Fast, accurate and simulation-free stochastic mapping
Fast, accurate and simulation-free stochastic mapping
复制标题
DOI：
10.1098/rstb.2008.0176
复制
发表时间：
2008-12-27
影响因子：
6.3
通讯作者：
Suchard, Marc A.
中科院分区：
文献类型：
--
作者：
Minin, Vladimir N.;Suchard, Marc A.
将离散性状的进化轨迹映射到系统发育树上在进化生物学中受到了相当多的关注。给定系统发育树末端的性状观测值，研究人员通常对性状在树上何处改变其状态以及某些变化在树的某些部分是否更具优势感兴趣。在基于模型的系统发育框架中，这些问题转化为对进化轨迹的概率特性进行表征。当前评估这些特性的方法依赖于计算成本高昂的模拟。在本文中，我们提出了一种高效的、无需模拟的算法，用于计算两个重要且普遍存在的进化轨迹特性。第一个是性状变化的平均数量，其中变化可分为感兴趣的类别（例如同义/非同义突变）。平均进化回报是第二个特性，它与性状处于每个状态的时间成比例地累积。为了说明我们结果的有用性，我们首先使用我们的无需模拟的随机映射来对两个进化性状之间的相关性进行后验预测检验。最后，我们将同义突变和非同义突变映射到HIV宿主内系统发育树的分支上，并比较末端分支和内部分支上的选择压力。
Mapping evolutionary trajectories of discrete traits onto phylogenies receives considerable attention in evolutionary biology. Given the trait observations at the tips of a phylogenetic tree, researchers are often interested where on the tree the trait changes its state and whether some changes are preferential in certain parts of the tree. In a model-based phylogenetic framework, such questions translate into characterizing probabilistic properties of evolutionary trajectories. Current methods of assessing these properties rely on computationally expensive simulations. In this paper, we present an efficient, simulation-free algorithm for computing two important and ubiquitous evolutionary trajectory properties. The first is the mean number of trait changes, where changes can be divided into classes of interest (e. g. synonymous/non-synonymous mutations). The mean evolutionary reward, accrued proportionally to the time a trait occupies each of its states, is the second property. To illustrate the usefulness of our results, we first employ our simulation-free stochastic mapping to execute a posterior predictive test of correlation between two evolutionary traits. We conclude by mapping synonymous and non-synonymous mutations onto branches of an HIV intrahost phylogenetic tree and comparing selection pressure on terminal and internal tree branches.