Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13457-62. doi: 10.1073/pnas.1310914110. Epub 2013 Jul 24.
We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r(2) = 0.65) in contrast to Alu repeats, which show little correlation (r(2) = 0.07). We estimate that the "rate" of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation--the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time.
我们分析了 83 个完全测序的大型猿类基因组中的移动元件插入，预测了总共 49452 个固定和多态的 Alu 和长散布元件 1（L1）插入，这些插入在人类参考组装中不存在，并将每个逆转录转座事件分配到大型猿类进化过程中的不同时间点。我们使用这些无同源性标记构建了人类和大型猿类的基于移动元件插入的系统发育，并证明它们在区分猿亚种和种群方面具有不同的能力。在这种情况下，我们发现 L1 多样性与单核苷酸多态性杂合度之间存在良好的相关性（r(2) = 0.65），与 Alu 重复序列形成对比，后者相关性很小（r(2) = 0.07）。我们估计，在这些谱系中，Alu 逆转座的“速率”差异了 15 倍。人类、黑猩猩和倭黑猩猩显示出最高的 Alu 积累率--后两者自 150 万年前分化以来一直如此。相比之下，L1 插入率保持相对稳定，差异不到三倍。我们得出结论，Alu 逆转座是最近人类-大型猿类进化过程中最具可变性的遗传变异形式，在非常短的进化时间内出现增加和减少。
