Abstract
High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies1–3. However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the deluge of new genomes4. In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties5,6 and, thus, the timescale of placental mammal evolution remains contentious7–10. Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Paleogene8 and show crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Paleocene/Eocene. Our new Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. As such, our approach can be used to tackle other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets.
