Individual Identification and Paternity Determination in Chimpanzees (Pan troglodytes) Using Human Short Tandem Repeat (STR) Markers

We studied 155 human short tandem repeat (STR) DNA markers in chimpanzees (Pan troglodytes) via the polymerase chain reaction (PCR). There is no difference in number of alleles per locus among STRs of different motif length (di-, tri-, or tetranucleotide repeats). We investigated 42 of the most informative STRs in greater detail using DNA isolated from a panel of 41 African-born, captive-housed chimpanzees. They reveal a wealth of genetic variability in chimpanzees, with an average of six alleles and 70.6% heterozygosity. The average paternity exclusion probability is 51.6%, and the best three STRs jointly provide >95% mean exclusion probability. Used in combination to define a multiple-locus genotype, the five most informative focal STRs can potentially uniquely identify every chimpanzee alive in the world. Although the subjects are of unknown geographical origin, homozygosity tests indicate little evidence for population subdivision. These markers represent the basis of a powerful battery of genetic tests, including individual identification, e.g., in poaching, paternity testing, or reconstruction of pedigrees among captive and wild chimpanzee breeding populations.     

Erythroblastosis models. II. Materno-fetal incompatibility in chimpanzee

Erythroblastosis fetalis represents a significant hazard for successful management of pregnancy in man and in marmosets, but not in crab-eating macaques. Materno-fetal blood group incompatibility in chimpanzee is described as a contributing factor in the death of an infant. The findings indicate that parental blood groups should be taken into consideration when breeding chimpanzees.     

Gene flow in wild chimpanzee populations: what genetic data tell us about chimpanzee movement over space and time

The isolation of phylogenetically distinct primate immunodeficiency viruses from at least seven wild-born, captive chimpanzees indicates that viruses closely related to HIV-1 may be endemic in some wild chimpanzee populations. The search for the chimpanzee population or populations harbouring these viruses is therefore on. This paper attempts to answer the question of whether or not such populations of chimpanzees are likely to exist at all, and, if so, where they are likely to be found. We summarize what is known about gene flow in wild populations of chimpanzees, both between major phylogeographical subdivisions of the species, and within these subdivisions. Our analysis indicates that hitherto undocumented reproductively isolated chimpanzee populations may in fact exist. This conclusion is based on the observation that, despite limited geographical sampling and limited numbers of genetic loci, conventional notions of the nature and extent of chimpanzee gene flow have recently been substantially revised. Molecular genetic studies using mitochondrial DNA sequences and hypervariable nuclear microsatellite markers have indicated the existence of heretofore undocumented barriers to chimpanzee gene flow. These studies have identified at least one population of chimpanzees genetically distinct enough to be classified into a new subspecies (Pan troglodytes vellerosus). At the same time, they have called into question the long-accepted genetic distinction between eastern chimpanzees (Pan troglodytes schweinfurthii) and western equatorial chimpanzees (Pan troglodytes troglodytes). The same studies have further indicated that gene flow between local populations is more extensive than was previously thought, and follows patterns sometimes inconsistent with those documented through direct behavioural observation. Given the apparently incomplete nature of the current understanding of chimpanzee gene flow in equatorial Africa, it seems reasonable to speculate that a chimpanzee population or populations may exist which both harbour the putative HIV-1 ancestor, and which have remained reproductively isolated from other chimpanzee populations over the time-scale relevant to the evolution of the SIVcpz-HIV-1 complex of viruses. Continued extensive sampling of wild chimpanzee populations, both for their genes and their viruses, should be performed quickly considering the high probability of extinction that many wild chimpanzee populations face today. The history of human-chimpanzee contacts is discussed.     

Blood groups in the species survival plan®, European endangered species program,and managed in situ populations of bonobo (Pan paniscus), common chimpanzee (Pan troglodytes), gorilla (Gorilla ssp.), and orangutan (Pongo pygmaeus ssp.)

