Estimating Correlated Rates of Trait Evolution with Uncertainty
Estimating Correlated Rates of Trait Evolution with Uncertainty
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DOI：
10.1093/sysbio/syy067
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发表时间：
2019-05-01
影响因子：
6.5
通讯作者：
Harmon, L. J.
中科院分区：
文献类型：
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作者：
Caetano, D. S.;Harmon, L. J.
性状间的相关进化是由于遗传约束、个体发育和选择而发生的，对表型进化的轨迹具有重要影响。例如，进化整合模式的转变可能允许谱系探索形态空间的新区域。在这里，我们使用系统发育树来研究几种特征的进化速度及其在进化分支和时间上的进化相关性模式。我们使用映射到系统发育分支的制度来测试进化整合的变化，同时结合与性状进化和祖先制度相关的不确定性，使用贝叶斯马尔可夫链蒙特卡罗对模型的所有参数进行联合估计。我们实现了使用汇总统计来测试基于一系列可以直接与生物学假设相关的模型属性的状态转移。此外，我们将Felsenstein的剪枝算法推广到具有多速率域的多变量布朗运动模型。我们进行了大量的模拟，以探索该方法在一系列场景下的性能。最后，我们提供了两个测试用例；中心科鱼类一种新的口腔形态的进化，以及变色蜥往返加勒比海岛屿期间特征进化轨迹的转变。
Correlated evolution among traits, which can happen due to genetic constraints, ontogeny, and selection, can have an important impact on the trajectory of phenotypic evolution. For example, shifts in the pattern of evolutionary integration may allow the exploration of novel regions of the morphospace by lineages. Here, we use phylogenetic trees to study the pace of evolution of several traits and their pattern of evolutionary correlation across clades and over time. We use regimes mapped to the branches of the phylogeny to test for shifts in evolutionary integration while incorporating the uncertainty related to trait evolution and ancestral regimes with joint estimation of all parameters of the model using Bayesian Markov chain Monte Carlo. We implemented the use of summary statistics to test for regime shifts based on a series of attributes of the model that can be directly relevant to biological hypotheses. In addition, we extend Felsenstein's pruning algorithm to the case of multivariate Brownian motion models with multiple rate regimes. We performed extensive simulations to explore the performance of the method under a series of scenarios. Finally, we provide two test cases; the evolution of a novel buccal morphology in fishes of the family Centrarchidae and a shift in the trajectory of evolution of traits during the radiation of anole lizards to and from the Caribbean islands.