Whole-genome sequencing of six Mauritian Cynomolgus macaques (Macaca fascicularis) reveals a genome-wide pattern of polymorphisms under extreme population bottleneck.
Whole-genome sequencing of six Mauritian Cynomolgus macaques (Macaca fascicularis) reveals a genome-wide pattern of polymorphisms under extreme population bottleneck.
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DOI：
10.1093/gbe/evv033
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发表时间：
2015-03-23
影响因子：
3.3
通讯作者：
Blancher A
中科院分区：
文献类型：
--
作者：
Osada N;Hettiarachchi N;Adeyemi Babarinde I;Saitou N;Blancher A
食蟹猴（Macaca fascicularis）在世纪左右被人类引入毛里求斯岛。蒙古食蟹猴独特的人口统计学历史提供了一个机会，不仅可以研究生物医学研究中成熟的非人灵长类动物的遗传背景，还可以了解极端人口瓶颈对基因组多态性模式的影响。我们对6只猕猴的全基因组进行了测序，并获得了每个个体基因组序列的平均20倍覆盖率。核苷酸多样性的总体水平比马来西亚食蟹猴小23%，并且观察到低频多态性减少。此外，我们还证实，马来西亚食蟹猴在遗传上更接近马来西亚人口的代表，而不是印度支那人口的代表。过量的非同义多态性在低频率，这已被观察到在许多其他物种中，是不是很强的样本，杂合的非同义多态性相对于同义多态性的比例是较高的个体在马来西亚猕猴比马来西亚猕猴。这些模式表明，极端的种群瓶颈使得净化选择被种群中遗传漂变的力量所压倒。最后，我们通过使用六个样本的全基因组位点频谱来估计创始个体的数量。假设一个简单的人口统计场景，一个单一的瓶颈，然后是指数增长，估计的创始人数量（2020人）与以前的估计基本一致。
Cynomolgus macaques (Macaca fascicularis) were introduced to the island of Mauritius by humans around the 16th century. The unique demographic history of the Mauritian cynomolgus macaques provides the opportunity to not only examine the genetic background of well-established nonhuman primates for biomedical research but also understand the effect of an extreme population bottleneck on the pattern of polymorphisms in genomes. We sequenced the whole genomes of six Mauritian cynomolgus macaques and obtained an average of 20-fold coverage of the genome sequences for each individual. The overall level of nucleotide diversity was 23% smaller than that of the Malaysian cynomolgus macaques, and a reduction of low-frequency polymorphisms was observed. In addition, we also confirmed that the Mauritian cynomolgus macaques were genetically closer to a representative of the Malaysian population than to a representative of the Indochinese population. Excess of nonsynonymous polymorphisms in low frequency, which has been observed in many other species, was not very strong in the Mauritian samples, and the proportion of heterozygous nonsynonymous polymorphisms relative to synonymous polymorphisms is higher within individuals in Mauritian than Malaysian cynomolgus macaques. Those patterns indicate that the extreme population bottleneck made purifying selection overwhelmed by the power of genetic drift in the population. Finally, we estimated the number of founding individuals by using the genome-wide site frequency spectrum of the six samples. Assuming a simple demographic scenario with a single bottleneck followed by exponential growth, the estimated number of founders (∼20 individuals) is largely consistent with previous estimates.