School of Biological Sciences, University of Reading, Reading, UK.
Methods Mol Biol. 2022;2569:255-266. doi: 10.1007/978-1-0716-2691-7_12.
The fossil record is the best evidence of the characteristics of extinct species, but only a narrow range of traits fossilize or survive the fossilization process. Lacking fossil or other evidence about the past, ancestral states can be reconstructed. Three pieces of information are combined when reconstructing ancestral states: extant or known trait values (data); the evolutionary history, linking the species of interest (phylogeny); and the evolutionary model of trait change. These reconstructed ancestral states can be interpreted as our best guess as to the route evolution took, given the distribution of the trait across species, the relationships among them, and our model of evolution. Because the information we use to reconstruct the past is often not known without error, uncertainty about their true values should be accounted for when reconstructing ancestral states. In this chapter we describe how ancestral states can be reconstructed using a Bayesian framework implemented in the software BayesTraits to account for uncertainty in the phylogenetic tree and the model of evolution.
化石记录是已灭绝物种特征的最佳证据，但只有一小部分特征可以化石化或在化石化过程中幸存下来。由于缺乏过去的化石或其他证据，可以重建祖先状态。在重建祖先状态时，需要结合以下三种信息：现存或已知特征值（数据）；将感兴趣的物种联系起来的进化历史（系统发育）；以及特征变化的进化模型。这些重建的祖先状态可以被解释为我们根据特征在物种中的分布、它们之间的关系以及我们的进化模型，对进化所走的路线的最佳猜测。由于我们用于重建过去的信息通常不能无误地获知，因此在重建祖先状态时应该考虑到其真实值的不确定性。在本章中，我们将描述如何使用贝叶斯框架（在软件 BayesTraits 中实现）来重建祖先状态，以考虑到系统发育树和进化模型中的不确定性。