Blood groups of humans and great apes have long been considered similar, although they are not interchangeable between species. In this study, human monoclonal antibody technology was used to assign human ABO blood groups to whole blood samples from great apes housed in North American and European zoos and in situ managed populations, as a practical means to assist blood transfusion situations for these species. From a subset of each of the species (bonobo, common chimpanzee, gorilla, and orangutans), DNA sequence analysis was performed to determine blood group genotype. Bonobo and common chimpanzee populations were predominantly group A, which concurred with historic literature and was confirmed by genotyping. In agreement with historic literature, a smaller number of the common chimpanzees sampled were group O, although this O blood group was more often present in wild‐origin animals as compared with zoo‐born animals. Gorilla blood groups were inconclusive by monoclonal antibody techniques, and genetic studies were inconsistent with any known human blood group. As the genus and, specifically, the Bornean species, orangutans were identified with all human blood groups, including O, which had not been reported previously. Following this study, it was concluded that blood groups of bonobo, common chimpanzees, and some orangutans can be reliably assessed by human monoclonal antibody technology. However, this technique was not reliable for gorilla or orangutans other than those with blood group A. Even in those species with reliable blood group detection, blood transfusion preparation must include cross‐matching to minimize adverse reactions for the patient. Zoo Biol 30:427–444, 2011. © 2010 Wiley‐Liss, Inc.     

Genetic and ‘cultural’ similarity in wild chimpanzees

The question of whether animals possess ‘cultures’ or ‘traditions’ continues to generate widespread theoretical and empirical interest. Studies of wild chimpanzees have featured prominently in this discussion, as the dominant approach used to identify culture in wild animals was first applied to them. This procedure, the ‘method of exclusion,’ begins by documenting behavioural differences between groups and then infers the existence of culture by eliminating ecological explanations for their occurrence. The validity of this approach has been questioned because genetic differences between groups have not explicitly been ruled out as a factor contributing to between-group differences in behaviour. Here we investigate this issue directly by analysing genetic and behavioural data from nine groups of wild chimpanzees. We find that the overall levels of genetic and behavioural dissimilarity between groups are highly and statistically significantly correlated. Additional analyses show that only a very small number of behaviours vary between genetically similar groups, and that there is no obvious pattern as to which classes of behaviours (e.g. tool-use versus communicative) have a distribution that matches patterns of between-group genetic dissimilarity. These results indicate that genetic dissimilarity cannot be eliminated as playing a major role in generating group differences in chimpanzee behaviour.     

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.     

Understanding the classics: the unifying concepts of transgressive segregation,inbreeding depression and heterosis and their central relevance for crop breeding

Transgressive segregation and heterosis are the reasons that plant breeding works. Molecular explanations for both phenomena have been suggested and play a contributing role. However, it is often overlooked by molecular genetic researchers that transgressive segregation and heterosis are most simply explained by dispersion of favorable alleles. Therefore, advances in molecular biology will deliver the most impact on plant breeding when integrated with sources of heritable trait variation – and this will be best achieved within a quantitative genetics framework. An example of the power of quantitative approaches is the implementation of genomic selection, which has recently revolutionized animal breeding. Genomic selection is now being applied to both hybrid and inbred crops and is likely to be the major source of improvement in plant breeding practice over the next decade. Breeders’ ability to efficiently apply genomic selection methodologies is due to recent technology advances in genotyping and sequencing. Furthermore, targeted integration of additional molecular data (such as gene expression, gene copy number and methylation status) into genomic prediction models may increase their performance. In this review, we discuss and contextualize a suite of established quantitative genetics themes relating to hybrid vigour, transgressive segregation and their central relevance to plant breeding, with the aim of informing crop researchers outside of the quantitative genetics discipline of their relevance and importance to crop improvement. Better understanding between molecular and quantitative disciplines will increase the potential for further improvements in plant breeding methodologies and so help underpin future food security.     

The genetic demography of a chimpanzee colony

Chimpanzees used for biomedical research must be bred in captivity because of restrictions on importation. Because they are large and expensive animals, population sizes at breeding facilities are limited. This implies that inbreeding at some level is inevitable and that genetic management techniques should be employed to minimize matings between related individuals. The purpose of this paper is to consider the genetic history of the chimpanzee colony at the Southwest Foundation for Biomedical Research (SFBR) and to suggest ways in which genetic variability may be affected by management schemes. A total of 339 chimpanzees resided at SFBR between January, 1980, and January, 1990. Although only one mating between related individuals has occurred so far, the average level of kinship in the colony and between potential breeders is increasing. Population structure techniques were employed to assess the mating patterns which have occurred and to explore the degree of change in the characteristics of potential mates. A “gene dropping” simulation method was used to predict expected levels of heterozygosity and strategies for maintaining variability by increasing the breeding portion of the population were evaluated using a simulation approach. © 1995 Wiley-Liss, Inc.     

