Phylogenetic Analysis Using Levy Processes: Finding Jumps in the Evolution of Continuous Traits
Phylogenetic Analysis Using Levy Processes: Finding Jumps in the Evolution of Continuous Traits
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DOI：
10.1093/sysbio/sys086
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发表时间：
2013-03-01
影响因子：
6.5
通讯作者：
Liang, Mason
中科院分区：
文献类型：
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作者：
Landis, Michael J.;Schraiber, Joshua G.;Liang, Mason
高斯过程是一类随机过程，包括布朗运动和奥恩斯坦-乌伦贝克过程，广泛用于模拟统计系统发育中的连续性状进化。在这样的过程中，系统发育树顶端的观察结果具有多元高斯分布，这可能会导致在某些进化条件下的次优模型规范，如间断平衡或适应性辐射模型中所假设的那样。为了考虑非正态分布的连续性状演化，我们引入了一种在将连续性状演化建模为 Levy 过程时计算后验概率的方法。通过数据模拟和模型测试，我们确定单速率布朗运动（BM）和带有跳跃的 Levy 过程在比较数据中产生不同的模式。然后我们分析了 126 只灵长类动物的体重和颅内体积测量结果。我们拒绝单率 BM，转而支持每个性状都有跳跃的 Levy 过程，导致类人猿最近共同祖先的谱系显示出反对单率 BM 的特别有力的证据。
Gaussian processes, a class of stochastic processes including Brownian motion and the Ornstein-Uhlenbeck process, are widely used to model continuous trait evolution in statistical phylogenetics. Under such processes, observations at the tips of a phylogenetic tree have a multivariate Gaussian distribution, which may lead to suboptimal model specification under certain evolutionary conditions, as supposed in models of punctuated equilibrium or adaptive radiation. To consider non-normally distributed continuous trait evolution, we introduce a method to compute posterior probabilities when modeling continuous trait evolution as a Levy process. Through data simulation and model testing, we establish that single-rate Brownian motion (BM) and Levy processes with jumps generate distinct patterns in comparative data. We then analyzed body mass and endocranial volume measurements for 126 primates. We rejected single-rate BM in favor of a Levy process with jumps for each trait, with the lineage leading to most recent common ancestor of great apes showing particularly strong evidence against single-rate BM.