Kado Tomoyuki, Yoshimaru Hiroshi, Tsumura Yoshihiko, Tachida Hidenori
Department of Biology, Faculty of Sciences, Kyushu University, Ropponmatsu, Fukuoka 810-8560, Japan.
Genetics. 2003 Aug;164(4):1547-59. doi: 10.1093/genetics/164.4.1547.
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.
我们研究了一种针叶树——日本柳杉的核苷酸变异，以及该物种与其亲缘关系最近的物种——落羽杉在七个核基因座（Acl5、Chi1、Ferr、GapC、HemA、Lcyb和Pat）上的差异。日本柳杉的样本采集自三个地区，即关东 - 东海、北陆和岩手。在这些样本中未发现明显的地理分化。然而，核苷酸多态性的频率谱显示中频变异过多，这表明该种群在过去并非随机交配且种群大小并非恒定。沉默位点的平均核苷酸多样性π为0.00383。然而，沉默位点的π值在不同基因座间存在差异。基因座间多态性与分化的比较（HKA检验）表明，Acl5基因座的多态性显著较低。我们还在Lcyb基因座观察到替换多态性几乎显著过量。这些结果表明某些基因座可能受到自然选择作用。仅在Chi1基因座检测到一次基因内重组，在其他基因座未检测到。种群重组率4Nr较低似乎是由于重组率r较低和种群大小N较小所致。
