DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato)

Genetics

Volumn 164, Issue 4, 2003, Pages 1547-1559

  Kado, Tomoyuki ^a   Yoshimaru, Hiroshi ^b   Tsumura, Yoshihiko ^b   Tachida, Hidenori ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b FORESTRY AND FOREST PRODUCTS RESEARCH INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONIFER; DNA POLYMORPHISM; GENE LOCUS; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; JAPANESE CEDAR; NATURAL SELECTION; NUCLEOTIDE SEQUENCE; POPULATION SIZE; PRIORITY JOURNAL; SPECIES DIFFERENTIATION;

ALLELES; BASE SEQUENCE; CHROMOSOME MAPPING; CRYPTOMERIA; DNA; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HAPLOTYPES; JAPAN; LINKAGE (GENETICS); LINKAGE DISEQUILIBRIUM; MOLECULAR SEQUENCE DATA; MUTATION; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SELECTION (GENETICS); SPECIES SPECIFICITY; TAXODIUM; VARIATION (GENETICS);

CONIFEROPHYTA; CRYPTOMERIA; CRYPTOMERIA JAPONICA; CUPRESSACEAE; EMBRYOPHYTA; JAPONICA; TAXODIUM DISTICHUM;

EID: 0041817580     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (61)

1. AGUADÉ, M., 2001 Nucleotide sequence variation at two genes of the phenylpropanoid pathway, the FAH1 and F3H genes, in Arabidopsis thaliana. Mol. Biol. Evol. 18: 1-9.
2. ARNOLD, C. A., and J. C. LOWTHER, 1955 A new Cretaceous conifer from northern Alaska. Am. J. Bot. 42: 522-528.
3. BANDELT, H. J., P. FORSTER and A. ROHL, 1999 Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16: 37-48.
4. BEGUN, D. J., and C. F. AQUADRO, 1992 Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
5. CHAGNE, D., C. LALANNE, D. MADUR, S. KUMAR, J. M. FRIGERIO et al., 2002 A high density genetic map of maritime pine based on AFLPs. Ann. For. Sci. 59: 627-636.
6. CHARLESWORTH, B., T. H. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
7. DVORNYK, V., A. SIRVIO, M. MIKKONEN and O. SAVOLAINEN, 2002 Low nucleotide diversity at the pall locus in the widely distributed Pinus sylvestris. Mol. Biol. Evol. 19: 179-188.
8. FILATOV, D. A., and D. CHARLESWORTH, 1999 DNA polymorphism, haplotype structure and balancing selection in the Leavenworthia PgiC locus. Genetics 153: 1423-1434.
9. FU, Y. X., 1997 Statistical tests of neutrality for DNA samples from a population. Genetics 147: 915-925.
10. FU, Y. X., and W. H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
11. GADEK, P. A., D. L. ALPERS, M. M. M. HESLEWOOD and C. J. QUINN, 2000 Relationships within Cupressaccae sensu lato: a combined morphological and molecular approach. Am. J. Bot. 87: 1044-1057.
12. GRATTAPAGLIA, D., and R. SEDEROFF, 1994 Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-test-cross: mapping strategy and RAPD markers. Genetics 137: 1121-1137.
13. HAMRICK, J. L., and M. J. W. GODT, 1990 Allozyme diversity in plant species, pp. 43-63 in Plant Population Genetics, Breeding and Genetic Resources, edited by A. H. D. BROWN, M. T. CLEGG, A. L. KAHLER and B. S. WEIR. Sinauer Associates, Sunderland, MA.
14. HAMRICK, J. L., and M. J. W. GODT, 1996 Effects of life history traits on genetic diversity in plant species. Philos. Trans. R. Soc. Lond. B 351: 1291-1298.
15. HANZAWA, Y., T. TAKAHASHI, A. J. MICHAEL, D. BURTIN, D. LONG et al., 2000 ACAULIS5, an Arabidopsis gene required for stem elongation, encodes a spermine synthase. EMBO J. 19: 4248-4256.
16. HARPENDING, H. C., 1994 Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66: 591-600.
17. HAYASHI, Y., 1960 Taxonomical and Phytogeographical Study of Japanese Conifers. Norin-Shuppan, Tokyo (in Japanese).
18. HIZUME, M., T. KONDO, F. SHIBATA and R. ISHIZUKA, 2001 Flow cytometric determination of genome size in the Taxodiaceae, Cupressaceae sensu stricto and Sciadopityaceae. Cytologia 66: 307-311.
19. HUDSON, R. R., 1987 Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50: 245-250.
20. HUDSON, R. R., 1990 Gene genealogy and the coalescent process, pp. 1-44 in Oxford Surveys in Evolutionary Biology, edited by P. H. HARVEY and L. PARTRIDGE. Oxford University Press, New York.
21. HUDSON, R. R., 2000 A new statistic for detecting genetic differentiation. Genetics 155: 2011-2014.
22. HUDSON, R. R., and N. L. KAPLAN, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
23. HUDSON, R. R., M. KREITMAN and M. AGUADÉ, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
24. HUDSON, R. R., M. SLATKIN and W. P. MADDISON, 1992 Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
25. INNAN, H., F. TAJIMA, R. TERAUCHI and N. T. MIYASHITA, 1996 Intragenic recombination in the Adh locus of the wild plant Arabidopsis thaliana. Genetics 143: 1761-1770.
26. IWATA, H., T. UJINO-IHARA, K. YOSHIMURA, K. NAGASAKA, Y. MUKAI et al., 2001 Cleaved amplified polymorphic sequence markers in sugi, Cryptomeria japonica D. Don, and their locations on a linkage map. Theor. Appl. Genet. 103: 881-895.
