The geographic apportionment of mitochondrial genetic diversity in east African chimpanzees, Pan troglodytes schweinfurthii

This study is a geographically systematic genetic survey of the easternmost subspecies of chimpanzee, Pan troglodytes schweinfurthii. DNA was noninvasively collected in the form of shed hair from chimpanzees of known origin in Uganda, Rwanda, Tanzania, and Zaire. Two hundred sixty-two DNA sequences from hypervariable region 1 of which of the mitochondrial control region were generated. Eastern chimpanzees display levels of mitochondrial genetic variation which are low and which are similar to levels observed in humans (Homo sapiens). Also like humans, between 80% and 90% of the genetic variability within the eastern chimpanzees is apportioned within populations. Spatial autocorrelation analysis shows that genetic similarity between eastern chimpanzees decreases clinically with distance, in a pattern remarkably similar to one seen for humans separated by equivalent geographic distances. Eastern chimpanzee mismatch distributions (frequency distributions of pairwise genetic differences between individuals) are similar in shape to those for humans, implying similar population histories of recent demographic expansion. The overall pattern of genetic variability in eastern chimpanzees is consistent with the hypothesis that the subject has responded demographically to paleoclimatically driven changes in the distribution of eastern African forests during the recent Pleistocene.      

Different selective pressures shape the molecular evolution of color vision in chimpanzee and human populations

A population genetic analysis of the long-wavelength opsin (OPN1LW, "red") color vision gene in a global sample of 236 human nucleotide sequences had previously discovered nine amino acid replacement single nucleotide polymorphisms, which were found at high frequencies in both African and non-African populations and associated with an unusual haplotype diversity. Although this pattern of nucleotide diversity is consistent with balancing selection, it has been argued that a recombination "hot spot" or gene conversion within and between X-linked color vision genes alone may explain these patterns. The current analysis investigates a closely related primate with trichromatism to determine whether color vision gene amino acid polymorphism and signatures of adaptive evolution are characteristic of humans alone. Our population sample of 56 chimpanzee (Pan troglodytes) OPN1LW sequences shows three singleton amino acid polymorphisms and no unusual recombination or linkage disequilibrium patterns across the approximately 5.5-kb region analyzed. Our comparative population genetic approach shows that the patterns of OPN1LW variation in humans and chimpanzees are consistent with positive and purifying selection within the two lineages, respectively. Although the complex role of color vision has been greatly documented in primate evolution in general, it is surprising that trichromatism has followed very different selective trajectories even between humans and our closest relatives.     

Analysis of chimpanzee history based on genome sequence alignments

Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously available. We show that bonobos and common chimpanzees were separated ~1,290,000 years ago, western and other common chimpanzees ~510,000 years ago, and eastern and central chimpanzees at least 50,000 years ago. We infer that the central chimpanzee population size increased by at least a factor of 4 since its separation from western chimpanzees, while the western chimpanzee effective population size decreased. Surprisingly, in about one percent of the genome, the genetic relationships between humans, chimpanzees, and bonobos appear to be different from the species relationships. We used PCR-based resequencing to confirm 11 regions where chimpanzees and bonobos are not most closely related. Study of such loci should provide information about the period of time 5–7 million years ago when the ancestors of humans separated from those of the chimpanzees.     

Unconstrained cranial evolution in Neandertals and modern humans compared to common chimpanzees

A variety of lines of evidence support the idea that neutral evolutionary processes (genetic drift, mutation) have been important in generating cranial differences between Neandertals and modern humans. But how do Neandertals and modern humans compare with other species? And how do these comparisons illuminate the evolutionary processes underlying cranial diversification? To address these questions, we used 27 standard cranial measurements collected on 2524 recent modern humans, 20 Neandertals and 237 common chimpanzees to estimate split times between Neandertals and modern humans, and between Pan troglodytes verus and two other subspecies of common chimpanzee. Consistent with a neutral divergence, the Neandertal versus modern human split-time estimates based on cranial measurements are similar to those based on DNA sequences. By contrast, the common chimpanzee cranial estimates are much lower than DNA-sequence estimates. Apparently, cranial evolution has been unconstrained in Neandertals and modern humans compared with common chimpanzees. Based on these and additional analyses, it appears that cranial differentiation in common chimpanzees has been restricted by stabilizing natural selection. Alternatively, this restriction could be due to genetic and/or developmental constraints on the amount of within-group variance (relative to effective population size) available for genetic drift to act on.     

