Phylogeny of Rungwecebus Figure 1. Distribution of Papio [modified after 63] and Rungwecebus (blue boxes), and collecting sites of samples. Blue dot = origin of the Rungwecebus sample [2] from the Southern Highlands of Tanzania. A second population of Rungwecebus was found in the Udzungwa Mountains [1]. Names of baboon collecting sites and their geographical coordinates are given in Table S1. doi:10.1371/journal.pone.0004859.g001 to the extremely low levels of variation and hence, the relationships among baboons and the kipunji cannot be resolved unambiguously using these data. Our mitochondrial data sets included all seven papionin genera. Furthermore, the 25 baboon individuals represented all five Papio species (P. papio, P. hamadryas, P. anubis, P. cynocephalus, P. ursinus) and covered most of the genus’ geographic distribution. Phyloge- netic tree reconstructions for the three individual loci (Figures S1, S2, S3) and the concatenated data set with 1486 bp in length (Figure 2) revealed mainly identical and highly supported relationships, with only a few remaining unresolved or with low support. We found strong support for the division of African papionins into two major clades, one with Mandrillus and Cercocebus, and the other with Lophocebus, Theropithecus, Papio and Rungwecebus. Among the latter, a common origin of Papio and Rungwecebus was highly supported, but the relationship between this clade and either Lophocebus or Theropithecus was not well resolved. Within the Papio+Rungwecebus clade, we found several strongly supported haplogroups. However, these did not correspond to the tradition- ally recognized baboon species, and with the exception of P. papio, all other baboon taxa were para- or polyphyletic. In contrast, we found a strong geographical signal with local populations forming monophyletic haplogroups irrespective of their species affiliations. This reflects clearly the discordance between mitochondrial phylogeny and baboon morphology. The same is also true for Rungwecebus, which did not represent a sister lineage to the Papio genus [2,6], but instead clustered with yellow baboons (P. cynocephalus) from southern Tanzania, Malawi, Zambia and with chacma baboons (P. ursinus) from Zimbabwe, northern Namibia and northern South Africa. These yellow and chacma baboons from south-east Africa represent local populations that are geographically closest to Rungwecebus (Figure 1). To test for the reliability of the depicted relationships, we evaluated alternative phylogenetic positions of Rungwecebus among papionins with the Kishino-Hasegawa (KH) [7] and Shimodaira-Hasegawa (SH) [8] tests. Accordingly, a sister grouping of Rungwecebus to Papio, Theropithecus, Lophocebus or a Cercocebus+Mandrillus clade was significantly rejected (P,0.001, Table 1). Each of our nuclear data sets comprised 11 sequences, of which five were derived from the five baboon species and the remaining six from representatives of the other papionin genera. Phylogenetic tree reconstructions for individual loci (Figures S4, S5, S6, S7, S8) and the concatenated data set of 4486 bp in length (Figure 3) provided similar tree topologies, although the resolution was relatively low, especially for single loci. As in the mitochondrial phylogeny, the nuclear data strongly supported a major division of PLoS ONE | www.plosone.org 2 March 2009 | Volume 4 | Issue 3 | e4859