posterior probability values (first: MP, second: NJ, third: ML, fourth: Bayesian). Dashes indicate values #50%. Red = P. papio, green = P. anubis, grey = P. hamadryas, yellow = P. cynocephalus, brown = P. ursinus. For abbreviations see Fig. 1 and Table S1. Found at: doi:10.1371/journal.pone.0004859.s001 (0.13 MB TIF) Figure S2 50% majority rule consensus tree (cladogram) based on COII sequences. Numbers on nodes represent bootstrap or posterior probability values (first: MP, second: NJ, third: ML, fourth: Bayesian). Dashes indicate values #50%. Red = P. papio, green = P. anubis, grey = P. hamadryas, yellow = P. cynocephalus, brown = P. ursinus. For abbreviations see Fig. 1 and Table S1. Found at: doi:10.1371/journal.pone.0004859.s002 (0.12 MB TIF) Figure S3 50% majority rule consensus tree (cladogram) based on 12SrRNA sequences. Numbers on nodes represent bootstrap or posterior probability values (first: MP, second: NJ, third: ML, fourth: Bayesian). Dashes indicate values #50%. Red = P. papio, green = P. anubis, grey = P. hamadryas, yellow = P. cynocephalus, brown = P. ursinus. For abbreviations see Fig. 1 and Table S1. Found at: doi:10.1371/journal.pone.0004859.s003 (0.09 MB TIF) Figure S4 50% majority rule consensus tree (cladogram) based on TSPY sequences. Numbers on nodes represent bootstrap or posterior probability values (first: MP, second: NJ, third: ML, fourth: Bayesian). Dashes indicate values #50%. Found at: doi:10.1371/journal.pone.0004859.s004 (0.09 MB TIF) Figure S5 50% majority rule consensus tree (cladogram) based on CD4 sequences. Numbers on nodes represent bootstrap or posterior probability values (first: MP, second: NJ, third: ML, fourth: Bayesian). Dashes indicate values #50%. Found at: doi:10.1371/journal.pone.0004859.s005 (0.10 MB TIF) Figure S6 50% majority rule consensus tree (cladogram) based on a 1,3-GT sequences. Numbers on nodes represent bootstrap or posterior probability values (first: MP, second: NJ, third: ML, fourth: Bayesian). Dashes indicate values #50%. Found at: doi:10.1371/journal.pone.0004859.s006 (0.09 MB TIF) Figure S7 50% majority rule consensus tree (cladogram) based on LPA sequences. Numbers on nodes represent bootstrap or posterior probability values (first: MP, second: NJ, third: ML, fourth: Bayesian). Found at: doi:10.1371/journal.pone.0004859.s007 (0.09 MB TIF) References 1. Jones T, Ehardt CL, Butynski TM, Davenport TRB, Mpunga NE, et al. (2005) The highland mangabey Lophocebus kipunji: a new species of African monkey. Science 308: 1161–1164. 2. Davenport TRB, Stanley WT, Sargis EJ, De Luca DW, Mpunga NE, et al. (2006) A new Genus of African monkey, Rungwecebus: Morphology, ecology, and molecular phylogenetics. Science 312: 1378–1381. 3. Davenport TRB, De Luca DW, Jones T, Mpunga NE, Machaga SJ, et al. (2008) The critically endangered kipunji Rungwecebus kipunji of southern Tanzania: first census and conservation status assessment. Oryx 42: 352–359. 4. Singleton M (2009) The phenetic affinities of Rungwecebus kipunji. J Hum Evol 56: 25–42. 5. Ehardt CL, Butynski TM (2006) The recently described highland mangabey, Lophocebus kipunji (Cercopithecoidea, Cercopithecinae): Current knowledge and conservation assessment. Primate Conserv 21: 81–87. 6. Olson LE, Sargis EJ, Stanley WT, Hildebrandt KBP, Davenport TRB (2008) Short communication: Additional molecular evidence strongly supports the distinction between the recently described African primate Rungwecebus kipunji (Cercopithecidae, Papionini) and Lophocebus. Mol Phylogenet Evol 48: 789–794. 7. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and their branching order of Hominoidea. J Mol Evol 29: 170–179. 8. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihood with applications to phylogenetic inference. Mol Biol Evol 16: 1114–1116. 