The complex evolutionary history of gorillas: insights from genomic data

Relatively little is known about the evolutionary and demographichistories of gorillas, one of our closest living relatives.In this study, we used samples from both western (Gorilla gorilla)and eastern (Gorilla beringei) gorillas to infer the timingof the split between these geographically disjunct populationsand to elaborate the demographic history of gorillas. Here wepresent DNA sequences from 16 noncoding autosomal loci from15 western gorillas and 3 eastern gorillas, including 2 noninvasivelysampled free-ranging individuals. We find that the genetic diversityof gorillas is similar to that of chimpanzees but almost twiceas high as that of bonobos and humans. A significantly positiveFu & Li's D was observed for western gorillas, suggestinga complex demographic history with a constant, long-term populationsize and ancestral population structure. Among different population-splitscenarios, our data suggest a complex history of western andeastern gorillas including an initial population split at around0.9–1.6 MYA and subsequent, primarily male-mediated geneflow until approximately 80,000–200,000 years ago. Furthermore,simulations revealed that more gene flow took place from easternto western gorilla populations than vice versa.     

Male-mediated gene flow in patrilocal primates

Background

Many group–living species display strong sex biases in dispersal tendencies. However, gene flow mediated by apparently philopatric sex may still occur and potentially alters population structure. In our closest living evolutionary relatives, dispersal of adult males seems to be precluded by high levels of territoriality between males of different groups in chimpanzees, and has only been observed once in bonobos. Still, male–mediated gene flow might occur through rare events such as extra–group matings leading to extra–group paternity (EGP) and female secondary dispersal with offspring, but the extent of this gene flow has not yet been assessed.

Methodology/Principal Findings

Using autosomal microsatellite genotyping of samples from multiple groups of wild western chimpanzees (Pan troglodytes verus) and bonobos (Pan paniscus), we found low genetic differentiation among groups for both males and females. Characterization of Y–chromosome microsatellites revealed levels of genetic differentiation between groups in bonobos almost as high as those reported previously in eastern chimpanzees, but lower levels of differentiation in western chimpanzees. By using simulations to evaluate the patterns of Y–chromosomal variation expected under realistic assumptions of group size, mutation rate and reproductive skew, we demonstrate that the observed presence of multiple and highly divergent Y–haplotypes within western chimpanzee and bonobo groups is best explained by successful male–mediated gene flow.

Conclusions/Significance

The similarity of inferred rates of male–mediated gene flow and published rates of EGP in western chimpanzees suggests this is the most likely mechanism of male–mediated gene flow in this subspecies. In bonobos more data are needed to refine the estimated rate of gene flow. Our findings suggest that dispersal patterns in these closely related species, and particularly for the chimpanzee subspecies, are more variable than previously appreciated. This is consistent with growing recognition of extensive behavioral variation in chimpanzees and bonobos.     

Non-invasive sampling and DNA amplification for paternity exclusion,community structure,and phylogeography in wild chimpanzees

Genetic studies of free-ranging primates have been seriously impeded by difficulties of sampling tissues, including the undesirability of bleeding habituated animals, of transporting frozen samples to the laboratory, and of the inherent inadequacies of accessible variation including allozymes, mtDNA RFLP patterns and DNA fingerprints. We have developed methods of non-invasive DNA sampling and DNA-level genotyping which, when combined with a hierarchical analysis of mtDNA sequences and hypervariable nDNA simple sequence repeat (microsatellite) loci size length polymorphisms, facilitate the resolution of most questions at the individual, social group (community), population, and species (phylogenetic) levels. This approach, based on DNA amplified from shed hair, represents an important new tool for the acquisition of genetic information and will facilitate the study and management of both captive and free-ranging chimpanzees (Pan troglodytes). Our hierarchical analysis of population genetics of chimpanzees has revealed high historical levels of gene flow and large effective population sizes, as well as substantial divergence between the West African subspecies and chimpanzees from central and East Africa. At the community level, closer relatedness among philopatric males than among females supports the view that kin selection has been an evolutionary force shaping male-male cooperation in this species. Results from our study of the now relatively isolated Gombe community suggest that habitat fragmentation affects population genetic structure and possibly population viability.     

