The Fossilized Birth Death Process with heterogeneous diversification rates unravels the link between diversification and specialisation to a carnivorous diet in Nimravidae (Carnivoraformes)

Abstract

Bayesian phylogenetic inference uses more and more complex diversification models as tree priors to test new macroevolutionary hypotheses. However, those models are usually developed in a neontological framework, despite the increasing number of datasets covering both extant and fossil taxa, as well as the fact that many clades are entirely extinct. In this paper, we develop the F-ClaDS model, a Fossilized-Birth-Death (FBD) version of the cladogenetic diversification rate shift (ClaDS) model, in BEAST2. ClaDS estimates partially inherited branch-specific rates from a phylogeny, providing a nuanced and detailed perspective of the variations in diversification across the tree. Our extension allows the integration of fossil samples directly into the phylogeny. We apply our new implementation to a dataset of 36 Nimravidae, a fully extinct carnivoraform clade that spanned from the Early Eocene to the Late Miocene, which species had different degrees of specialisation to a carnivorous diet. We show that using different tree priors does not affect substantially the topology of the inferred trees, but affects the ages of nodes and tips, as well as branch-lengths. F-ClaDS also recovers more species as sampled ancestors than the homogeneous FBD model. The branches with the highest speciation and extinction rates are those corresponding to the hypercarnivorous clades (Hoplophoneus and the barbourofelins), supporting the view that specialization to a hypercarnivorous diet can spur speciation, but also increase extinction risk, especially during times of global ecosystem change, potentially due to a high position in the trophic chain.