Data from: Phylogeny, palaeontology, and primates: do incomplete fossils bias the tree of life?

Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here, we apply a heuristic means to assess how a fossil's incompleteness detracts from inferring its phylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated the extinction of living species by deleting an extant taxon's molecular data and keeping only those morphological characters present in actual fossils. The choice of characters present in a given living taxon (the subject) was defined by those present in a given fossil (the template). By measuring congruence between a well-corroborated phylogeny to those incorporating artificial fossils, and by comparing real vs. random character distributions and states, we tested the information content of paleontological datasets and determined if extinction of a living species leads to bias in phylogeny reconstruction. We found a positive correlation between fossil completeness and topological congruence. Real fossil templates sampled for 36 or more of the 360 available morphological characters (including dental) performed significantly better than similarly complete templates with random states. Templates dominated by only one partition performed worse than templates with randomly sampled characters across partitions. The template based on the Eocene primate Darwinius masillae performs better than most other templates with a similar number of sampled characters, likely due to preservation of data across multiple partitions. Our results support the interpretation that Darwinius is strepsirhine, not haplorhine, and suggest that paleontological datasets are reliable in primate phylogeny reconstruction.

古生物系统学（Paleontological systematics）高度依赖经历过腐烂与化石化作用的形态学数据。本研究采用启发式方法，评估化石完整性缺失对其系统发育关系推断准确性的削弱程度。我们构建了灵长类的系统发育矩阵（phylogenetic matrix），通过删除现存类群（extant taxon）的分子数据（molecular data）、仅保留实际化石中存在的形态学特征（morphological characters），模拟现存物种的灭绝场景。给定现存类群（目标类群）的特征选取规则，由对应化石（模板）所具备的特征所界定。通过比对经过充分验证的系统发育树与纳入人工化石（artificial fossils）的系统发育树的拓扑一致性（topological congruence），并对比真实特征分布与随机特征分布及特征状态，我们评估了古生物学数据集的信息含量（information content），并检验了现存物种灭绝是否会导致系统发育重建（phylogeny reconstruction）出现偏差。研究结果显示，化石完整性与拓扑一致性之间存在显著正相关关系。针对360个可用形态学特征（含牙齿特征）中36个及以上特征进行采样的真实化石模板，其表现显著优于特征状态随机的同完整性模板。仅依赖单一特征分区（partition）的模板，性能劣于跨分区随机采样特征的模板。基于始新世灵长类达尔文猴（Darwinius masillae）的模板，在采样特征数量相近的各类模板中表现优于多数同类模板，这或得益于其多解剖分区的数据保存完整性。本研究结果支持“达尔文猴属于原猴类（strepsirhine），而非简鼻类（haplorhine）”的解读，并表明古生物学数据集在灵长类系统发育重建中具备可靠的应用价值。