Linkage disequilibrium in the North American Holstein population

Linkage disequilibrium was estimated using 7119 single nucleotide polymorphism markers across the genome and 200 animals from the North American Holstein cattle population. The analysis of maternally inherited haplotypes revealed strong linkage disequilibrium ( r ²   >   0.8) in genomic regions of ∼50 kb or less. While linkage disequilibrium decays as a function of genomic distance, genomic regions within genes showed greater linkage disequilibrium and greater variation in linkage disequilibrium compared with intergenic regions. Identification of haplotype blocks could characterize the most common haplotypes. Although maximum haplotype block size was over 1 Mb, mean block size was 26–113 kb by various definitions, which was larger than that observed in humans (∼10 kb). Effective population size of the dairy cattle population was estimated from linkage disequilibrium between single nucleotide polymorphism marker pairs in various haplotype ranges. Rapid reduction of effective population size of dairy cattle was inferred from linkage disequilibrium in recent generations. This result implies a loss of genetic diversity because of the high rate of inbreeding and high selection intensity in dairy cattle. The pattern observed in this study indicated linkage disequilibrium in the current dairy cattle population could be exploited to refine mapping resolution. Changes in effective population size during past generations imply a necessity of plans to maintain polymorphism in the Holstein population.     

Absence of the TAP2 human recombination hotspot in chimpanzees

Recent experiments using sperm typing have demonstrated that, in several regions of the human genome, recombination does not occur uniformly but instead is concentrated in “hotspots” of 1–2 kb. Moreover, the crossover asymmetry observed in a subset of these has led to the suggestion that hotspots may be short-lived on an evolutionary time scale. To test this possibility, we focused on a region known to contain a recombination hotspot in humans, TAP2, and asked whether chimpanzees, the closest living evolutionary relatives of humans, harbor a hotspot in a similar location. Specifically, we used a new statistical approach to estimate recombination rate variation from patterns of linkage disequilibrium in a sample of 24 western chimpanzees (Pan troglodytes verus). This method has been shown to produce reliable results on simulated data and on human data from the TAP2 region. Strikingly, however, it finds very little support for recombination rate variation at TAP2 in the western chimpanzee data. Moreover, simulations suggest that there should be stronger support if there were a hotspot similar to the one characterized in humans. Thus, it appears that the human TAP2 recombination hotspot is not shared by western chimpanzees. These findings demonstrate that fine-scale recombination rates can change between very closely related species and raise the possibility that rates differ among human populations, with important implications for linkage-disequilibrium based association studies.     

Distances éntre l'homme et les singes anthropoïdes basées sur la mobilité électrophorétique des protéines et enzymes

Electrophoretic mobilities of ten homologous serum proteins and enzymes in Man and anthropoid apes led to estimations of the genetic distances between five species (Homo, Pan, Gorilla, Pongo and Symphalangus). The separation of the Symphalangus (Siamang) lineage from that leading to the great apes and Man is obvious. Less evident is the cluster containing only humans and chimpanzees, and also the fact that orang-utans are placed closer to Man than gorillas.     

Brief Communication: Quantitative‐ and molecular‐genetic differentiation in humans and chimpanzees: Implications for the evolutionary processes underlying cranial diversification

Estimates of the amount of genetic differentiation in humans among major geographic regions (e.g., Eastern Asia vs. Europe) from quantitative‐genetic analyses of cranial measurements closely match those from classical‐ and molecular‐genetic markers. Typically, among‐region differences account for ～10% of the total variation. This correspondence is generally interpreted as evidence for the importance of neutral evolutionary processes (e.g., genetic drift) in generating among‐region differences in human cranial form, but it was initially surprising because human cranial diversity was frequently assumed to show a strong signature of natural selection. Is the human degree of similarity of cranial and DNA‐sequence estimates of among‐region genetic differentiation unusual? How do comparisons with other taxa illuminate the evolutionary processes underlying cranial diversification? Chimpanzees provide a useful starting point for placing the human results in a broader comparative context, because common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the extant species most closely related to humans. To address these questions, I used 27 cranial measurements collected on a sample of 861 humans and 263 chimpanzees to estimate the amount of genetic differentiation between pairs of groups (between regions for humans and between species or subspecies for chimpanzees). Consistent with previous results, the human cranial estimates are quite similar to published DNA‐sequence estimates. In contrast, the chimpanzee cranial estimates are much smaller than published DNA‐sequence estimates. It appears that cranial differentiation has been limited in chimpanzees relative to humans. Am J Phys Anthropol 154:615–620, 2014. © 2014 Wiley Periodicals, Inc.     

