Ancestral state reconstruction, rate heterogeneity, and the evolution of reptile viviparity

Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. Although methods for identifying evolutionary rate shifts in continuous characters have attracted recent attention (e.g. Eastman et al., 2011, Stack et al., 2011), such methods for discrete characters have only very recently been developed (Beaulieu et al., 2013, Beaulieu and O’Meara 2014) and have yet to be widely used. However, ancestral state reconstructions of discrete characters are being performed on increasingly large phylogenies, where it is likely that evolutionary rates will vary greatly between different clades (Beaulieu and O’Meara 2014). Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. Th...

几乎所有用于离散性状（discrete characters）祖先状态重建（ancestral state reconstruction）的模型，均存在一项核心假设：即目标性状在整棵系统发育树（phylogenetic tree）的所有分支上均以统一速率进化。尽管针对连续性状（continuous characters）的进化速率偏移（evolutionary rate shifts）识别方法近年来已受到广泛关注（如Eastman等人，2011；Stack等人，2011），但面向离散性状的同类方法直至近年才得以提出（Beaulieu等人，2013；Beaulieu与O’Meara，2014），且尚未得到广泛应用。然而，当前离散性状的祖先状态重建工作正逐步应用于规模日益扩大的系统发育树数据集，而不同进化枝（clade）间的进化速率很可能存在显著差异（Beaulieu与O’Meara，2014）。本研究阐明了若未考虑此类进化速率异质性（evolutionary rate variability），将会导致结果出现严重异常（且大概率错误）；而三种能够适配速率变异的方法，则可得到与之相反、更具合理性且更为稳健的重建结果。Th...