School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Mol Biol Evol. 2017 May 1;34(5):1055-1065. doi: 10.1093/molbev/msx056.
Relatively little is known about the evolutionary history of the African green monkey (genus Chlorocebus) due to the lack of sampled polymorphism data from wild populations. Yet, this characterization of genetic diversity is not only critical for a better understanding of their own history, but also for human biomedical research given that they are one of the most widely used primate models. Here, I analyze the demographic and selective history of the African green monkey, utilizing one of the most comprehensive catalogs of wild genetic diversity to date, consisting of 1,795,643 autosomal single nucleotide polymorphisms in 25 individuals, representing all five major populations: C. a. aethiops, C. a. cynosurus, C. a. pygerythrus, C. a. sabaeus, and C. a tantalus. Assuming a mutation rate of 5.9 × 10-9 per base pair per generation and a generation time of 8.5 years, divergence time estimates range from 523 to 621 kya for the basal split of C. a. aethiops from the other four populations. Importantly, the resulting tree characterizing the relationship and split-times between these populations differs significantly from that presented in the original genome paper, owing to their neglect of within-population variation when calculating between population-divergence. In addition, I find that the demographic history of all five populations is well explained by a model of population fragmentation and isolation, rather than novel colonization events. Finally, utilizing these demographic models as a null, I investigate the selective history of the populations, identifying candidate regions potentially related to adaptation in response to pathogen exposure.
由于缺乏来自野生种群的采样多态性数据，人们对非洲绿猴（属 Chlorocebus）的进化历史知之甚少。然而，这种遗传多样性的特征不仅对于更好地了解它们自身的历史至关重要，而且对于人类生物医学研究也至关重要，因为它们是最广泛使用的灵长类动物模型之一。在这里，我利用迄今为止最全面的野生遗传多样性目录之一，对非洲绿猴的人口统计学和选择历史进行了分析，该目录由 25 个个体的 1795643 个常染色体单核苷酸多态性组成，代表了所有五个主要种群：C. a. aethiops、C. a. cynosurus、C. a. pygerythrus、C. a. sabaeus 和 C. a. tantalus。假设突变率为每个碱基对每个世代 5.9×10-9，世代时间为 8.5 年，从 C. a. aethiops 与其他四个种群的基础分裂开始，分歧时间估计范围为 523 到 621 kya。重要的是，由于在计算种群间分歧时忽略了种群内的变异，因此由此产生的描述这些种群之间关系和分裂时间的树与原始基因组论文中呈现的树有很大的不同。此外，我发现所有五个种群的人口历史都可以很好地用种群碎片化和隔离的模型来解释，而不是新的殖民化事件。最后，我利用这些人口统计学模型作为一个零假设，研究了种群的选择历史，确定了可能与应对病原体暴露的适应相关的候选区域。
