NICHOLS, 1996 Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Lond. Ser. B 263: 1619-1626.
2. COCKERHAM, C. C., and B. S. WEIR, 1987 Correlations, descent measures: drift with migration and mutation. Proc. Natl. Acad. Sci. USA 84: 8512-8514.
3. EL MOUSADIK, A., and R. J. PETIT, 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.
4. ENDLER, J. A., 1986 Natural Selection in the Wild. Princeton University Press, Princeton, NJ.
5. EXCOFFIER, L., P. E. SMOUSE and J. M. QUATTRO, 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
6. FELSENSTEIN, J., 1995 PHYLIP (phylogeny inference package). Ver. 3.57c. Department of Genetics, University ofWashington, Seattle.
7. FU, Y. X., 1996 New statistical tests of neutrality for DNA samples from a population. Genetics 143: 557-570.
8. GOUDET, J., 2000 FSTAT: a program to estimate and test gene diversities and fixation indices. Ver. 2.9.1. (http://www2.unil.ch/popgen/ softwares/fstat.htm).
9. HAMRICK, J. L., M. J. W. GODT and S. L. SHERMAN-BROYLERS, 1992 Factors influencing levels of genetic diversity in woody plant species. New Forests 6: 95-124.
10. HAYASHI, Y., 1960 Taxonomical and phytogeographical study of Japanese conifers. Norin-Shuppan, Tokyo (in Japanese).
11. HUDSON, R. R., and N. KAPLAN, 1988 The coalescent process in models with selection and recombination. Genetics 120: 831-840.
12. HUDSON, R. R., M. KREITMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
13. IWATA, H., T. IHARA-UJINO, K. YOSHIMURA, K. NAGASAKA and Y. TSUMURA, 2001 Cleaved amplified polymorphic sequence markers in sugi, Cryptomeria japonica D. Don, and their locations on the linkage map. Theor. Appl. Genet. 103: 881-895.
14. KAWAMURA, T., 1977 Fossil pollen study on distribution of Cryptomeria japonica forest. I. Akita Prefecture. Kafun 11: 8-20 (in Japanese).
15. LEWIS, P. O., and D. ZAYKIN, 2002 GDA. (http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php).
16. MANTEL, N., 1967 The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209-220.
17. MAURICIO, R., 2001 Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology. Nature Rev. Genet. 2: 370-381.
18. MCDONALD, J. H. and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
19. MURAI, S., 1947 Major forestry tree species in the Tohoku region and their varietal problems, pp. 131-151 in Kokudo Saiken Zourin Gijutsu Kouenshu. Aomori Rinyukai, Aomori, Japan.
20. NEI, M., 1972 Genetic distance between populations. Am. Nat. 106: 283-292.
21. NEI, M., 1973 Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA 70: 3321-3323.
22. NEI, M., 1977 F-statistics and analysis of gene diversity in subdivided populations. Ann. Hum. Genet. 41: 225-233.
23. NEI, M., 1978 Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.
24. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
25. NEI, M., and R. K. CHESSER, 1983 Estimation of fixation indices and gene diversities. Ann. Hum. Genet. 47: 253-259.
26. NIKAIDO, A. M., T. UJINO, H. IWATA, K. YOSHIMURA, H. YOSHIMARU et al., 2000 AFLP and CAPS linkage maps of Cryptomeria japonica. Theor. Appl. Genet. 100: 825-831.
27. OHBA, K., 1993 Clonal forestry with sugi (Cryptomeria japonica), pp. 66-90 in Clonal Forestry II, Conservation and Application, edited by M. R. AHUJA and W. J. LIBBY. Springer-Verlag, Berlin.
28. PETIT, R. J., I. AGUINAGALDE, J.-L. DE BEAULIEU, C. BITTKAU, S. BREWER et al., 2003 Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300: 1563-1565.
29. PRITCHARD, J. K., M. STEPHENS and P. DONNELLY, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
30. RIESEBERG, L. H., J. WHITTON and K. GARDNER, 1999 Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics 152: 713-727.
31. SAITOU, N., and M. NEI, 1987 A neighbor-joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 44: 406-425.
32. SCHNEIDER, S., J. M. KUEFFER, D. ROESSLI and L. EXCOFFIER, 1997 Arlequin, Version 2.0: software for population genetic data analysis. Genetic and Biometry Laboratory, University of Geneva, Switzerland. (http://lgb.unige.ch/arlequin/).
33. SCOTTI-SAINTAGNE, C., S. MARIETTE, I. PORTH, P. G. GOICOECHEA, T. BARRENECHE et al., 2004 Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. & Q. petraea (Matt.) Liebl.]. Genetics 168: 1615-1626.