AVPR1A Variation in Chimpanzees (Pan troglodytes): Population Differences and Association with Behavioral Style

Primates and other mammals show measurable, heritable variation in behavioral traits such as gregariousness, timidity, and aggression. Connections among behavior, environment, neuroanatomy, and genetics are complex, but small genetic differences can have large effects on behavioral phenotypes. One of the best examples of a single gene with large effects on natural variation in social behavior is AVPR1A, which codes for a receptor of the peptide hormone arginine vasopressin. Work on rodents shows a likely causal association between AVPR1A regulatory polymorphisms and social behavior. Chimpanzees also show variation in the AVPR1A regulatory region, with some individuals lacking a ca. 350-bp segment corresponding to a putative functional element. Thus, chimpanzees have a “short” allele (segment deletion) and a “long” allele (no deletion) at this locus. Here we compare AVPR1A variation in two chimpanzee populations, and we examine behavioral and hormonal data in relation to AVPR1A genotypes. We genotyped AVPR1A in a captive population of western chimpanzees (Pan troglodytes verus, New Iberia Research Center; N = 64) for which we had quantitative measures of personality (based on 15 behavioral style indices, calculated from 3 yr of observational data), dominance rank, and baseline testosterone levels. We also provide the first assessment of AVPR1A genotype frequencies in a wild eastern chimpanzee population (Pan troglodytes schweinfurthii, Ngogo community, Kibale National Park, Uganda; N = 26). Our results indicated that the AVPR1A long allele was associated with a “smart” social personality in captive western chimpanzees, independent of testosterone levels. Although the frequency of the long allele was relatively low in captive western chimpanzees (0.23), it was the major allele in wild eastern chimpanzees (0.62). Our finding that allele and genotype frequencies for the AVPR1A polymorphism differ among chimpanzee populations also highlights the need for comparative studies —across subspecies and research sites— in primate behavioral genetics.     

The Human Semicircular Canals Orientation Is More Similar to the Bonobos than to the Chimpanzees

For some traits, the human genome is more closely related to either the bonobo or the chimpanzee genome than they are to each other. Therefore, it becomes crucial to understand whether and how morphostructural differences between humans, chimpanzees and bonobos reflect the well known phylogeny. Here we comparatively investigated intra and extra labyrinthine semicircular canals orientation using 260 computed tomography scans of extant humans (Homo sapiens), bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Humans and bonobos proved more similarities between themselves than with chimpanzees. This finding did not fit with the well established chimpanzee – bonobo monophyly. One hypothesis was convergent evolution in which bonobos and humans produce independently similar phenotypes possibly in response to similar selective pressures that may be associated with postural adaptations. Another possibility was convergence following a “random walk” (Brownian motion) evolutionary model. A more parsimonious explanation was that the bonobo-human labyrinthine shared morphology more closely retained the ancestral condition with chimpanzees being subsequently derived. Finally, these results might be a consequence of genetic diversity and incomplete lineage sorting. The remarkable symmetry of the Semicircular Canals was the second major finding of this article with possible applications in taphonomy. It has the potential to investigate altered fossils, inferring the probability of post-mortem deformation which can lead to difficulties in understanding taxonomic variation, phylogenetic relationships, and functional morphology.     

Evolution of a HOXB6 intergenic region within the great apes and humans

Data accumulated over the past decade from several loci suggest that nonhuman primates have a greater amount of intraspecific genetic variation relative to humans. In phylogenetic reconstructions among primates that are based on genetic data, therefore, it becomes essential to adequately sample the population(s) being analyzed. Inadequate sampling may not only underestimate variation within any given population, but such an underestimate may confound any phylogenetic or population-specific conclusions implied by the data. Here we present inter- and intraspecific data on the molecular evolution of an approximately 1.0 kb intergenic HOXB6 sequence among humans, common chimpanzees, pygmy chimpanzees, gorillas and orangutans. To date, this study represents the most comprehensive investigation of a noncoding nuclear locus among the great apes and humans that examines the nature and amount of intraspecific variation in DNA sequences. Not only do these HOXB6 data continue to support earlier findings that Homo sapiens sapiens has less genetic variation than any great ape species (Ruano et al., 1992; Deinard & Kidd, 1995), but they strongly suggest that a high level of genetic polymorphism existed within the common ancestor of the African ape clade (Homo-Pan-Gorilla). Despite detecting two nucleotide substitutions linking Pan and Homo, we caution against concluding that the HOXB6 data definitively support a Homo-Pan clade to the exclusion of Gorilla. Rather, we believe that taking into consideration the level of genetic polymorphism that is likely to have existed within the common ancestor, the most prudent conclusion that can be made from all available data, including morphological, karyotypic and genetic data, may be that speciation among Homo-Pan-Gorilla is best represented by a "trichotomy".     

