title: Molecular phylogenetic analysis of the Papionina using concatenation and species tree methods.
abstract: The Papionina is a geographically widespread subtribe of African cercopithecid monkeys whose evolutionary history is of particular interest to anthropologists. The phylogenetic relationships among arboreal mangabeys (Lophocebus), baboons (Papio), and geladas (Theropithecus) remain unresolved. Molecular phylogenetic analyses have revealed marked gene tree incongruence for these taxa, and several recent concatenated phylogenetic analyses of multilocus datasets have supported different phylogenetic hypotheses. To address this issue, we investigated the phylogeny of the Lophocebus + Papio + Theropithecus group using concatenation methods, as well as alternative methods that incorporate gene tree heterogeneity to estimate a 'species tree.' Our compiled DNA sequence dataset was ∼56 kb pairs long and included 57 independent partitions. All analyses of concatenated alignments strongly supported a Lophocebus + Papio clade and a basal position for Theropithecus. The Bayesian concordance analysis supported the same phylogeny. A coalescent-based Bayesian method resulted in a very poorly resolved species tree. The topological agreement between concatenation and the Bayesian concordance analysis offers considerable support for a Lophocebus + Papio clade as the dominant relationship across the genome. However, the results of the Bayesian concordance analysis indicate that almost half the genome has an alternative history. As such, our results offer a well-supported phylogenetic hypothesis for the Papio/Lophocebus/Theropithecus trichotomy, while at the same time providing evidence for a complex evolutionary history that likely includes hybridization among lineages.
authors.affiliation: Department of Anthropology, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA. Electronic address: elaine.guevara@yale.edu.
authors.forename: Elaine E
authors.initials: EE
authors.lastname: Guevara
authors.affiliation: Department of Anthropology, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA; Program in Anthropology, The Graduate Center, City University of New York, 365 5th Avenue, New York, NY 10016, USA; Program in Biology, The Graduate Center, City University of New York, 365 5th Avenue, New York, NY 10016, USA; New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, USA. Electronic address: msteiper@hunter.cuny.edu.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Steiper
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics*; D016663:Cercopithecinae / Q000235:genetics*; D044708:DNA, Concatenated / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D044708:DNA, Concatenated; D004272:DNA, Mitochondrial
keywords: Bayesian concordance; Gene tree heterogeneity; Mangabeys; Multispecies coalescent; Primate evolution; Supermatrix