DOI: 10.5061/dryad.9tm42
title: Data from: Mitogenomics of the Old World monkey tribe Papionini

description: Background: The evolutionary history of the Old World monkey tribe
 Papionini comprising the genera Macaca, Mandrillus, Cercocebus,
 Lophocebus, Theropithecus, Rungwecebus and Papio is still matter of
 debate. Although the African Papionini (subtribe Papionina) are generally
 considered to be the sister lineage to the Asian Papionini (subtribe
 Macacina), previous studies based on morphological data, nuclear or
 mitochondrial sequences have shown contradictory phylogenetic
 relationships among and within both subtribes. To further elucidate the
 phylogenetic relationships among papionins and to estimate divergence ages
 we generated mitochondrial genome data and combined them with previously
 published sequences. Results: Our mitochondrial gene tree comprises 33
 papionins representing all genera of the tribe except Rungwecebus. In
 contrast to most previous studies, the obtained phylogeny suggests a
 division of the Papionini into three main mitochondrial clades with
 similar ages: 1) Papio, Theropithecus, Lophocebus; 2) Mandrillus,
 Cercocebus; and 3) Macaca; the Mandrillus + Cercocebus clade appears to be
 more closely related to Macaca than to the other African Papionini.
 Further, we find paraphyletic relationships within the
 Mandrillus + Cercocebus clade as well as in Papio. Relationships among
 Theropithecus, Lophocebus and Papio remain unresolved. Divergence ages
 reveal initial splits within the three mitochondrial clades around the
 Miocene/Pliocene boundary and differentiation of Macaca species groups
 occurred on a similar time scale as those found between genera of the
 subtribe Papionina. Conclusion: Due to the largely well-resolved
 mitochondrial phylogeny, our study provides new insights into the
 evolutionary history of the Papionini. Results show some contradictory
 relationships in comparison to previous analyses, notably the paraphyly
 within the Cercocebus + Mandrillus clade and three instead of only two
 major mitochondrial clades. Divergence ages among species groups of
 macaques are similar to those among African Papionini genera, suggesting
 that diversification of the mitochondrial genome is of a similar magnitude
 in both subtribes. However, since our mitochondrial tree represents just a
 single gene tree that most likely does not reflect the true species tree,
 extensive nuclear sequence data is required to illuminate the true species
 phylogeny of papionins and to trace possible ancient hybridization events
 among lineages.
description: Liedigk Add.file-1
 Alignment mtDNA 38.nexAdditional file 1: Basic
 alignment of complete mitochondrial genomes from 38 catarrhine primate
 taxa. (nexus format)Liedigk_Add.file-1_Alignment_mtDNA_38.nexLiedigk_Add.file-2_TabS1Additional file 2: Table S1. Divergence ages among catarrhine primates in Ma (95% credibility intervals) estimated with uncorrelated and auto-correlated relaxed clock models. (docx)Liedigk_Add.file-3_FigS1Additional file 3: Figure S1. Nucleotide composition among Papionini and outroup taxa. (pptx)Liedigk_Add.file-4_FigS2Additional file 4: Figure S2. Ultrametric tree of Papionini and outgroup taxa as inferred from dataset 2. Tree topologies as inferred from Bayesian (MrBayes) as well as from ML (RAxML) estimations were mainly identical with some exceptions. All unlabelled branches show ML BP of 100% and Bayesian PP of 1.0. Values below are indicated at respective nodes. Taxa indicated with a are arranged differently in the ML (RAxML) and Bayesian tree (MrBayes): ((P. anubis west2, P. anubis west1) P. papio); ((C. torquatus, C. atys), ((C. chrysogaster, M. leucophaeus), M. sphinx)). Red ellipse indicates main difference to figure 1. * = sequences were newly generated in this study. (pptx)Liedigk_Add.file-5_FigS3Additional file 5: Figure S3: Tree topology including divergence dates as estimated with an auto-correlated relaxed clock model as implemented in PhyloBayes 3.3. Time scale shows million years before present. * = sequences were newly generated in this study. (pptx)Liedigk_Add.file-6_FigS4Additional file 6: Figure S4: Tree topology including divergence dates as estimated with an uncorrelated relaxed clock model as implemented in PhyloBayes 3.3. Time scale shows million years before present. * = sequences were newly generated in this study. (pptx)Liedigk_Add.file-7_TabS2Additional file 7: Table S2. Studied species and individuals along with their GenBank accession numbers. (xls)