27. KAKKAR, R. J., and V. K. SAWHNEY, 2002 Polyamine research in plants - a changing perspective. Physiol. Plant. 116: 281-292.
28. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 "Hitchhiking effect" revisited. Genetics 123: 887-899.
29. KAWABE, A., and N. T. MIYASHITA, 1999 DNA variation in the basic chitinase locus (ChiB) region of the wild plant Arabidopsis thaliana. Genetics 153: 1445-1453.
30. KUITTINEN, H., and M. AGUADÉ, 2000 Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana. Genetics 155: 863-872.
31. KUSUMI, J., Y. TSUMURA, H. YOSHIMARU and H. TACHIDA, 2000 Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnFIGS region, and trnL intron sequences. Am. J. Bot. 87: 1480-1488.
32. KUSUMI, J., Y. TSUMURA, H. YOSHIMARU and H. TACHIDA, 2002 Molecular evolution of nuclear genes in Cupressaceae, a group of conifer trees. Mol. Biol. Evol. 19: 736-747.
33. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favorable gene. Genet. Res. 23: 23-35.
34. McDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
35. MIYASHITA, N. T., A. KAWABE and H. INNA, 1999 DNA variation in the wild plant Arabidopsis thaliana revealed by amplified fragment length polymorphism analysis. Genetics 152: 1723-1731.
36. MIYOSHI, N., T. FUHIKI and Y. MORITA, 1999 Palynology of a 250-m core from Lake Biwa: a 430,000-year record of glacial-interglacial vegetation change in Japan. Rev. Paleobot. Palynol. 104: 267-283.
37. MORIYAMA, E. N., and J. R. POWELL, 1996 Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13: 261-277.
38. MUKAI, Y., Y. SUYAMA, Y. TSUMURA, T. KAWAHARA, H. YOSHIMARU et al., 1995 A linkage map for sugi (CRIPTOMERIA-JAPONICA) based on RFLP, RAPD and isozyme loci. Theor. Appl. Genet. 90: 835-840.
39. MURAI, S., 1947 Major forest tree species in the Tohoku region and their varietal problems, pp. 131-151 in Kokudo Saiken Zourin Gijutsu Kouenshu, edited by AOMORI-RINYU-KYOUKAI, Aomori-rinyu-kyoukai, Aomori (in Japanese).
40. NACHMAN, M. W., V. L. BAUER, S. L. CROWELL and C. F. AQUADRO, 1998 DNA variability and recombination rate at X-linked loci in humans. Genetics 150: 1133-1141.
41. NIKAIDO, A. M., T. UJINO, H. IWATA, K. YOSHIMURA, H. YOSHIMURA et al., 2000 AFLP and CAPS linkage maps of Cryptomeria japonica. Theor. Appl. Genet. 100: 825-831.
42. 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, New York.
43. OHTA, T., 1992 The nearly neutral theory of molecular evolution. Annu. Rev. Syst. Ecol. 23: 263-286.
44. RAMOS-ONSINS, S. E., and J. ROZAS, 2002 Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 19: 2092-2100.
45. ROZAS, J., and R. ROZAS, 1999 DnaSP version 3.0: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
46. SAVOLAINEN, O., C. H. LANGLEY, B. P. LAZZARO and H. FREVILLE, 2000 Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana. Mol. Biol. Evol. 17: 645-655.
47. STAHL, E. A., G. DWYER, R. MAURICIO, M. KREITMAN and J. BERGELSON, 1999 Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature 400: 667-671.
48. TACHIDA, H., 2000 Molecular evolution in a multisite nearly neutral mutation model. J. Mol. Evol. 50: 69-81.
49. TAJIMA, F., 1989a Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
50. TAJIMA, F., 1989b The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
51. TAJIMA, F., 1995 Effect of non-random sampling on the estimation of parameters in population genetics. Genet. Res. 66: 267-276.
52. TAKAHARA, H., 1998 Sugi-rin no hensen, pp. 207-223 in Nippon Rettou Syokusei-si, edited by Y. YASUDA and N. MIYOUSHI. Asakura-Shoten, Tokyo (in Japanese).
53. TODA, R., 1973 Tree breeding, pp. 1-45 in History of Forestry, edited by JAPAN FORESTRY ASSOCIATION. Japan Forestry Association, Tokyo (in Japanese).
54. 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.
55. TSUKADA, M., 1982 Cryptomeria japonica: glacial refugia and late-glacial and postglacial migration. Ecology 63: 1091-1105.
56. TSUMURA, Y., and N. TOMARU, 1999 Genetic diversity of Cryptomeria japonica using co-dominant markers based on sequenced-tagged sites. Theor. Appl. Genet. 98: 396-404.
57. 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.
58. TSUMURA, Y., N. TOMARU, Y. SUYAMA, and S. BACCHUS, 1999 Genetic diversity and differentiation of Taxodium in the southeastern United States using cleaved amplified polymorphic sequences. Heredity 83: 229-238.
59. 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.
60. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
61. YASUE, M., K. OGIYAMA, S. SUTO, H. TSUKAHARA, F. MIYAHARA et al., 1987 Geographical differentiation of natural Cyptomeria stands analyzed by diterpene hydrocarbon constituents of individual trees. J. Jpn. For. Soc. 69: 152-156.