title: DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato).
abstract: We investigated the nucleotide variation of a conifer, Cryptomeria japonica, and the divergence between this species and its closest relative, Taxodium distichum, at seven nuclear loci (Acl5, Chi1, Ferr, GapC, HemA, Lcyb, and Pat). Samples of C. japonica were collected from three areas, Kantou-Toukai, Hokuriku, and Iwate. No apparent geographic differentiation was found among these samples. However, the frequency spectrum of the nucleotide polymorphism revealed excesses of intermediate-frequency variants, which suggests that the population was not panmictic and a constant size in the past. The average nucleotide diversity, pi, for silent sites was 0.00383. However, values of pi for silent sites vary among loci. Comparisons of polymorphism to divergence among loci (the HKA test) showed that the polymorphism at the Acl5 locus was significantly lower. We also observed a nearly significant excess of replacement polymorphisms at the Lcyb locus. These results suggested possibilities of natural selection acting at some of the loci. Intragenic recombination was detected only once at the Chi1 locus and was not detected at the other loci. The low level of population recombination rate, 4Nr, seemed to be due to both low level of recombination, r, and small population size, N.
authors.affiliation: Department of Biology, Faculty of Sciences, Kyushu University, Ropponmatsu, Fukuoka 810-8560, Japan.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Kado
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yoshimaru
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Tsumura
authors.forename: Hidenori
authors.initials: H
authors.lastname: Tachida
mesh_terms: D000483:Alleles; D001483:Base Sequence / Q000235:genetics; D002874:Chromosome Mapping; D032485:Cryptomeria / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D019143:Evolution, Molecular; D008040:Genetic Linkage; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D007564:Japan; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D009154:Mutation; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D012641:Selection, Genetic; D013045:Species Specificity; D032489:Taxodium / Q000235:genetics
chemical_list: D004247:DNA