Luisi Pierre, Alvarez-Ponce David, Pybus Marc, Fares Mario A, Bertranpetit Jaume, Laayouni Hafid
Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
Integrative Systems Biology Group, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), Spain Biology Department, University of Nevada, Reno Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
Genome Biol Evol. 2015 Apr 2;7(4):1141-54. doi: 10.1093/gbe/evv055.
Genes vary in their likelihood to undergo adaptive evolution. The genomic factors that determine adaptability, however, remain poorly understood. Genes function in the context of molecular networks, with some occupying more important positions than others and thus being likely to be under stronger selective pressures. However, how positive selection distributes across the different parts of molecular networks is still not fully understood. Here, we inferred positive selection using comparative genomics and population genetics approaches through the comparison of 10 mammalian and 270 human genomes, respectively. In agreement with previous results, we found that genes with lower network centralities are more likely to evolve under positive selection (as inferred from divergence data). Surprisingly, polymorphism data yield results in the opposite direction than divergence data: Genes with higher centralities are more likely to have been targeted by recent positive selection during recent human evolution. Our results indicate that the relationship between centrality and the impact of adaptive evolution highly depends on the mode of positive selection and/or the evolutionary time-scale.
基因经历适应性进化的可能性各不相同。然而,决定适应性的基因组因素仍知之甚少。基因在分子网络的背景下起作用,一些基因占据着比其他基因更重要的位置,因此可能承受更强的选择压力。然而,正选择如何分布在分子网络的不同部分仍未完全了解。在这里,我们分别通过比较10个哺乳动物基因组和270个人类基因组,使用比较基因组学和群体遗传学方法推断正选择。与先前的结果一致,我们发现网络中心性较低的基因在正选择下更有可能进化(从分歧数据推断)。令人惊讶的是,多态性数据产生的结果与分歧数据相反:在近期人类进化过程中,中心性较高的基因更有可能受到近期正选择的靶向作用。我们的结果表明,中心性与适应性进化影响之间的关系高度依赖于正选择模式和/或进化时间尺度。