title: Genomics, biogeography, and the diversification of placental mammals.
abstract: Previous molecular analyses of mammalian evolutionary relationships involving a wide range of placental mammalian taxa have been restricted in size from one to two dozen gene loci and have not decisively resolved the basal branching order within Placentalia. Here, on extracting from thousands of gene loci both their coding nucleotide sequences and translated amino acid sequences, we attempt to resolve key uncertainties about the ancient branching pattern of crown placental mammals. Focusing on approximately 1,700 conserved gene loci, those that have the more slowly evolving coding sequences, and using maximum-likelihood, Bayesian inference, maximum parsimony, and neighbor-joining (NJ) phylogenetic tree reconstruction methods, we find from almost all results that a clade (the southern Atlantogenata) composed of Afrotheria and Xenarthra is the sister group of all other (the northern Boreoeutheria) crown placental mammals, among boreoeutherians Rodentia groups with Lagomorpha, and the resultant Glires is close to Primates. Only the NJ tree for nucleotide sequences separates Rodentia (murids) first and then Lagomorpha (rabbit) from the other placental mammals. However, this nucleotide NJ tree still depicts Atlantogenata and Boreoeutheria but minus Rodentia and Lagomorpha. Moreover, the NJ tree for amino acid sequences does depict the basal separation to be between Atlantogenata and a Boreoeutheria that includes Rodentia and Lagomorpha. Crown placental mammalian diversification appears to be largely the result of ancient plate tectonic events that allowed time for convergent phenotypes to evolve in the descendant clades.
authors.affiliation: Perinatology Research Branch, National Institute of Child Health and Human Development/National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA. dwildman@med.wayne.edu
authors.forename: Derek E
authors.initials: DE
authors.lastname: Wildman
authors.forename: Monica
authors.initials: M
authors.lastname: Uddin
authors.forename: Juan C
authors.initials: JC
authors.lastname: Opazo
authors.forename: Guozhen
authors.initials: G
authors.lastname: Liu
authors.forename: Vincent
authors.initials: V
authors.lastname: Lefort
authors.forename: Stephane
authors.initials: S
authors.lastname: Guindon
authors.forename: Olivier
authors.initials: O
authors.lastname: Gascuel
authors.forename: Lawrence I
authors.initials: LI
authors.lastname: Grossman
authors.forename: Roberto
authors.initials: R
authors.lastname: Romero
authors.forename: Morris
authors.initials: M
authors.lastname: Goodman
mesh_terms: D000818:Animals; D044822:Biodiversity; D016678:Genome / Q000235:genetics*; D023281:Genomics; D005843:Geography; D008322:Mammals / Q000235:genetics* / Q000502:physiology*; D010802:Phylogeny; D010920:Placenta / Q000502:physiology*