Table 1. Log likelihoods for alternative tree topologies. tree topology Rungwecebus clusters within Papio Rungwecebus sister lineage to Papio Rungwecebus sister lineage to Theropithecus Rungwecebus sister lineage to Lophocebus Rungwecebus sister lineage to (Mandrillus+Cercocebus) doi:10.1371/journal.pone.0004859.t001 lineages+Rungwecebus (clade S) from northern baboon lineages (clade N) occurred 2.19 million years ago (mya) (95% confidence limit [CI]: 1.50–2.98 mya) (Table 2, Figure 2). Among northern baboons, western populations including P. papio and P. anubis (clade W) and eastern populations with P. hamadryas, P. anubis and P. cynocephalus (clade E) diverged from each other 1.69 (1.04–2.41) mya. The southern clade including Rungwecebus is further divided into three subgroups. P. ursinus (PU5, PU6) from the South and West of southern Africa (clade S1) diverged from the remaining southern populations 2.02 (1.37–2.79) mya and most likely represent Cape chacmas (P. (u.) ursinus). Afterwards, 1.36 (0.82– 2.01) mya, P. cynocephalus from central Zambia (PC6, PC7; clade S2), which represent Kinda baboons (P. (c.) kindae) [9–11], were separated from additional populations of P. cynocephalus and P. ursinus as well as from Rungwecebus (clade S3). Rungwecebus diverged from its closest related baboon haplotype (PC4) 0.35 (0.09–0.67) mya. The distinct subclade of P. ursinus within clade S3 most likely represents grey-footed chacmas (P. (u.) griseipes) [9–11]. Figure 3. Phylogenetic position of Rungwecebus in relation to Papio and other members of the Papionini - nuclear DNA phylogeny. The phylogram is based on the neighbor-joining algorithm and by applying the TrN+I model of sequence evolution. Marked * nodes yielded bootstrap values of $98% (for MP, NJ and ML) or posterior probability values of 1.0 (Bayesian). For abbreviations and geographic origin of baboon sequences see Figure 1 and Table S1. doi:10.1371/journal.pone.0004859.g003 PLoS ONE | www.plosone.org 4 March 2009 | Volume 4 | Issue 3 | e4859 Phylogeny of Rungwecebus mitochondrial DNA - Log Likelihood 5653.26440 5728.00367 5736.60755 5738.32191 5750.55459 KH/SH test best tree P,0.001 P,0.001 P,0.001 P,0.001 nuclear DNA - Log Likelihood KH/SH test 7373.63688 7369.50337 7416.41553 7416.41553 7490.88793 P = 0.578; P = 0.604 best tree P,0.05 P,0.05 P,0.001 Discussion Based on its morphology [1,5], the kipunji was first regarded as a mangabey of the genus Lophocebus. However, subsequent genetic, cranial morphometric and ecological analyses provided evidence for the uniqueness of the kipunji and led to its being placed into a new genus [2,4,6]. Moreover, the then available genetic data suggested a sister taxon relationship of Rungwecebus with Papio and not with Lophocebus or any other papionin genus [2,6]. In contrast to Davenport et al. [2] and Olson et al. [6] we found no clear sister taxon relationship between the kipunji and the baboon clade. Instead, our analyses of mitochondrial sequences of the kipunji demonstrated that this lineage clusters closely with baboon lineages that lie nearest to it geographically (i.e. yellow baboons from southern Tanzania, Malawi and eastern Zambia and chacma baboons from Zambia, Zimbabwe, northern Namibia and northern South Africa). In contrast, nuclear sequence data give some indication that Rungwecebus is a sister taxon to Papio and not nested within the baboon clade. Although, this relationship is only weakly supported by the available nuclear data, morpholog- ical and ecological data clearly provide evidence for the distinctiveness of Rungwecebus and its separation from Papio [3,4]. Likewise for Papio, discordance between the mitochondrial phylogeny and the traditional classification into five clearly differentiated species [12,13] was found. Incomplete lineage sorting of mitochondrial DNA could be a possible explanation of such discrepancies, but then Rungwecebus would be expected to cluster with more ancient baboon lineages and not specifically with geographically-adjacent baboon haplotypes. The same is also true for baboon lineages, where local populations form monophyletic groups irrespective of their species affiliations. Hence, the observed discrepancy between mitochondrial data on the one hand and morphological, ecological (and nuclear) data on the other hand raises questions about the evolutionary history of Rungwecebus and Papio. A possible explanation could be that Rungwecebus is actually a member of the genus Papio as suggested by the mitochondrial data and thus does not warrant placement into its own genus. In support of such a hypothesis, the mitochondrial sequence data yield a relatively recent divergence time (i.e. 0.35 [0.09–0.67] mya) between Rungwecebus and geographically-associated baboon line- ages. If Rungwecebus belongs within Papio, its unique morphological and ecological characteristics, which are clearly different from that of baboons [2,5], would reflect recently acquired autapomorphies. Kipunjis are more arboreal than baboons [2,5] and hence, depend on woodland habitats. During the Pleistocene, climatic changes led to shifts in the distribution of forest habitats and savannah biotopes [14–18]. During such events baboon populations might have become isolated and adapted to forest or woodland habitats, resulting in a new and distinct morphotype, the kipunji. However,