Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees
Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees
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DOI：
10.1093/molbev/msz049
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发表时间：
2019-05-01
影响因子：
10.7
通讯作者：
Liu, Jun S.
中科院分区：
文献类型：
--
作者：
Hu, Zhirui;Sackton, Timothy B.;Liu, Jun S.
DNA序列在进化过程中的保守性是功能的一个强有力的指标，序列保守性的获得或丧失可以用来推断整个进化过程中功能的变化。在一个基因组中特定谱系的进化速率的变化可以表明共享的功能转变，因此可以用来检测表型趋同的基因组相关性。然而，现有的方法不允许容易地检测速率变化的模式，这导致检测收敛速率变化或其他复杂的进化场景的挑战。在这里，我们介绍PhyloAcc，一种新的贝叶斯方法来模拟整个基因组中保守元素的取代率变化。该方法假设系统发生树上每个分支的替代率为几个类别，估计每个类别的替代率，并检测替代率的变化作为类别切换的后验概率。模拟结果表明，PhyloAcc可以检测多个目标物种的速率变化的基因组区域比以前的方法更好，并具有更高的精度重建复杂的模式的取代率变化比流行的贝叶斯松弛时钟模型。我们展示了PhyloAcc在两个经典的收敛表型的例子：鸟类的飞行损失和哺乳动物向海洋生物的过渡。在每一种情况下，我们的方法揭示了许多保守的非外显子元件的加速表型收敛谱系的例子。我们的方法是广泛适用于任何一组保守的元素，其中多个率的变化，预计在一个同源性。
Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved nonexonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.