The Limits of the Constant-rate Birth–Death Prior for Phylogenetic Tree Topology Inference

作者：Mark P. Khurana, Neil Scheidwasser, Matthew J. Penn, Samir Bhatt, David A. Duchêne · 发表于：Systematic Biology · 年份：2023 · DOI：10.1093/sysbio/syad075 · 被引用次数：6 · 研究领域：Genomics and Phylogenetic Studies、Evolution and Paleontology Studies、Evolution and Genetic Dynamics

Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example, with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which the crBD model differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD model trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used Bayesian methods and crBD priors with those that used other non-crBD priors and non-Bayesian methods (i.e., maximum likelihood methods), we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolut...