Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.
Evolution. 2013 Jun;67(6):1823-30. doi: 10.1111/evo.12047. Epub 2013 Feb 4.
Stochastic population processes may cause differences between species histories and gene histories. These processes are assumed to only influence the most recent divergences in the tree of life; however, there may be underappreciated potential for microevolutionary processes to impact deep divergences. I used multispecies coalescent models to determine the impact of stochastic processes on deep phylogenomic histories. Here I show phylogenomic discordance between gene histories and species histories is expected at deep divergences for many eukaryotic taxa, and the probability of discordance increases with population size, generation time, and the number of species in the tree. Five eukaryotic clades (angiosperms, birds, harpaline beetles, mammals, and nymphalid butterflies) demonstrate significant discordance potential at divergences over 50 million years old, and this discordance potential is independent of the age of divergence. These findings demonstrate population processes acting over very short timescales will leave a lasting impact on genomic histories, even for divergence events occurring tens to hundreds of millions of years ago.
随机种群过程可能导致物种历史和基因历史之间存在差异。这些过程被认为仅影响生命之树中最近的分歧；然而，微观进化过程可能对深度分歧产生尚未被充分认识的潜在影响。我使用多物种合并模型来确定随机过程对深度系统发育历史的影响。在这里，我表明对于许多真核生物类群，在深度分歧中，基因历史和物种历史之间存在系统发育分歧是预期的，分歧的概率随着种群大小、世代时间和树上物种的数量而增加。五个真核类群（被子植物、鸟类、哈巴龙甲虫、哺乳动物和蛱蝶科蝴蝶）在超过 5000 万年的分歧中表现出显著的分歧潜力，而且这种分歧潜力与分歧的年龄无关。这些发现表明，即使对于发生在数千万到数亿年前的分歧事件，作用于非常短时间尺度的种群过程也将对基因组历史产生持久的影响。
