Puttick Mark N
School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
Biol Lett. 2016 Aug;12(8). doi: 10.1098/rsbl.2016.0392.
Ancestral state reconstruction of discrete character traits is often vital when attempting to understand the origins and homology of traits in living species. The addition of fossils has been shown to alter our understanding of trait evolution in extant taxa, but researchers may avoid using fossils alongside extant species if only few are known, or if the designation of the trait of interest is uncertain. Here, I investigate the impacts of fossils and incorrectly coded fossils in the ancestral state reconstruction of discrete morphological characters under a likelihood model. Under simulated phylogenies and data, likelihood-based models are generally accurate when estimating ancestral node values. Analyses with combined fossil and extant data always outperform analyses with extant species alone, even when around one quarter of the fossil information is incorrect. These results are especially pronounced when model assumptions are violated, such as when there is a trend away from the root value. Fossil data are of particular importance when attempting to estimate the root node character state. Attempts should be made to include fossils in analysis of discrete traits under likelihood, even if there is uncertainty in the fossil trait data.
在试图理解现存物种性状的起源和同源性时，离散性状特征的祖先状态重建往往至关重要。已表明添加化石会改变我们对现存分类单元中性状进化的理解，但如果已知的化石很少，或者感兴趣性状的指定不确定，研究人员可能会避免将化石与现存物种一起使用。在这里，我在似然模型下研究化石和编码错误的化石在离散形态特征祖先状态重建中的影响。在模拟系统发育和数据下，基于似然的模型在估计祖先节点值时通常是准确的。即使大约四分之一的化石信息不正确，结合化石和现存数据的分析总是优于仅使用现存物种的分析。当模型假设被违反时，例如当存在远离根值的趋势时，这些结果尤其明显。在试图估计根节点性状状态时，化石数据尤为重要。即使化石性状数据存在不确定性，也应尝试在似然分析中纳入化石来分析离散性状。
