一项针对灵长类动物进化中重要非编码元件的全基因组筛选。
A genome-wide screen for noncoding elements important in primate evolution.
作者信息
Bush Eliot C, Lahn Bruce T
机构信息
Department of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA.
出版信息
BMC Evol Biol. 2008 Jan 23;8:17. doi: 10.1186/1471-2148-8-17.
BACKGROUND
A major goal in the study of human evolution is to identify key genetic changes which occurred over the course of primate evolution. According to one school of thought, many such changes are likely to be found in noncoding sequence. An approach to identifying these involves comparing multiple genomes to identify conserved regions with an accelerated substitution rate in a particular lineage. Such acceleration could be the result of positive selection.
RESULTS
Here we develop a likelihood ratio test method to identify such regions. We apply it not only to the human terminal lineage, as has been done in previous studies, but also to a number of other branches in the primate tree. We present the top scoring elements, and compare our results with previous studies. We also present resequencing data from one particular element accelerated on the human lineage. These data indicate that the element lies in a region of low polymorphism in humans, consistent with the possibility of a recent selective sweep. They also show that the AT to GC bias for polymorphism in this region differs dramatically from that for substitutions.
CONCLUSION
Our results suggest that screens of this type will be helpful in unraveling the complex set of changes which occurred during primate evolution.
背景
人类进化研究的一个主要目标是确定在灵长类动物进化过程中发生的关键基因变化。根据一种观点，许多这样的变化可能存在于非编码序列中。识别这些变化的一种方法是比较多个基因组，以确定在特定谱系中具有加速替换率的保守区域。这种加速可能是正选择的结果。
结果
在这里，我们开发了一种似然比检验方法来识别这些区域。我们不仅像以前的研究那样将其应用于人类终端谱系，还将其应用于灵长类谱系树中的许多其他分支。我们展示了得分最高的元件，并将我们的结果与以前的研究进行了比较。我们还展示了来自人类谱系上加速的一个特定元件的重测序数据。这些数据表明，该元件位于人类低多态性区域，这与近期选择性清除的可能性一致。它们还表明，该区域多态性的AT到GC偏差与替换偏差有很大差异。
结论
我们的结果表明，这种类型的筛选将有助于揭示灵长类动物进化过程中发生的复杂变化集。
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