No 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 limited 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 calibrations. 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.

Calibrations published in the Fossil Calibration Series are accessioned into the Fossil Calibration Database (www.fossilcalibrations.org). The Database is a dynamic tool for finding up-to-date calibrations, and calibration data will be updated and annotated as interpretations change. In contrast, the Fossil Calibration papers are a permanent published record of the information on which the calibrations were originally based. Please refer to the Database for the latest data.

Estimates of the time of origin for placental mammals from DNA studies span nearly the duration of the Cretaceous period (145 to 65 million years ago), with a maximum of 129 million years ago and a minimum of 78 million years ago. Palaeontologists too are divided on the timing. Some support a deep Cretaceous origin by allying certain middle Cretaceous fossils (97-90 million years old) from Uzbekistan with modern placental lineages, whereas others support the origin of crown group Placentalia near the close of the Cretaceous. This controversy has yet to be addressed by a comprehensive phylogenetic analysis that includes all well-known Cretaceous fossils and a wide sample of morphology among Tertiary and recent placentals. Here we report the discovery of a new well-preserved mammal from the Late Cretaceous of Mongolia and a broad-scale phylogenetic analysis. Our results exclude Cretaceous fossils from Placentalia, place the origin of Placentalia near the Cretaceous/Tertiary (K/T) boundary in Laurasia rather than much earlier within the Cretaceous in the Southern Hemisphere, and place afrotherians and xenarthrans in a nested rather than a basal position within Placentalia.

Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157–170 Ma, crown Placentalia diverged 86–100 Ma, and crown Atlantogenata diverged 84–97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.