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.

古生物系统学高度依赖历经腐烂与化石化作用的形态学数据。本研究采用启发式方法，评估化石的不完备性如何削弱其系统发育关系的推断精度。我们构建了灵长类的系统发育矩阵，并通过删除现存分类群的分子数据、仅保留实际化石中存在的形态学性状，模拟现存物种的灭绝过程。特定现存分类群（即研究对象）的保留性状选择，由特定化石（即参照模板）所具备的性状定义。我们通过衡量经过充分佐证的系统发育树与纳入人工模拟化石的系统发育树之间的拓扑一致性，并对比真实性状与随机性状的分布模式及性状状态，检验了古生物学数据集的信息含量，同时探究现存物种的灭绝是否会导致系统发育重建出现偏差。研究发现，化石完备性与拓扑一致性呈显著正相关。在360个可获取的形态学性状（包括齿列性状）中，选取36个及以上性状构建的真实化石参照模板，其表现显著优于性状状态随机选取的同等完备性参照模板。仅单一性状分区主导的参照模板，其表现差于跨多性状分区随机选取性状的参照模板。基于始新世灵长类达尔文猴（Darwinius masillae）的参照模板，在选取性状数量相近的前提下，其表现优于绝大多数其他参照模板，这可能得益于其多性状分区的数据保存完整性。本研究结果支持‘达尔文猴为原猴亚目（strepsirhine）而非简鼻亚目（haplorhine）’的分类解读，同时表明古生物学数据集在灵长类系统发育重建中具备可靠性。