Hematologic and serum biochemical reference intervals for the chimpanzee (Pan troglodytes) categorized by age and sex

Normal reference range intervals for hematologic and serum biochemical values in the chimpanzee (Pan troglodytes) have seldom been reported. The few studies that have been conducted either report values on the basis of a small number of animals, report values for all age groups or both sexes combined, or were designed specifically to document the effect of a particular condition on the normal range of hematologic and serum biochemical values. On the basis of data collected from 133 chimpanzees over a 17-year period, empirically based clinical reference ranges were derived to provide a guide for basic diagnostic and clinical care of chimpanzees. For either sex within each of four age groups, there is a table that summarizes serum biochemical and a table that summarizes hematologic values. These values are compared with prior values, and their importance in the care and well being of captive chimpanzee populations is discussed.     

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.     

Genetic research with nonhuman primates: serving the needs of mankind Symposium summary and future prospects

The wide array of papers delivered at this symposium, ranging from population genetics to molecular genetics, is convincing evidence that genetic research with nonhuman primates is in full bloom. In fact, progress has been quite remarkable considering that a significant number of pedigreed colonies of nonhuman primates have been available for less than 25 years, which is hardly enough time to raise 3 generations of chimpanzees, 5 generations of baboons or 6 generations of rhesus monkeys. Were it not for these pedigreed colonies, we would not have been privileged to have this assemblage of papers on behavior, social structure, predisposition to disease and management of breeding colonies. It is indeed exciting that preliminary evidence has been obtained for major genes that play a role in susceptibility to dyslipoproteinemias in baboons, and that monoclonal antibodies and DNA markers are helping us to understand cholesterol metabolism. And thanks to computers, we can now rank animals in a colony in terms of their useful genotypes as well as their productivity. One can not help but be impressed with the commonality of humans and nonhuman primates at the structural and functional levels. For example, the major histocompatibility systems and the maternal-fetal relationships are very similar. We heard that this similarity is even more striking at the chromosomal, biochemical and DNA levels. A provocative question yet to be answered is, “what accounts for the obvious differences between humans and nonhuman primates in view of these incredible similarities?” In light of these advances, this symposium was at the cutting edge of primate genetics and the papers published in this issue of Genetica are certain to be hallmarks in the literature.     

Chimpanzee tool technology in the Goualougo Triangle, Republic of Congo

With the exception of humans, chimpanzees show the most diverse and complex tool-using repertoires of all extant species. Specific tool repertoires differ between wild chimpanzee populations, but no apparent genetic or environmental factors have emerged as definitive forces shaping variation between populations. However, identification of such patterns has likely been hindered by a lack of information from chimpanzee taxa residing in central Africa. We report our observations of the technological system of chimpanzees in the Goualougo Triangle, located in the Republic of Congo, which is the first study to compile a complete tool repertoire from the Lower Guinean subspecies of chimpanzee (Pan troglodytes troglodytes). Between 1999 and 2006, we documented the tool use of chimpanzees by direct observations, remote video monitoring, and collections of tool assemblages. We observed 22 different types of tool behavior, almost half of which were habitual (shown repeatedly by several individuals) or customary (shown by most members of at least one age-sex class). Several behaviors considered universals among chimpanzees were confirmed in this population, but we also report the first observations of known individuals using tools to perforate termite nests, puncture termite nests, pound for honey, and use leafy twigs for rain cover. Tool behavior in this chimpanzee population ranged from simple tasks to hierarchical sequences. We report three different tool sets and a high degree of tool-material selectivity for particular tasks, which are otherwise rare in wild chimpanzees. Chimpanzees in the Goualougo Triangle are shown to have one of the largest and most complex tool repertoires reported in wild chimpanzee populations. We highlight new insights from this chimpanzee population to our understanding of ape technological systems and evolutionary models of tool-using behavior.     

