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，而利用化石记录中分类单元（taxa）的首次出现与末次出现事件推断此类速率的研究，已有悠久历史。解析多样性动态的核心，在于对所有支系（lineages）的未观测物种形成与灭绝时间生成无偏估计，但受限于现有数据的复杂特性，对这些参数的推断颇具挑战。本研究提出一种全新的概率框架，可基于化石记录联合估算物种专属的物种形成与灭绝时间，以及内在生灭过程（birth-death process）的速率。该框架允许速率随时间独立变化，并在模型中显式纳入保存与采样概率，以估算每个支系的真实存续时长。我们实现了一套贝叶斯算法，通过探索不同的多样化（diversification）模型来评估速率转移的存在性。对一系列模拟数据集的测试表明，即便模型的基本假设被违背，或是数据存在不同程度的缺失，本方法仍具备出色的准确性与鲁棒性（robustness）。最后，我们以犀科（Rhinocerotidae）哺乳动物的多样化过程为例，展示了本方法的应用，并揭示了该类群的一段复杂演化历史：物种形成与灭绝速率先后发生多次独立的时间性转移，最终导致该类群先扩张后衰退。本研究所采用的生灭过程的估计参数，可直接与基于定年分子系统发育（phylogeny）得到的参数进行对比。因此，本模型为整合系统发育与化石信息以推断宏观演化（macroevolutionary）过程迈出了重要一步。