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中的变异模式，是进化生物学领域的核心研究议题之一。目前已有诸多系统发育比较方法（phylogenetic comparative methods, PCMs）可实现此类分析任务。然而，现有PCMs仅能定位针对系统发育整体分支的速率转变，却无法识别预期出现在单个物种与支系层面的速率变化——例如岛屿脊椎动物的体型进化速率更快这一经典假说。此外，尽管化石在解析性状变异与进化过程中极具科学价值，但多数PCMs无法处理包含化石类群的系统发育树。 2. 我们开发了一种基于系统发育岭回归的系统发育比较方法，将其命名为RRphylo，该方法可为系统发育的每一条分支分配独立的进化速率，既可定位针对整个演化支的速率转变，也可识别与独立树末端类群相关的速率变化。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研究案例：一是鸟颈类与哺乳类的飞行演化历程，二是岛屿哺乳类的体型进化模式——这两类类群通常被认为分别与陆生、大陆物种处于不同的进化速率调控范围中。 3. RRphylo在各类实验条件下均表现优异。模拟实验结果表明，其I型错误率与II型错误率均处于较低水平。我们通过分析得到了确凿的统计学证据，证明飞行会加速脊椎动物的体型进化速率，而类群体型变得极大会减缓该进化速率。此外，我们的研究结果显示，岛屿哺乳类的体型进化速率并未显著高于大陆物种。 4. RRphylo是一种新型系统发育比较方法，非常适合利用化石数据估算表型进化速率的变异与转变。除了可用于检测进化速率的变异模式外，该方法还可拓展应用于诸多后续研究问题，例如随时间推移的进化速率演化动态、祖先状态估算，以及随时间变化的表型趋势预测。