The quantitative genetics of the prevalence of infectious diseases: hidden genetic variation due to indirect genetic effects dominates heritable variation and response to selection

Infectious diseases have profound effects on life, both in nature and agriculture. However, a quantitative genetic theory of the host population for the endemic prevalence of infectious diseases is almost entirely lacking. While several studies have demonstrated the relevance of transmission of infections for heritable variation and response to selection, current quantitative genetics ignores transmission. Thus, we lack concepts of breeding value and heritable variation for endemic prevalence, and poorly understand response of endemic prevalence to selection. Here, we integrate quantitative genetics and epidemiology, and propose a quantitative genetic theory for the basic reproduction number R₀ and for the endemic prevalence of an infection. We first identify the genetic factors that determine the prevalence. Subsequently, we investigate the population-level consequences of individual genetic variation, for both R0 and the endemic prevalence. Next, we present expressions for the breeding value and heritable variation, for endemic prevalence and individual binary disease status, and show that these depend strongly on the prevalence. Results show that heritable variation for endemic prevalence is substantially greater than currently believed, and increases strongly when prevalence decreases, while heritability of disease status approaches zero. As a consequence, response of the endemic prevalence to selection for lower disease status accelerates considerably when prevalence decreases, in contrast to classical predictions. Finally, we show that most heritable variation for the endemic prevalence is hidden in indirect genetic effects, suggesting a key role for kin-group selection in the evolutionary history of current populations and for genetic improvement in animals and plants.     

Analysis of hematologic findings in healthy and sick adult chimpanzees (Pan troglodytes)

In order to assess the validity of interspecies extrapolation of hematological information, reference values obtained on 63 captive adult chimpanzees were compared with normal values for man. The discriminative power of both chimpanzee and human reference values was tested by the ability of each to identify abnormalities in the blood in 15 sick chimpanzees. The results indicated that human criteria could be applied to most chimpanzee red cell values but species differences were found in erythrocyte sedimentation rates and neutrophil counts.     

Muscle architecture of the common chimpanzee (Pan troglodytes): perspectives for investigating chimpanzee behavior

Thorpe et al. (Am J Phys Anthropol 110:179–199, 1999) quantified chimpanzee (Pan troglodytes) muscle architecture and joint moment arms to determine whether they functionally compensated for structural differences between chimpanzees and humans. They observed enough distinction to conclude that musculoskeletal properties were not compensatory and suggested that chimpanzees and humans do not exhibit dynamically similar movements. These investigators based their assessment on unilateral limb musculatures from three male chimpanzees, of which they called one non-adult representative. Factors such as age, sex, and behavioral lateralization may be responsible for variation in chimpanzee muscle architecture, but this is presently unknown. While the full extent of variation in chimpanzee muscle architecture due to such factors cannot be evaluated with data presently available, the present study expands the chimpanzee dataset and provides a preliminary glimpse of the potential relevance of these factors. Thirty-seven forelimb and 36 hind limb muscles were assessed in two chimpanzee cadavers: one unilaterally (right limbs), and one bilaterally. Mass, fiber length, and physiological cross-sectional area (PCSA) are reported for individual muscles and muscle groups. The musculature of an adult female is more similar in architectural patterns to a young male chimpanzee than to humans, particularly when comparing muscle groups. Age- and sex-related intraspecific differences do not obscure chimpanzee-human interspecific differences. Side asymmetry in one chimpanzee, despite consistent forelimb directional asymmetry, also does not exceed the magnitude of chimpanzee-human differences. Left forelimb muscles, on average, usually had higher masses and longer fiber lengths than right, while right forelimb muscles, on average, usually had greater PCSAs than left. Most muscle groups from the left forelimb exhibited greater masses than right groups, but group asymmetry was significant only for the manual digital muscles. The hind limb exhibited less asymmetry than the forelimb in most comparisons. Examination of additional chimpanzees would clarify the full range of inter- and intra-individual variation.     

