title: The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.
abstract: 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.
authors.affiliation: Department of Biology, The National University of Ireland, Maynooth, Ireland School of Earth Sciences, University of Bristol, United Kingdom james.tarver@bristol.ac.uk davide.pisani@bristol.ac.uk.
authors.forename: James E
authors.initials: JE
authors.lastname: Tarver
authors.affiliation: Department of Genetics, Evolution and Environment, University College London, United Kingdom School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom.
authors.forename: Mario
authors.initials: M
authors.lastname: Dos Reis
authors.affiliation: Department of Computer Science, University of Texas at Austin Department of Electrical and Computer Engineering, University of California, San Diego.
authors.forename: Siavash
authors.initials: S
authors.lastname: Mirarab
authors.affiliation: Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Life Sciences, University of Leeds.
authors.forename: Raymond J
authors.initials: RJ
authors.lastname: Moran
authors.affiliation: School of Earth Sciences, University of Bristol, United Kingdom.
authors.forename: Sean
authors.initials: S
authors.lastname: Parker
authors.affiliation: School of Earth Sciences, University of Bristol, United Kingdom.
authors.forename: Joseph E
authors.initials: JE
authors.lastname: O'Reilly
authors.affiliation: Mount Desert Island Biological Laboratory, Salisbury Cove, Maine.
authors.forename: Benjamin L
authors.initials: BL
authors.lastname: King
authors.affiliation: Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Life Sciences, University of Leeds.
authors.forename: Mary J
authors.initials: MJ
authors.lastname: O'Connell
authors.affiliation: Museum of Zoology, University of Cambridge, United Kingdom.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Asher
authors.affiliation: Department of Computer Science, University of Texas at Austin Department of Electrical and Computer Engineering, University of California, San Diego Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign.
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
authors.affiliation: Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Peterson
authors.affiliation: School of Earth Sciences, University of Bristol, United Kingdom.
authors.forename: Philip C J
authors.initials: PC
authors.lastname: Donoghue
authors.affiliation: School of Earth Sciences, University of Bristol, United Kingdom School of Biological Sciences, University of Bristol, United Kingdom james.tarver@bristol.ac.uk davide.pisani@bristol.ac.uk.
authors.forename: Davide
authors.initials: D
authors.lastname: Pisani
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D005260:Female; D005580:Fossils; D049810:Genetic Speciation; D016678:Genome; D008322:Mammals / Q000145:classification / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D010920:Placenta / Q000033:anatomy & histology*; D011247:Pregnancy
chemical_list: D035683:MicroRNAs
keywords: genome; mammalian; microRNA; palaeontology; phylogeny; placental