Data from: A new method for testing evolutionary rate variation and shifts in phenotypic evolution

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.1. 量化表型进化速率及其在系统发育树（phylogenetic trees）上的变异模式，是进化生物学领域的核心议题之一。当前已有诸多系统发育比较方法（phylogenetic comparative methods, PCMs）可实现此类任务。然而，现有PCMs仅能定位系统发育整体分支区段的进化速率转移事件，却无法识别预期出现在单个物种及支系水平的速率变化——例如岛屿脊椎动物的体型进化速率普遍更快这一假说。此外，尽管化石可为解析性状变异与进化过程提供极具价值的信息，但绝大多数PCMs均无法处理化石系统发育数据。 2. 本研究开发了一种基于系统发育岭回归（phylogenetic ridge regression）的PCM，命名为RRphylo，该方法可为系统发育的每一条分支分配进化速率，并可定位与整个演化支（clades）以及非关联树末端相关的进化速率转移事件。我们通过模拟系统发育树与模拟数据集对RRphylo进行了性能测试，以评估其在不同实验条件下的表现。随后，我们将该方法应用于两个真实案例场景：一是鸟颈类群（ornithodirans）与哺乳类的飞行能力进化，二是岛屿哺乳类的体型进化——这两类类群的进化速率范围通常分别不同于陆生及大陆物种。 3. RRphylo在各类实验条件下均表现优异。模拟实验结果显示，该方法的一类错误率（Type I error rate）与二类错误率（Type II error rate）均较低。本研究发现了强有力的证据，表明飞行能力的演化可加快脊椎动物的体型进化速率，而巨型体型的获得则会减缓该速率。不过，岛屿哺乳类的体型进化速率并未显著快于大陆哺乳类。 4. RRphylo是一种新型PCM，可用于估算基于化石数据的表型进化速率变异与速率转移事件。除了可用于检测进化速率变异外，该方法还可应用于诸多后续研究问题，例如进化速率的时间动态演化、祖先状态估算以及表型随时间的变化趋势分析。