Fifty years of chimpanzee demography at Taronga Park Zoo

There has been a captive Pan troglodytes colony at Taronga Park Zoo in Sydney, Australia, since the mid-1930s. Demographic data on these animals were first analyzed in 1986; however, further information collected for 15 years since then is now available. The reproductive histories of 33 females in the colony have been recorded, and these data form the largest collection of captive chimpanzee data from a setting that has involved natural breeding conditions since the mid-1960s. These data were analyzed in conjunction with data from wild populations to establish the degree of variability present within chimpanzee reproductive parameters, and to identify which distinctive life history characteristics persist in well-provisioned, natural-fertility populations. The age at first birth for the chimpanzee females is 9.8 yr on average (n=16), which is 1-4.8 yr earlier than the average for wild populations. In line with this accelerated reproduction, birth intervals are also significantly shorter than those in noncaptive chimpanzee populations. The median birth interval for all surviving infants (based on a Kaplan-Meier survival analysis) is 49 months (n=43) compared to 62+ months for wild groups. At the same time, infant mortality remains high. The data confirm distinctive features of the life history of common chimpanzees, including later maturation, long birth intervals, a relatively invariant fertility schedule, and high juvenile mortality. However, aspects of both fertility and mortality are significantly related to social circumstances, indicating that in common chimpanzees, as in humans, life history characters may represent ecological and social adaptations rather than species-fixed characteristics.     

Polymorphic microsatellite DNA amplification customized for chimpanzee paternity testing

DNA segments containing GT/AC dinucleotide repeats in the chimpanzee (Pan troglodytes) genome were screened. Thirteen transformedE. coli colonies were identified with the (GT)₁₀ probe to have chimpanzee DNA fragments containing (GT)_n repeats. These potentially polymorphic (variable n) DNA segments were sequenced. Primers for the polymerase chain reaction (PCR) amplifying these DNA segments were designed. Six pairs of primers yielded polymorphic PCR products. Three of them revealed considerable length polymorphisms and heterozygosities in a group of captive chimpanzees. For studies on chimpanzees in the wild and in captivity, these primers should be useful for paternity testing, for investigating genetic variations, and for improving the genetic maintenance of breeding colonies. The strategy adopted in the present study to obtain PCR primers amplifying polymorphic microsatellite DNA segments may well be applicable to almost all eukaryotic organisms.     

A chimpanzee-passaged human immunodeficiency virus isolate is cytopathic for chimpanzee cells but does not induce disease.

The human immunodeficiency virus type 1 (HIV-1) readily infects both humans and chimpanzees, but the pathologic outcomes of infection in these two species differ greatly. In attempts to identify virus-cell interactions that might account for this differential pathogenicity, chimpanzee peripheral blood lymphocytes and bone marrow macrophages were assessed in vitro for their ability to support the replication of several HIV-1 isolates. Although the IIIb, RF, and MN isolates did not readily infect chimpanzee peripheral blood lymphocytes, an isolate of HIV-1 passaged in vivo in chimpanzees not only replicated well in both chimpanzee peripheral blood lymphocytes and bone marrow macrophages but also was cytopathic for chimpanzee CD4+ lymphocytes. Because no evidence of HIV-induced disease has been observed in chimpanzees infected with this isolate, in vitro replication to high titers with concomitant loss of CD4+ cells is not, in this instance, a correlate of pathogenicity. These observations, therefore, indicate that caution must be used when making extrapolations from in vitro data to in vivo pathogenesis.     

Census and distribution of chimpanzees in Côte D’Ivoire

Most methods of estimating chimpanzee population densities rely on nest counts. We tested the most frequently used techniques on a known chimpanzee community living in the rainforest of the Taï National Park, Côte d’Ivoire. The best density estimates are given by counts that assume groups of nests to be distributed randomly and that use the mean group size for homogenous habitat but the median for heterogenous habitats. Correction for real forest cover within the region should be made because chimpanzees make nests only in forested regions. This method gave the exact chimpanzee density for the Taï population, i.e. 1.7 nest builders/km². For the nationwide survey, we first estimated the chimpanzee density for different types of habitat (e.g. intact primary forest: 1.64 chimpanzees/km²; degraded forests: 0.4 chimpanzees/km²; human encroached forests and mosaic habitats: 0.09 chimpanzees/km²). Second, we estimated the total forest cover of the country with satellite pictures. This gave an estimated chimpanzee population in Côte d’Ivoire of about 11,676 ± 1,168 individuals, which equals the number of spectators at a soccer game in an average European town. Sadly, only three National Parks may have chimpanzee populations large enough to be viable, whereas the rest are scattered and isolated small populations that are already threatened in their survival.