Mello Beatriz, Schrago Carlos G
Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
Evol Bioinform Online. 2019 Jun 13;15:1176934319855988. doi: 10.1177/1176934319855988. eCollection 2019.
The recent surge of genomic data has prompted the investigation of substitution rate variation across the genome, as well as among lineages. Evolutionary trees inferred from distinct genomic regions may display branch lengths that differ between loci by simple proportionality constants, indicating that rate variation follows a pacemaker model, which may be attributed to lineage effects. Analyses of genes from diverse biological clades produced contrasting results, supporting either this model or alternative scenarios where multiple pacemakers exist. So far, an evaluation of the pacemaker hypothesis for all great apes has never been carried out. In this work, we tested whether the evolutionary rates of hominids conform to pacemakers, which were inferred accounting for gene tree/species tree discordance. For higher precision, substitution rates in branches were estimated with a calibration-free approach, the relative rate framework. A predominant evolutionary trend in great apes was evidenced by the recovery of a large pacemaker, encompassing most hominid genomic regions. In addition, the majority of genes followed a pace of evolution that was closely related to the strict molecular clock. However, slight rate decreases were recovered in the internal branches leading to humans, corroborating the hominoid slowdown hypothesis. Our findings suggest that in great apes, life history traits were the major drivers of substitution rate variation across the genome.
近期基因组数据的激增促使人们对全基因组以及不同谱系间的替换率变化进行研究。从不同基因组区域推断出的进化树可能显示，不同基因座之间的分支长度仅通过简单的比例常数就存在差异，这表明速率变化遵循一种起搏器模型，这种差异可能归因于谱系效应。对来自不同生物类群的基因进行分析得出了相互矛盾的结果，这些结果要么支持该模型，要么支持存在多个起搏器的其他情况。到目前为止，从未对所有大型猿类的起搏器假说进行过评估。在这项研究中，我们测试了原始人类的进化速率是否符合起搏器模型，该模型是在考虑基因树/物种树不一致的情况下推断出来的。为了获得更高的精度，我们采用了一种无需校准的方法——相对速率框架来估计分支中的替换率。通过恢复一个涵盖大多数原始人类基因组区域的大型起搏器，证明了大型猿类中存在一种主要的进化趋势。此外，大多数基因遵循与严格分子钟密切相关的进化速率。然而，在通向人类的内部分支中发现了轻微的速率下降，这证实了类人猿减速假说。我们的研究结果表明，在大型猿类中，生活史特征是全基因组替换率变化的主要驱动因素。
