Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

Abstract

The fossil record suggests a rapid radiation of placental mammals following the Cretaceous - Paleogene (K - Pg) mass extinction 65 million years ago (Ma); nevertheless, molecular time estimates, while highly variable, are generally much older. Early molecular studies suffer from inadequate dating methods, reliance on the molecular clock, and simplistic and over-confident interpretations of the fossil record. More recent studies have used Bayesian dating methods that circumvent those issues, but the use of lim- ited data has led to large estimation uncertainties, precluding a decisive conclusion on the timing of mammalian diversifications. Here we use a powerful Bayesian method to analyse 36 nuclear genomes and 274 mitochondrial genomes (20.6 million base pairs), combined with robust but flexible fossil cali- brations. Our posterior time estimates suggest that marsupials diverged from eutherians 168 - 178 Ma, and crown Marsupialia diverged 64 - 84 Ma. Placentalia diverged 88 - 90 Ma, and present-day placental orders (except Primates and Xenarthra) originated in a ~20 Myr window (45 - 65 Ma) after the K - Pg extinction. Therefore we reject a pre K - Pg model of placental ordinal diversification. We suggest other infamous instances of mismatch between molecular and palaeontological divergence time estimates will be resolved with this same approach. © 2012 The Royal Society.