Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka 4118540, Japan.
Genetics. 2013 Nov;195(3):1027-35. doi: 10.1534/genetics.113.156703. Epub 2013 Sep 11.
The ratio of genetic diversity on X chromosomes relative to autosomes in organisms with XX/XY sex chromosomes could provide fundamental insight into the process of genome evolution. Here we report this ratio for 24 cynomolgus monkeys (Macaca fascicularis) originating in Indonesia, Malaysia, and the Philippines. The average X/A diversity ratios in these samples was 0.34 and 0.20 in the Indonesian-Malaysian and Philippine populations, respectively, considerably lower than the null expectation of 0.75. A Philippine population supposed to derive from an ancestral population by founding events showed a significantly lower ratio than the parental population, suggesting a demographic effect for the reduction. Taking sex-specific mutation rate bias and demographic effect into account, expected X/A diversity ratios generated by computer simulations roughly agreed with the observed data in the intergenic regions. In contrast, silent sites in genic regions on X chromosomes showed strong reduction in genetic diversity and the observed X/A diversity ratio in the genic regions cannot be explained by mutation rate bias and demography, indicating that natural selection also reduces the level of polymorphism near genes. Whole-genome analysis of a female cynomolgus monkey also supported the notion of stronger reduction of genetic diversity near genes on the X chromosome.
性染色体为 XX/XY 的生物中，X 染色体相对于常染色体的遗传多样性比率可以为基因组进化过程提供重要的见解。本文报告了来自印度尼西亚、马来西亚和菲律宾的 24 只食蟹猴（Macaca fascicularis）的这一比率。在这些样本中，印度尼西亚-马来西亚种群和菲律宾种群的平均 X/A 多样性比率分别为 0.34 和 0.20，远低于 0.75 的预期值。一个假定通过奠基事件从祖先种群中衍生出来的菲律宾种群的比率明显低于母体种群，表明这种减少是由种群效应引起的。考虑到性染色体特有突变率偏倚和种群效应，计算机模拟生成的预期 X/A 多样性比率与基因间区域的观察数据大致吻合。相比之下，X 染色体上基因区域的沉默位点的遗传多样性明显降低，基因区域观察到的 X/A 多样性比率不能用突变率偏倚和种群动态来解释，这表明自然选择也降低了基因附近多态性的水平。对一只雌性食蟹猴的全基因组分析也支持了 X 染色体上基因附近遗传多样性减少更为强烈的观点。