34. STORZ, J. F., 2005 Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol. Ecol. 14: 671-688.
35. STROBECK, C., 1983 Expected linkage disequilibrium for a neutral locus linked to a chromosomal arrangement. Genetics 103: 545-555.
36. TAJIMA, F., 1989 Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
37. TAKAHARA, H., 1998 Distribution history of Cryptomeria forest, pp. 207-223 in Vegetation History of the Japanese Archipelago, edited by Y. YASUDA and N. MIYOUSHI. Asakura-Shoten, Tokyo.
38. TAKAHASHI, T., N. TANI, H. TAIRA and Y. TSUMURA, 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.
39. TANI, N., T. TAKAHASHI, H. IWATA, Y. MUKAI, T. UJINO-IHARA et al., 2003 A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed tags. Genetics 165: 1551-1568.
40. TOMARU, N., Y. TSUMURA and K. OHBA, 1994 Genetic variation and population differentiation in natural populations of Cryptomeria japonica. Plant Species Biol. 9: 191-199.
41. TSUKADA, M., 1983 Vegetation and climate during the last glacial maximum in Japan. Quatern. Res. 19: 212-235.
42. TSUKADA, M., 1986 Altitudinal and latitudinal migration of Cryptomeria japonica for the past 20,000 years in Japan. Quatern. Res. 26: 135-152.
43. TSUKADA, M., 1988 Japan, pp. 458-518 in Handbook of Vegetation Science, Vol. VII, Vegetation History, edited by B. HUNTLEY and T. WEBB III. Kluwer, Dordrecht, The Netherlands.
44. TSUMURA, Y., and K. OHBA, 1993 Genetic structure of geographical marginal populations of Cryptomeria japonica. Can. J. For. Res. 23: 859-863.
45. TSUMURA, Y., and N. TOMARU, 1999 Genetic diversity of Cryptomeria japonica using co-dominant DNA markers based on sequenced-tagged site. Theor. Appl. Genet. 98: 396-404.
46. TSUMURA, Y., K. YOSHIMURA, N. TOMARU and K. OHBA, 1995 Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theor. Appl. Genet. 91: 1222-1236.
47. TSUMURA, Y., Y. SUYAMA, K. YOSHIMURA, N. SHIRATO and Y. MUKAI, 1997 Sequence-tagged-sites (STSs) of cDNA clones in Cryptomeria japonica and their evaluation as molecular markers in conifers. Theor. Appl. Genet. 94: 764-772.
48. TSUMURA, Y., A. MATSUMOTO, N. TANI, T. UJINO-IHARA, T. KADO et al., 2007 Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implication for management and conservation. Heredity (in press).
49. UJINO-IHARA, T., K. YOSHIMURA, Y. UGAWA, H. YOSHIMARU, K. NAGASAKA et al., 2000 Expression analysis of ESTs derived from the inner bark of Cryptomeria japonica. Plant Mol. Biol. 43: 451-457.
50. UJINO-IHARA, T., H. KANAMORI, H. YAMANE, Y. TAGUCHI, N. NAMIKI et al., 2005 Comparative analysis of expressed sequence tags of conifers and angiosperms reveals sequences specifically conserved in conifers. Plant Mol. Biol. 59: 895-907.
51. VASEMÄGI, A., and C. R. PRIMMER, 2005 Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Mol. Ecol. 14: 3623-3642.
52. VASEMÄGI, A., J. NILSSON and C. R. PRIMMER, 2005 Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Mol. Biol. Evol. 22: 1067-1076.
53. VITALIS, R., K. DAWSON and P. BOURSOT, 2001 Interpretation of variation across marker loci as evidence of selection. Genetics 158: 1811-1823.
54. VITALIS, R., K. DAWSON, P. BOURSOT and K. BELKHIR, 2003 DetSel 1.0: a computer program to detect markers responding to selection. J. Hered. 94: 429-431.
55. WRIGHT, S., 1922 Coefficients of inbreeding and relationship. Am. Nat. 56: 330-338.
56. WRIGHT, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.
57. YAMAZAKI, T., 1995 Cryptomeriaceae, pp. 264, in Flora of Japan. Vol I, Pteridophyta and Gymnospermae, edited by K. IWATSUKI, T. YAMAZAKI, D.E. BOUFFORD and H. OHBA. Kodansha, Tokyo
58. YASUE, M., K. OGIYAMA, S. SUTO, H. TSUKAHARA, F. MIYAHARA et al., 1987 Geographical differentiation of natural Cryptomeria stands analyzed by diterpene hydrocarbon constituents of individual trees. J. Jpn. For. Soc. 69: 152-156.