Online Appendix and Cetacean Datasets for: The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology

Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, i.e. lacking morphological and molecular data, which we call occurrences, provide invaluable information to reconstruct the past number of lineages. Here, we present new methodological developments around the Fossilized Birth-Death Process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) cons...系统发育动力学模型（Phylodynamic models）通常旨在基于分子序列数据，联合推断系统发育关系、模型参数，以及近年来新增的随时间推移的支系数量。在流行病学和宏进化（macroevolution）研究领域中，这类模型可分别用于估算随时间推移的既往感染人数（流行率，prevalence）或既往物种类群数量（古多样性，paleodiversity）。近年来涌现出"全证据"（total-evidence）分析方法，该方法在统一的贝叶斯推断框架下，整合现生与历史采样个体的分子与形态学数据。即便是仅以采样时间为特征、缺乏形态学与分子数据的采样个体——我们将其称为出现记录（occurrences）——也能为重建随时间推移的既往支系数量提供极具价值的信息。 本研究围绕化石出生死亡过程（Fossilized Birth-Death Process）提出了新的方法学进展，可实现（i）将出现记录数据纳入似然函数；（ii）cons...