Linda Vigilant

• Max Planck Institute for Evolutionary Anthropology

How populations adapt to their environment is a fundamental question in biology. Yet, we know surprisingly little about this process, especially for endangered species, such as nonhuman great apes. Chimpanzees, our closest living relatives, are particularly notable because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether...

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whet...

Reproductive inequality, or reproductive skew, drives natural selection, but has been difficult to assess, particularly for males in species with promiscuous mating and slow life histories, such as bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Although bonobos are often portrayed as more egalitarian than chimpanzees, genetic studies hav...

Mechanisms of inheritance remain poorly defined for many fitness-mediating traits, especially in long-lived animals with protracted development. Using 6,123 urinary samples from 170 wild chimpanzees, we examined the contributions of genetics, non-genetic maternal effects, and shared community effects on variation in cortisol levels, an established...

We were contacted by a colleague following the publication of our paper, who made us aware of a potential bias introduced by our treatment of random intercepts in our statistical models. In our models of dyadic behavior, the assignment of an individual to the“ID1” versus “ID2” position in each row of data was determined alphabetically, as our targe...

The wide application of high-throughput DNA sequencing methods in the typing of human and non-human MHC genes since the last decade has boosted the generation of big data in immunogenetics, where the identification of thousands of alleles defined at very high resolution can now be used to investigate detailed molecular variation at the individual l...

Associating with kin provides individual benefits but requires that these relationships be detectable. In humans, facial phenotype matching might help assess paternity; however, evidence for it is mixed. In chimpanzees, concealing visual cues of paternity may be beneficial due to their promiscuous mating system and the considerable risk of infantic...

The ultimate payoff of behaviours depends not only on their direct impact on an individual, but also on the impact on their relatives. Local relatedness—the average relatedness of an individual to their social environment—therefore has profound effects on social and life history evolution. Recent work has begun to show that local relatedness has th...

Evolutionary theories predict that sibling relationships will reflect a complex balance of cooperative and competitive dynamics. In most mammals, dispersal and death patterns mean that sibling relationships occur in a relatively narrow window during development, and/or only with same-sex individuals. Besides humans, one notable exception are mounta...

Evolutionary theories predict that sibling relationships will reflect a complex balance of cooperative and competitive dynamics. In most mammals, dispersal and death patterns mean that sibling relationships occur in a relatively narrow window during development, and/or only with same-sex individuals. Besides humans, one notable exception are mounta...

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Afr...

A fine characterization of the HLA molecular profiles of populations from distinct origins and ethnical backgrounds is essential for both clinical issues in histocompatibility and transplantation and fundamental research in population and evolutionary genetics. Recent developments of high throughput sequencing technologies (including NGS) have allo...

Studies of the evolutionary relationships among gorilla populations using autosomal and mitochondrial sequences suggest that male-mediated gene flow may have been important in the past, but data on the Y-chromosomal relationships among the gorilla subspecies are limited. Here, we genotyped blood and noninvasively collected fecal samples from 12 cap...

Paleoclimate reconstructions have enhanced our understanding of how past climates have shaped present-day biodiversity. We hypothesize that the geographic extent of Pleistocene forest refugia and suitable habitat fluctuated significantly in time during the late Quaternary for chimpanzees (Pan troglodytes). Using bioclimatic variables representing m...

Glucocorticoids, such as cortisol, mediate homeostatic processes, allowing individuals to adjust to fluctuating environments. The regulation of circadian cortisol responses, a key homeostatic function, has been shown to be heritable. However, to understand better the role of parental care in shaping physiological functioning in long-lived mammals w...

Extended breeding bonds and direct paternal care are rare in group-living species with high levels of male–male competition. In polygynandrously mating savannah baboons, many males form close ties (primary associations) to certain females outside the mating context. These relationships have likely evolved as a form of male parenting effort because...

Like many animals, adult male chimpanzees often compete for a limited number of mates. They fight other males as they strive for status that confers reproductive benefits and use aggression to coerce females to mate with them. Nevertheless, small-bodied, socially immature adolescent male chimpanzees, who cannot compete with older males for status n...

Humans are unusual among animals for continuing to provision and care for their offspring until adulthood. This "prolonged dependency" is considered key for the evolution of other notable human traits, such as large brains, complex societies, and extended postreproductive lifespans. Prolonged dependency must therefore have evolved under conditions...

Across vertebrates, species with intense male mating competition and high levels of sexual dimorphism in body size generally exhibit dimorphism in age-specific fertility. Compared with females, males show later ages at first reproduction and earlier reproductive senescence because they take longer to attain adult body size and musculature, and main...

Social rank is positively correlated with reproductive success in numerous species, albeit demographic factors often influence those patterns. In multimale primate species, reproductive skew tends to decrease with increasing numbers of males and sexually receptive females. Alpha male chimpanzees (Pan troglodytes) often sire a disproportionate, thou...

Aim Paleoclimate reconstructions have enhanced our understanding of how past climates may have shaped present-day biodiversity. We hypothesize that habitat stability in historical Afrotropical refugia played a major role in the habitat suitability and persistence of chimpanzees ( Pan troglodytes ) during the late Quaternary. We aimed to build a dyn...

