Data from: Bayesian estimation of speciation and extinction from incomplete fossil occurrence data

The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.

物种多样性的时间动态由物种形成（speciation）与灭绝（extinction）速率的变化所塑造，学界利用化石记录中类群的首现与末现数据推断此类速率的研究历史悠久。理解多样性动态，核心在于对所有谱系（lineage）未被观测到的物种形成与灭绝时间开展无偏估计，但由于可用数据的复杂特性，对这些参数的推断颇具挑战。本文提出一种全新的概率框架，可基于化石记录联合估算物种特异性的物种形成与灭绝时间，以及潜在生灭过程（birth-death process）的速率。该框架允许速率随时间独立变化，并将保存与采样概率显式纳入模型，以估算每个谱系的真实寿命。我们实现了一种贝叶斯算法（Bayesian algorithm），通过探索多样化模型的备选方案来评估速率转变的存在。在一系列模拟数据集上的测试表明，即便潜在假设被违背、数据存在不同程度的不完备性，我们的方法仍具备准确性与稳健性。最后，我们以犀科（Rhinocerotidae）哺乳动物的多样化历程为例展示了本方法的应用，揭示了该类群经历物种形成与灭绝速率反复且独立的时间转变的复杂历史，最终导致类群的扩张与随后的衰退。本文所实现的生灭过程估计参数，可直接与定年分子系统发育所得参数进行比较。因此，本模型为整合系统发育与化石信息以推断宏观演化过程（macroevolutionary processes）迈出了重要一步。