The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results thus support and extend the African origin hypothesis of human mtDNA evolution.

About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.

Summary Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

Noninvasive samples are useful for molecular genetic analyses of wild animal populations. However, the low DNA content of such samples makes DNA amplification difficult, and there is the potential for erroneous results when one of two alleles at heterozygous microsatellite loci fails to be amplified. In this study we describe an assay designed to measure the amount of amplifiable nuclear DNA in low DNA concentration extracts from noninvasive samples. We describe the range of DNA amounts obtained from chimpanzee faeces and shed hair samples and formulate a new efficient approach for accurate microsatellite genotyping. Prescreening of extracts for DNA quantity is recommended for sorting of samples for likely success and reliability. Repetition of results remains extensive for analysis of microsatellite amplifications beginning from low starting amounts of DNA, but is reduced for those with higher DNA content.

For animals living in mixed-sex social groups, females who form strong social bonds with other females live longer and have higher offspring survival [1-3]. These bonds are highly nepotistic, but sometimes strong bonds may also occur between unrelated females if kin are rare [2, 3] and even among postdispersal unrelated females in chimpanzees and horses [4, 5]. Because of fundamental differences between the resources that limit reproductive success in females (food and safety) and males (fertilizations), it has been predicted that bonding among males should be rare and found only for kin and among philopatric males [6] like chimpanzees [7-9]. We studied social bonds among dispersing male Assamese macaques (Macaca assamensis) to see whether males in multimale groups form differentiated social bonds and whether and how males derive fitness benefits from close bonds. We found that strong bonds were linked to coalition formation, which in turn predicted future social dominance, which influenced paternity success. The strength of males' social bonds was directly linked to the number of offspring they sired. Our results show that differentiated social relationships exert an important influence on the breeding success of both sexes that transcends contrasts in relatedness.

Fossils and molecular data are two independent sources of information that should in principle provide consistent inferences of when evolutionary lineages diverged. Here we use an alternative approach to genetic inference of species split times in recent human and ape evolution that is independent of the fossil record. We first use genetic parentage information on a large number of wild chimpanzees and mountain gorillas to directly infer their average generation times. We then compare these generation time estimates with those of humans and apply recent estimates of the human mutation rate per generation to derive estimates of split times of great apes and humans that are independent of fossil calibration. We date the human-chimpanzee split to at least 7-8 million years and the population split between Neanderthals and modern humans to 400,000-800,000 y ago. This suggests that molecular divergence dates may not be in conflict with the attribution of 6-to 7-million-y-old fossils to the human lineage and 400,000-yold fossils to the Neanderthal lineage.hominin | molecular dating | primate | speciation O ver 40 y ago, Sarich and Wilson used immunological data to propose that humans and African great apes diverged only about 5 million y ago, some three to four times more recently than had been assumed on the basis of the fossil record (1). Although contentious at the time (e.g., ref. 2), this divergence has since been repeatedly estimated from DNA sequence data at 4-6 million years ago (Ma) (3-8). However, this estimate is incompatible with the attribution of fossils older than 6 Ma to the human lineage. Although the assignment of fossils such as the ∼6 Ma Orrorin (9) and the 6-7 Ma Sahelanthropus (10) to the human lineage remains controversial (11), it is also possible that the divergence dates inferred from DNA sequence data are too recent.The total amount of sequence differences observed today between two evolutionary lineages can be expressed as the sum of two values: the sequence differences that accumulated since gene flow ceased between the lineages ("split time") and the sequence differences that correspond to the diversity in the common ancestor of both lineages. The extent of variation in the ancestral species may be estimated from the variance of DNA sequence differences observed across different parts of the genome between the species today, which will be larger the greater the level of variation in the ancestral population. By subtracting this value from the total amount of sequence differences, the sequence differences accumulated since the split can be estimated. The rate at which DNA sequence differences accumulate in the genome ("mutation rate") is needed to then convert DNA sequence differences into split times.In prior research, mutation rates have been calculated using species split times estimated from the fossil record as calibration points. For calculating split times between present-day humans and great apes, calibration points that assume DNA sequence differences between humans and orangutans...

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We have analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from ten countries in Africa. We find that chimpanzee population sub-structure makes genetic information a good predictor of geographic origin at country and regional scales. Most strikingly, multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200 and 550 thousand years ago (Kya), probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another possibly more recent contact (after 200 Kya), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.

The complex cooperative behavior exhibited by wild chimpanzees generates considerable theoretical and empirical interest, yet we know very little about the mechanisms responsible for its evolution. Here, we investigate the influence of kinship on the cooperative behavior of male chimpanzees living in an unusually large community at Ngogo in Kibale National Park, Uganda. Using long-term field observations and molecular genetic techniques to identify kin relations between individuals, we show that male chimpanzees clearly prefer to affiliate and cooperate with their maternal brothers in several behavioral contexts. Despite these results, additional analyses reveal that the impact of kinship is limited; paternal brothers do not selectively affiliate and cooperate, probably because they cannot be reliably recognized, and the majority of highly affiliative and cooperative dyads are actually unrelated or distantly related. These findings add to a growing body of research that indicates that animals cooperate with each other to obtain both direct and indirect fitness benefits and that complex cooperation can occur between kin and nonkin alike.Pan troglodytes ͉ genotyping ͉ kin recognition ͉ microsatellites ͉ relatedness