Data from: A parametric method for assessing diversification rate variation in phylogenetic trees

Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a tree using a variety of standard statistical distributions. PRC can identify subclades of the tree where diversification-rates are at variance with the remainder of the tree. A randomization test can be used to evaluate how often such variance would appear by chance alone. The method also allows for comparison of diversification-rate among a priori defined groups. Further, the application of the PRC method is not restricted to monophyletic groups. We examined the performance of PRC using simulated data which showed that PRC has acceptable false positive rates and statistical power to detect rate variation. We apply the PRC method to the well-studied radiation of North American Plethodon salamanders, and support the inference that the large-bodied P. glutinosus clade has a higher historical rate of diversification compared to other Plethodon salamanders.

系统发育假说（phylogenetic hypotheses）常被用于探究某类群演化历史中的多样化速率变化模式。多样化速率变异的分布特征可用于推断驱动支系形成模式的潜在生态与演化过程。现有多数方法均通过时间维度考察速率变异，而用于比较类群间多样化速率差异的方法则相对有限。本文提出一种全新方法——参数化速率比较法（parametric rate comparison, PRC），该方法采用多种标准统计分布，对系统发育树内各支系的多样化速率进行直接比对；PRC能够识别出系统发育树中多样化速率与其余支系存在显著偏离的亚支，借助随机化检验可评估此类偏离仅由随机因素产生的概率；该方法还支持对先验定义的类群间多样化速率进行比较，且其应用范围并不局限于单系类群（monophyletic groups）。本研究通过模拟数据对PRC的性能进行了测试，结果显示PRC的假阳性率处于可接受区间，且具备检测速率变异的统计效力。我们将PRC方法应用于研究较为充分的北美无肺螈属（Plethodon）辐射演化案例，验证支持了此前的推断：体型较大的黏滑无肺螈（P. glutinosus）亚支的历史多样化速率高于其他无肺螈属类群。