Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits
Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits
复制标题
自动识别连续和离散特征宏观进化速率异质性的快速似然计算
DOI：
10.1093/sysbio/syac035
复制
发表时间：
2022
影响因子：
6.5
通讯作者：
Uyeda, ed., Josef
中科院分区：
文献类型：
--
作者：
Grundler, Michael C.;Rabosky, Daniel L.;Zapata, Felipe;Uyeda, ed., Josef
了解整个生命树的表型差异需要确定进化速率在系统发育上何时何地发生变化。因此，宏观进化的主要方法论挑战是开发准确推断表型进化速率的谱系间变异的方法。在这里，我们描述了一种推断连续性状和离散性状的谱系间进化率异质性的方法。该方法假设特征的当前分布是由恒定速率过程混合产生的可变速率过程形成的，并使用单遍树遍历算法来估计分支特定的进化速率。通过在适当的情况下采用动态规划优化技术和近似最大似然估计器，我们的方法可以快速探索表型进化的速度和模式。模拟表明该方法可以高精度地重建性状进化速率。该方法应用于有鳞爬行动物繁殖和龟体尺寸的数据集，恢复了先前研究确定的速率异质性模式，但计算成本降低了多个数量级。我们的结果扩展了可用于检测宏观进化速率异质性的工具集，并指出了快速、近似方法在研究大规模生物多样性动态方面的实用性。 [布朗运动；连续字符；离散字符；宏观进化；马尔可夫过程；率异质性。]
Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to data sets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large-scale biodiversity dynamics. [Brownian motion; continuous characters; discrete characters; macroevolution; Markov process; rate heterogeneity.]