Demographic history and genetic differentiation in apes

Comparisons of genetic variation between humans and great apes are hampered by the fact that we still know little about the demographics and evolutionary history of the latter species. In addition, characterizing ape genetic variation is important because they are threatened with extinction, and knowledge about genetic differentiation among groups may guide conservation efforts. We sequenced multiple intergenic autosomal regions totaling 22,400 base pairs (bp) in ten individuals each from western, central, and eastern chimpanzee groups and in nine bonobos, and 16,000 bp in ten Bornean and six Sumatran orangutans. These regions are analyzed together with homologous information from three human populations and gorillas. We find that whereas orangutans have the highest diversity, western chimpanzees have the lowest, and that the demographic histories of most groups differ drastically. Special attention should therefore be paid to sampling strategies and the statistics chosen when comparing levels of variation within and among groups. Finally, we find that the extent of genetic differentiation among "subspecies" of chimpanzees and orangutans is comparable to that seen among human populations, calling the validity of the "subspecies" concept in apes into question.     

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human–chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1–1.5, 1.1–0.76 and 0.25–0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.     

The sampling scheme matters: Pan troglodytes troglodytes and P. t. schweinfurthii are characterized by clinal genetic variation rather than a strong subspecies break

Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian‐cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between‐subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions. Am J Phys Anthropol 156:181–191, 2015. © 2014 Wiley Periodicals, Inc.     

Estimating effective population size from linkage disequilibrium: severe bias in small samples

Effective population size (N _e) is a central concept in evolutionary biology and conservation genetics. It predicts rates of loss of neutral genetic variation, fixation of deleterious and favourable alleles, and the increase of inbreeding experienced by a population. A method exists for the estimation of N _e from the observed linkage disequilibrium between unlinked loci in a population sample. While an increasing number of studies have applied this method in natural and managed populations, its reliability has not yet been evaluated. We developed a computer program to calculate this estimator of N _e using the most widely used linkage disequilibrium algorithm and used simulations to show that this estimator is strongly biased when the sample size is small (<‰100) and below the true N _e. This is probably due to the linkage disequilibrium generated by the sampling process itself and the inadequate correction for this phenomenon in the method. Results suggest that N _e estimates derived using this method should be regarded with caution in many cases. To improve the method’s reliability and usefulness we propose a way to determine whether a given sample size exceeds the population N _e and can therefore be used for the computation of an unbiased estimate.     

Genetic Sampling of Unhabituated Chimpanzees (Pan troglodytes schweinfurthii) in Gishwati Forest Reserve, an Isolated Forest Fragment in Western Rwanda

Many primate populations currently live in forest fragments. These populations are often unhabituated, elusive, and contain few individuals, making them difficult to study through direct observation. Noninvasive genetic methods are useful for surveying these unhabituated populations to infer the number and sex of individuals and the genetic diversity of the population. We conducted genetic analysis on 70 fecal samples from eastern chimpanzees (Pan troglodytes schweinfurthii) in Gishwati Forest Reserve, a forest fragment in western Rwanda. We genotyped all but two of these samples using 12 autosomal and 13 Y-chromosome microsatellite markers previously used in analyses of other chimpanzee populations. The genetic data show that these samples represent a minimum of 19 individuals (7 females, 12 males). However, because we may not have sampled all individuals in the population, we also performed mark-recapture analysis with the genetic data and found that the entire population likely numbers between 19 and 29 individuals. These results are consistent with opportunistic observations of at least 19 individual chimpanzees. Levels of variation at the Y-chromosome microsatellites were similar to those observed in other chimpanzee communities, suggesting that the chimpanzees in this forest are members of a single community. These results provide a baseline count of the number of male and female chimpanzees in the Gishwati Forest Reserve, and the data provide the potential for follow-up studies aimed at tracking individuals over time, thus aiding conservation management of this unhabituated population.     

Termite fishing by wild chimpanzees: new data from Ugalla, western Tanzania

Chimpanzees manufacture flexible fishing probes to fish for termites in Issa, Ugalla, western Tanzania. These termite-fishing tools are similar in size and material to those used by long-studied communities of chimpanzees in western Tanzania (Pan troglodytes schweinfurthii) and in West Africa (P. t. verus), but not central African populations (P. t. troglodytes). This report adds to the patchwork of evidence of termite-fishing tool use behaviour by chimpanzees across Africa.