Ood (ML), and maximum parsimony (MP) algorithms as implemented in MEGA version 5 [37]. Haplogroups were classified based on the clusters resolved in tree constructions with statistical verification of 1,000 replications of bootstrap.(TIF)Table SPopulation Data AnalysisThe mtDNA diversity within populations was estimated in terms of haplotype (gene) diversity, mean number of pairwise difference, and nucleotide diversity [38] using the program Arlequin version 2.000 [39]. 166518-60-1 Genetic differentiation between populations was quantified from calculations of intra- and interpopulation distances with pairwise FST distance [40] and average pairwise difference [38].Comparison of six clades of haplotypes with mean number of pairwise haplotype differences. Mean number of pairwise haplotype differences was compared within and between clades shown in Figure 2. Values of the diagonal indicate average number of pairwise differences within clades. Those above the diagonal are average number of pairwise differences between clades and below the diagonal are corrected average pairwise differences. Estimates were obtained assuming Tamura-Nei mutation model using the software Arlequin version 2.000 (Schneider et al. 2000). Numbers in parentheses give the number of haplotypes in each clade. (TIF)Estimation of the Riverine Effect on Genetic Distance among PopulationsAccording to the riverine barrier hypothesis, the genetic similarity between populations separated by a river should be higher in the headwaters (where the river is narrower) than in its lower parts [41]. We compared three geographical indices against genetic distance. Straight distance indicated the length of the straight line linking two study sites. Detoured distance indicated the 15481974 length of a bent line that linked two study sites. The bent line had not to cross any large tributary (Figure 1), and to detour until the headwater to reach the opposite bank [7]. The center of the location of each population was roughly estimated as the center of gravity for the sampling places in each study population. These two types of geographical distances were measured using QGIS (ver. 1.8.0). The number of tributaries indicated the number of times rivers crossed the straight line on the satellite map (Google Earth). A riverine was regarded as a tributary only when it was estimated to be at least as wide as the Luo River on the satelliteTable S3 Comparison of population distances with results of test for 
their statistical significance. Values below the diagonal indicate estimates of population pairwise FST calculated assuming Tamura-Nei mutation model. Values above the diagonal indicate P values of permutaion test (n = 1,023) for the null hypothesis of FST = 0 by the software Arlequin version 2.000 (Schneider et al. 2000). (TIF)AcknowledgmentsWe thank the Centre de Recherche en Ecologie et Foresterie (CREF), Ministere de la Recherche Scientifique (MIN), the African Wildlife ` Solvent Yellow 14 Foundation (AWF), the World Wide Fund for Nature (WWF), the DRC staff of the Zoological Society of Milwaukee’s Bonobo and Congo Biodiversity Initiative (ZSM), the Institut Congolais pour la Conservation de la Nature (ICCN), ICCN Salonga National Park guards and the Tshuapa-Lomami-Lualaba (TL2) Project for field research assistance, and Andrew Fowler, Laure Deruti and Menard Mbende for field collaboration. ?Author ContributionsPerformed the field research: HT. Contributed to sampling work in the field: TS JH TH NT GR PG JD AC MM KY SD CD. Conce.Ood (ML), and maximum parsimony (MP) algorithms as implemented in MEGA version 5 [37]. Haplogroups were classified based on the clusters resolved in tree constructions with statistical verification of 1,000 replications of bootstrap.(TIF)Table SPopulation Data AnalysisThe mtDNA diversity within populations was estimated in terms of haplotype (gene) diversity, mean number of pairwise difference, and nucleotide diversity [38] using the program 
Arlequin version 2.000 [39]. Genetic differentiation between populations was quantified from calculations of intra- and interpopulation distances with pairwise FST distance [40] and average pairwise difference [38].Comparison of six clades of haplotypes with mean number of pairwise haplotype differences. Mean number of pairwise haplotype differences was compared within and between clades shown in Figure 2. Values of the diagonal indicate average number of pairwise differences within clades. Those above the diagonal are average number of pairwise differences between clades and below the diagonal are corrected average pairwise differences. Estimates were obtained assuming Tamura-Nei mutation model using the software Arlequin version 2.000 (Schneider et al. 2000). Numbers in parentheses give the number of haplotypes in each clade. (TIF)Estimation of the Riverine Effect on Genetic Distance among PopulationsAccording to the riverine barrier hypothesis, the genetic similarity between populations separated by a river should be higher in the headwaters (where the river is narrower) than in its lower parts [41]. We compared three geographical indices against genetic distance. Straight distance indicated the length of the straight line linking two study sites. Detoured distance indicated the 15481974 length of a bent line that linked two study sites. The bent line had not to cross any large tributary (Figure 1), and to detour until the headwater to reach the opposite bank [7]. The center of the location of each population was roughly estimated as the center of gravity for the sampling places in each study population. These two types of geographical distances were measured using QGIS (ver. 1.8.0). The number of tributaries indicated the number of times rivers crossed the straight line on the satellite map (Google Earth). A riverine was regarded as a tributary only when it was estimated to be at least as wide as the Luo River on the satelliteTable S3 Comparison of population distances with results of test for their statistical significance. Values below the diagonal indicate estimates of population pairwise FST calculated assuming Tamura-Nei mutation model. Values above the diagonal indicate P values of permutaion test (n = 1,023) for the null hypothesis of FST = 0 by the software Arlequin version 2.000 (Schneider et al. 2000). (TIF)AcknowledgmentsWe thank the Centre de Recherche en Ecologie et Foresterie (CREF), Ministere de la Recherche Scientifique (MIN), the African Wildlife ` Foundation (AWF), the World Wide Fund for Nature (WWF), the DRC staff of the Zoological Society of Milwaukee’s Bonobo and Congo Biodiversity Initiative (ZSM), the Institut Congolais pour la Conservation de la Nature (ICCN), ICCN Salonga National Park guards and the Tshuapa-Lomami-Lualaba (TL2) Project for field research assistance, and Andrew Fowler, Laure Deruti and Menard Mbende for field collaboration. ?Author ContributionsPerformed the field research: HT. Contributed to sampling work in the field: TS JH TH NT GR PG JD AC MM KY SD CD. Conce.