9. Burrell A (2008) Phylogenetics and Population Genetics of Central African Baboons. New York: New York University, Department of Anthropology. 308p. Phylogeny of Rungwecebus Figure S8 50% majority rule consensus tree (cladogram) based on Xq13.3 sequences. Numbers on nodes represent bootstrap or posterior probability values (first: MP, second: NJ, third: ML, fourth: Bayesian). Dashes indicate values #50%. Found at: doi:10.1371/journal.pone.0004859.s008 (0.09 MB TIF) Table S1 Origin of analyzed samples for mitochondrial DNA studies and their GenBank accession numbers (* marked samples were used also for the analysis of nuclear loci). Found at: doi:10.1371/journal.pone.0004859.s009 (0.38 MB DOC) Table S2 Species and GenBank accession numbers for nuclear DNA studies. For abbreviation and origin of baboon samples see Table S1. Found at: doi:10.1371/journal.pone.0004859.s010 (0.04 MB DOC) Table S3 Detailed information about primers, PCR conditions, applied substitution models, sequence length and number of polymorphic sites. Found at: doi:10.1371/journal.pone.0004859.s011 (0.04 MB DOC) Table S4 Mutational events including point mutations, deletions and insertions in the five nuclear loci. Found at: doi:10.1371/journal.pone.0004859.s012 (0.25 MB DOC) Acknowledgments We are grateful to Christina Oberdieck and Christiane Schwarz for their help in the laboratory, and Aliya Bauer, Olaf Behlert, Dawit Berhane, Umaru Buba, Elodie Ey, Kurt Hammerschmidt, Marie-Claude Huynen, Cuthbert Katsvanga, Christina Keller, Britta Kunz, Klaus Lorenz, Simone Teelen and Ymke Warren for their help in collecting baboon samples. We also thank the zoos in Berlin, Duisburg, Wuppertal and Rostock for blood samples from additional papionins. Clifford Jolly and Andy Burrell informed us that they found very similar results when they compared the respective sequences of their baboon samples from eastern Zambia with the sequences of kipunji. Author Contributions Conceived and designed the experiments: DZ. Analyzed the data: DZ CR. Wrote the paper: DZ MA CR. 10. Zinner D, Buba U, Nash S, Roos C. Pan-African voyagers. The phylo-geography of baboons. In: Sommer V, Ross C, eds. Primates of Gashaka. Socioecology and Conservation in Nigeria’s Biodiversity Hotspot. New York: Springer, In press. 11. Zinner D, Groeneveld LF, Keller C, Roos C. Mitochondrial phylogeography of baboons (Papio spp.) – Indication for introgressive hybridization? Subm. 12. Groves C (2001) Primate Taxonomy. Washington, DC: Smithsonian Institution Press. 350 p. 13. Grubb P, Butynski TM, Oates JF, Bearder SK, Disotell TD, et al. (2003) Assessment of the diversity of African primates. Int J Primatol 24: 1301– 1357. 14. Hamilton AC, Taylor D (1991) History of climate and forests in tropical Africa during the last 8 million years. Climatic Change 19: 65–78. 15. Turner A (1999) Evolution in African Plio-Pleistocene mammalian fauna: Correlation and causation. In: Bromage TG, Schrenk F, eds. African Biogeography, Climate Change & Human Evolution. Oxford: Oxford University Press. pp 76–87. 16. Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405: 907–913. 17. deMenocal PB (2004) African climate change and faunal evolution during the Pliocene-Pleistocene. Earth Planet Sc Lett 220: 3–24. 18. Tosi AJ (2008) Forest monkeys and Pleistocene refugia: a phylogeographic window onto the disjunct distribution of the Chlorocebus lhoesti species group. Zool J Linn Soc 154: 408–418. 19. Gautier-Hion A, Colyn M, Gautier JP (1999) Histoire Naturelle des Primates d’Afrique Centrale. Libreville, Gabon: ECOFAC. 162p. 20. Jolly CJ (2001) A proper study for mankind: Analogies from the Papionin monkeys and their implications for human evolution. Yrbk Phys Anthropol 44: 177–204. PLoS ONE | www.plosone.org 7 March 2009 | Volume 4 | Issue 3 | e4859