A new method for testing evolutionary rate variation and shifts in phenotypic evolution
A new method for testing evolutionary rate variation and shifts in phenotypic evolution
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DOI：
10.1111/2041-210x.12954
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发表时间：
2018-04-01
影响因子：
6.6
通讯作者：
Raia, Pasquale
中科院分区：
文献类型：
--
作者：
Castiglione, Silvia;Tesone, Gianmarco;Raia, Pasquale
1.量化表型进化率及其在系统发育树中的变异是进化生物学中的一个主要问题。一些系统发育比较方法（PCM）目前执行这样的任务。然而，现有的PCM可以定位与整个部分的进化有关的速率变化，但不是那些预计会发生在个别物种和谱系的水平，如与岛屿脊椎动物的身体大小变化更快的想法。尽管如此，大多数PCM不能处理化石遗传，尽管化石在理解性状变异和进化方面提供了非常有用的信息。我们开发了一个PCM的基础上系统发育脊回归，我们命名为RRphylo，它分配一个进化速率的每一个分支的进化史，并旨在定位有关整个分支的速率变化，以及不相关的树尖。我们在模拟树木和数据上测试RRphylo，以评估其在不同条件下的性能。然后，我们重复了它的应用与两个真实的案例情景，鸟类和哺乳动物的飞行进化和岛屿哺乳动物的身体大小进化，这通常被归类为不同的范围制度下进化比陆地和大陆物种分别。RRphylo在所有不同条件下都表现良好。仿真实验表明，该算法具有较低的I类和II类错误率。我们发现了重要的证据，证明飞行加速了脊椎动物体型进化的速度，而获得非常大的体型会减缓这一速度。尽管如此，岛屿哺乳动物的体型进化并不比大陆物种快。RRphylo是一个新的PCM理想估计的变化和变化的速度表型进化与化石数据。除了测试进化速率的变化，它是开放的各种进一步的问题，如速率随时间的演变，估计祖先的状态和随着时间的推移表型趋势的估计。
1. Quantifying phenotypic evolutionary rates and their variation across phylogenetic trees is a major issue in evolutionary biology. A number of phylogenetic comparative methods (PCMs) currently perform such task. However, available PCMs can locate rate shifts pertaining to entire portions of the phylogeny, but not those expected to occur at the level of individual species and lineages, such as with the idea that body size changes more rapidly in insular vertebrates. Still, most PCMs cannot deal with fossil phylogenies, albeit fossils provide highly desirable information when it comes to understand trait variation and evolution.2. We developed a PCM based on phylogenetic ridge regression, which we named RRphylo, which assigns an evolutionary rate to each branch of the phylogeny, and is designed to locate rate shifts relating to entire clades, as well as to unrelated tree tips. We tested RRphylo on simulated trees and data to assess its performance under different conditions. Then, we repeated its application with two real case scenarios, the evolution of flight in ornithodirans and mammals and body size evolution in insular mammals, which are usually subsumed to evolve under different range regimes than terrestrial and continental species respectively.3. RRphylo performs well across all different conditions. The simulation experiments demonstrated it has low Type I and Type II error rate. We found significant evidence that flight accelerates the rate of body size evolution in vertebrates, and that the acquisition of very large body size slows down the rate. Still, insular mammals body size evolution is not faster than in continental species.4. RRphylo is a new PCM ideal to estimate variation and shift in the rate of phenotypic evolution with fossil data. In addition to testing evolutionary rate variation, it is open to a variety of further questions, such as the evolution of rates in time, the estimation of ancestral states and the estimation of phenotypic trends over time.