Death is on our side: paleontological data drastically modify phylogenetic hypotheses

Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred using only data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes (such as ancestral states, paleobiogeography and diversification dynamics), the role fossils play in reconstructing phylogeny is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Based on taxon addition experiments on empirical data matrices, we show that the inclusion of paleontological data has a remarkable effect in phylogenetic inference. Fossils often have higher levels of topological influence than extant taxa, while inducing unique topological rearrangements. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any phylogenetic analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses.

化石是地球上曾经存在过的绝大多数物种的唯一遗留证据，为窥探塑造地球生命多样化进程的进化历史事件提供了直接窗口。系统发育（phylogeny）是我们理解进化过程的核心支撑，但常规上仅利用现存生物的可用数据进行推断。尽管已有研究表明，灭绝类群（extinct taxa）可为宏观进化（macroevolution）模式与过程（如祖先性状状态、古生物地理学（paleobiogeography）及多样化动态（diversification dynamics））的推断提供关键信息，但化石在系统发育重建中所扮演的角色仍存在争议。自分支系统学（phylogenetic systematics）萌芽早期以来，不同研究对化石的作用持有迥异观点：部分研究因化石记录的不完整性而否定其影响，部分研究则推崇化石能够颠覆系统发育假说的能力，还有研究认为化石的系统发育行为与现存类群并无二致。本研究基于经验数据矩阵开展类群添加实验（taxon addition experiments），结果显示纳入古生物数据（paleontological data）可对系统发育推断（phylogenetic inference）产生显著影响。相较于现存类群，化石通常对系统发育拓扑结构具有更强的影响力，同时能够引发独特的拓扑重排现象。此前已有多项研究针对化石的拓扑行为提出了一系列解释，例如化石保留了独特的形态特征，或是能够打破系统发育中的长枝效应。本研究构建了预测模型，结果表明：类群拥有独特的性状状态组合是其引发拓扑变化程度的首要预测因子；且在开展任何系统发育分析之前，即可在一定程度上预测各类群（包括化石类群与现存类群）的相对影响力。本研究结果证实了古生物数据在系统发育推断中的独特作用，强化了近期实证研究的共识；同时首次对其影响的决定因素开展了定量评估，这对于形态学分析与总证据分析（total-evidence analyses）的类群采样设计均具有广泛的指导意义。