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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, that is, lacking morphological and molecular data, which we call occurrences, provide invaluable information to estimate 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) consider piecewise-constant birth, death, and sampling rates; and (iii) estimate the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions. We finally illustrate our new implementation using two empirical data sets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the coronavirus disease 2019 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics. [Birth–death model; epidemiology; fossils; macroevolution; occurrences; phylogenetics; skyline.]

The systematic value of the middle-ear ossicles, in particular the malleus, has been long recognized for diverse groups. We present systematic work on the characters of the middle-ear ossicles of pinnipeds, focusing on until now poorly studied Southern Hemisphere species. Mallei were extracted from 16 specimens of pinnipeds belonging to five austral and one boreal species of Phocidae and two austral species of Otariidae. Several characters used in this study have been described previously, and some were here modified. Three new characters are here defined and analysed. All characters were mapped onto the phylogeny. Our character analysis shows the transformations that have occurred in the evolution of middle ear ossicles in pinnipeds and identifies diagnostic features of many of its clades. Beyond the identification of specific changes within eachclade, our study of pinniped ossicle evolution documents the occurrence of anatomical convergences with other groups of mammals that live in an aquatic environment, as has occurred in other organ systems as well., Contributions to Zoology, 87 (2)