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

Tomoyuki Kado, Hiroshi Yoshimaru, Yoshihiko Tsumura, Hidenori Tachida

Research output: Contribution to journalArticle

62 Citations (Scopus)

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, π, for silent sites was 0.00383. However, values of π 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, γ, and small population size, N.

Original languageEnglish
Pages (from-to)1547-1559
Number of pages13
JournalGenetics
Volume164
Issue number4
Publication statusPublished - Aug 1 2003

Fingerprint

Cupressaceae
Cryptomeria
Coniferophyta
Genetic Recombination
Nucleotides
Taxodium
DNA
Genetic Selection
Population Density
Population

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Kado, T., Yoshimaru, H., Tsumura, Y., & Tachida, H. (2003). DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics, 164(4), 1547-1559.

DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). / Kado, Tomoyuki; Yoshimaru, Hiroshi; Tsumura, Yoshihiko; Tachida, Hidenori.

In: Genetics, Vol. 164, No. 4, 01.08.2003, p. 1547-1559.

Research output: Contribution to journalArticle

Kado, T, Yoshimaru, H, Tsumura, Y & Tachida, H 2003, 'DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato)', Genetics, vol. 164, no. 4, pp. 1547-1559.
Kado T, Yoshimaru H, Tsumura Y, Tachida H. DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics. 2003 Aug 1;164(4):1547-1559.
Kado, Tomoyuki ; Yoshimaru, Hiroshi ; Tsumura, Yoshihiko ; Tachida, Hidenori. / DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). In: Genetics. 2003 ; Vol. 164, No. 4. pp. 1547-1559.
@article{7cf590c9a90b4ae98c161bf6a7e5aca1,
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, π, for silent sites was 0.00383. However, values of π 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, γ, and small population size, N.",
author = "Tomoyuki Kado and Hiroshi Yoshimaru and Yoshihiko Tsumura and Hidenori Tachida",
year = "2003",
month = "8",
day = "1",
language = "English",
volume = "164",
pages = "1547--1559",
journal = "Genetics",
issn = "0016-6731",
publisher = "Genetics Society of America",
number = "4",

}

TY - JOUR

T1 - DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato)

AU - Kado, Tomoyuki

AU - Yoshimaru, Hiroshi

AU - Tsumura, Yoshihiko

AU - Tachida, Hidenori

PY - 2003/8/1

Y1 - 2003/8/1

N2 - 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, π, for silent sites was 0.00383. However, values of π 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, γ, and small population size, N.

AB - 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, π, for silent sites was 0.00383. However, values of π 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, γ, and small population size, N.

UR - http://www.scopus.com/inward/record.url?scp=0041817580&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0041817580&partnerID=8YFLogxK

M3 - Article

VL - 164

SP - 1547

EP - 1559

JO - Genetics

JF - Genetics

SN - 0016-6731

IS - 4

ER -