Phylogenetic trees for the four extant species of African hominoids are presented, based on mtDNA control region-1 sequences from 1,158 unique haplotypes. We include 83 new haplotypes of western chimpanzees and bonobos. Phylogenetic analysis of this enlarged database, which takes intraspecific geographic variability into account, reveals different patterns of evolution among species and great heterogeneity in species-level variation. Several chimpanzee and bonobo clades (and even single social groups) have retained substantially more mitochondrial variation than is seen in the entire human species. Among the 811 human haplotypes, those that branch off early are predominantly but not exclusively African. Neighbor joining trees provide strong evidence that eastern chimpanzee and human clades have experienced reduced effective population sizes, the latter apparently since the Homo sapiens-neanderthalensis split. Application of topiary pruning resolves ambiguities in the phylogenetic tree that are attributable to homoplasies in the data set. The diverse patterns of mtDNA sequence variation seen in today's hominoid taxa probably ref lect historical differences in ecological plasticity, female-biased dispersal, range fragmentation over differing periods of time, and competition among social groups. These results are relevant to the origin of zoonotic diseases, including HIV-1, and call into question some aspects of the current taxonomic treatment and conservation management of gorillas and chimpanzees.In spite of the absence of relevant fossils, studies of genetic variation have settled the question of whether humans are more closely related to gorillas or chimpanzees in favor of the latter (1). However, most such comparative studies have been based on no more than six individuals of each taxon with the exception of humans (2-9). Furthermore, the individual apes used in these comparisons are typically of unknown geographic origin, and there has been a tendency to treat all chimpanzees as a homogeneous group. Advances in DNA sequencing technology and noninvasive genotyping (10-13) now permit a more thorough analysis of the geographic variation within and among mitochondrial DNA (mtDNA) sequences in each of the living African hominoids. The noncoding control region 1 (CR1) was selected for analysis because it is hypervariable and was thought to be relatively free from direct natural selection and therefore was thought to provide a less ambiguous record of mutational change and phylogenetic relationships (9).Here we present a comparison of genetic variation in all nine recognized taxa of African or African-derived hominoid: (i) western lowland gorilla (Gorilla g. gorilla); (ii) eastern moun- (14). We also include three other groups in our analyses: a Neandertal (Homo s. neanderthalensis) and Bornean and Sumatran orangutans (Pongo p. pygmaeus and Pongo p. abelii, respectively). Using common names except when ambiguous, we show that these taxa have very different amounts and patterns of genetic variation, with hum...

Di¡erences in social relationships among community members are often explained by di¡erences in genetic relationships. The current techniques of DNA analysis allow explicit testing of such a hypothesis. Here, we have analysed the genetic relationships for a community of wild bonobos (Pan paniscus) using nuclear and mitochondrial DNA markers extracted from faecal samples. Bonobos show an opportunistic and promiscuous mating behaviour, even with mates from outside the community. Nonetheless, we ¢nd that most infants were sired by resident males and that two dominant males together attained the highest paternity success. Intriguingly, the latter males are the sons of high-ranking females, suggesting an important in£uence of mothers on the paternity success of their sons. The molecular data support previous inferences on female dispersal and male philopatry. We ¢nd a total of ¢ve di¡erent mitochondrial haplotypes among 15 adult females, suggesting a frequent migration of females. Moreover, for most adult and subadult males in the group we ¢nd a matching mother, while this is not the case for most females, indicating that these leave the community during adolescence. Our study demonstrates that faecal samples can be a useful source for the determination of kinship in a whole community.

We show that nuclear DNA extracted from faeces of free living bonobos (Pan paniscus) can be used to amplify hypervariable simple sequence repeats, which can be used for paternity analysis and kinship studies. Of 130 DNA extractions of samples from 33 different animals, about two-thirds yielded PCR products at the first attempt. For several samples only a second extraction resulted in positive amplifications. Consistency tests revealed that in some cases only one of the two alleles was amplified. Presumably this is due to a very limited amount of bonobo DNA in the sample and we suggest therefore that a sample found to be homozygous at a given locus should be typed repeatedly for verification

SummaryStudies of captive populations of bonobos suggest that females are more gregarious than males. This seems to contradict assumed sex-differences in kinship deriving from a speciestypical dispersal pattern of female exogamy and male philopatry. Here we present data on spatial associations and af liative relations among members of one wild community (Eyengo) for which genetic relationships were identi ed by analysing mitochondrial and nuclear DNA. Our data from Lomako con rm the existence of spatial associations among resident females. In addition, they reveal strong social bonds between males and females. While most female-female associations did not last longer than one eld season, long-term associations occurred predominantly between mixed-sex dyads and involved both close kin and unrelated individuals. Differences in social grooming appeared to be related to patterns of spatial association rather than to kinship. It is suggested that under natural conditions social organisation of bonobos is characterised by strong inter-sexual bonds. Males may bene t from bonding with females by increased reproductivesuccess via rank acquisition. For females bene ts may derive from inclusive tness and reduced food competition. Preliminary evidence suggests that females also may bene t from protection by resident males against male intruders.