Phylogenetic signal and bias in paleontology

An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.

Methods
These files include both supplementary "data" and "materials" referred to Asher & Smith, Systematic Biology, "Phylogenetic Signal & Bias in Paleontology":

https://doi.org/10.1093/sysbio/syab072

如今，前所未有的海量研究证据已阐明了现存哺乳类与鸟类在生命之树（Tree of Life）上的系统发育（phylogeny）关系。本研究依托该生命之树，对五项已发表研究衍生出的六组数据集所包含的古生物学常用数据（骨骼与牙齿）的系统发育价值进行量化评估。我们提出三个相互关联的问题：1）此类数据能否充分还原生命之树中已明确的分支结构？2）基于形态学数据的研究其准确率是否普遍相近，抑或部分形态学数据集的表现优于其他数据集？3）无法形成化石的数据缺失是否会导致分类群（taxa）被错误置于误导性的基部分支位置？

将形态学数据并入DNA数据集通常可提升所得拓扑结构与经充分验证的生命之树的一致性，但该效果因形态学数据集而异。与化石联合分析时，缺失大量形态学特征的现生分类群会显著降低系统发育分辨率。通过移除缺失形态学数据的现生分类群以改善该问题的尝试，往往会因长枝伪迹（long-branch artefacts）导致准确率下降。本研究未发现任何证据表明，化石形成过程会导致灭绝类群被错误置于拓扑学上的基部分支或其附近位置。形态学数据是现生类群与化石共有的证据来源，无论采用何种系统发育估计方法，对化石开展系统发育分析时，纳入现生类群的分子与形态学采样数据均可极大提升分析效果。

方法
本数据集包含Asher与Smith发表于《Systematic Biology》的论文《Phylogenetic Signal & Bias in Paleontology》中提及的补充“数据”与“材料”：

https://doi.org/10.1093/sysbio/syab072