In polygynous and polygynandrous species, there is often intense male-male competition over access to females, high male reproductive skew, and more male investment in mating effort than parenting effort [1]. However, the benefits derived from mating effort and parenting effort may change over the course of males’ lives. In many mammalian species,...

The major histocompatibility complex (MHC) is central to the innate and adaptive immune responses of jawed vertebrates. Characteristic of the MHC are high gene density, gene copy number variation, and allelic polymorphism. Because apes and monkeys are the closest living relatives of humans, the MHCs of these non-human primates (NHP) are studied in...

The original version of this article contained a spelling error in the Acknowledgments regarding the name of the funding organisation supporting GM and JAH. UKRI-BBSCR should have been UKRI-BBSRC, as is now indicated correctly below.

Monitoring population size and growth over time is vital for the conservation of endangered species. Mountain gorillas Gorilla beringei beringei remain in two small populations that span the borders of the Democratic Republic of Congo, Rwanda and Uganda. Each population contains two subpopulations that receive differing levels of protection: the mo...

Background: The highly polymorphic genes of the major histocompatibility complex (MHC) class I are involved in defense against viruses and other intracellular pathogens. Although several studies found reduced MHC class I diversity in bonobos in comparison to the closely related chimpanzee, it is unclear if this lower diversity also influences the...

Genetic estimation of population sizes has been critical for monitoring cryptic and rare species; however, population estimates do not inherently reveal the permanence or stability of the population under study. Thus, it is important to monitor not only the number of individuals in a population, but also how they are associated in groups and how th...

The Chimpanzees of the Taï Forest - edited by Christophe Boesch November 2019

The major histocompatibility complex (MHC) class I genes play a critical role within the immune system, both by the presentation of antigens from intracellular pathogens to immunocompetent cells and by the interaction with killer cell immunoglobulin-like receptors (KIR) on natural killer cells (NK cells). Genes of the MHC are highly diverse, and MH...

In many group-living mammals, mothers may increase the reproductive success of their daughters even after they are nutritionally independent and fully grown [1]. However, whether such maternal effects exist for adult sons is largely unknown. Here we show that males have higher paternity success when their mother is living in the group at the time o...

Although infanticide by wild adult male chimpanzees has been reported from multiple sites, affiliative infant carrying by males is rare. We observed infant carrying by an alpha male chimpanzee at Bulindi (Uganda) on two consecutive mornings and collected faecal samples from the newborn infant female, her mother and all candidate fathers to determin...

Dispersal is a key event in the life of an animal and it influences individual reproductive success. Male mountain gorillas exhibit both philopatry and dispersal, resulting in a mixed one-male and multimale social organization. However, little is known about the relationship between male dispersal or philopatry and reproductive careers in Bwindi mo...

The selective advantage of male infanticide is enhancement of reproductive success of the aggressor. This implies that aggression is directed at individuals sired by others, infant loss shortens the mother's inter‐birth interval, and the aggressor has a greater likelihood of siring the next offspring of the victims’ mother. As these conditions are...

Long-term maleefemale bonds and bi-parental investment in offspring are hallmarks of human society. A key question is how these traits evolved from the polygynandrously mating multimale multifemale society that likely characterized the Pan-Homo ancestor. In all three species of savanna baboons, lactating females form strong ties (sometimes called "...

Large‐scale genomic studies of wild animal populations are often limited by access to high‐quality DNA. Although non‐invasive samples, such as feces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help overcome th...

Socioecological theory predicts that male parenting among mammals should be rare due to the large payoffs of prioritizing mating effort over parenting. Although these predictions are generally met, in some promiscuous primate species males overcome this by identifying their offspring, and providing benefits such as protection and resource access. M...

Habitat fragmentation is a leading threat to global biodiversity. Dispersal plays a key role in gene flow and population viability, but the impact of fragmentation on dispersal patterns remains poorly understood. Among chimpanzees, males typically remain in their natal communities while females often disperse. However, habitat loss and fragmentatio...

The social organization of a group‐living animal is defined by a balance between group dynamic events such as group formation, group dissolution, and dispersal events and group stability in membership and over time. Understanding these processes, which are relevant for questions ranging from disease transmission patterns to the evolution of polygyn...

In comparison to humans and chimpanzees, gorillas show low diversity at MHC class I genes (Gogo), as reflected by an overall reduced level of allelic variation as well as the absence of a functionally important sequence motif that interacts with killer cell immunoglobulin-like receptors (KIR). Here, we use recently generated large-scale genomic seq...

Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accurac...

Objectives: The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmente...

Target capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of non-invasive samples such as feces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution, and popul...

Major histocompatibility complex (MHC) class I genes are critically involved in the defense against intracellular pathogens. MHC diversity comparisons among samples of closely related taxa may reveal traces of past or ongoing selective processes. The bonobo and chimpanzee are the closest living evolutionary relatives of humans and last shared a com...

Vast, pristine ecosystems and their biodiversity are vanishing globally at frightening speed, but many large tracts of wilderness have not yet been systematically inventoried and important natural populations of threatened species remain poorly characterized. The forest-savanna ecotone of the Eastern Central African Republic (CAR) is one such poorl...

The two closest living relatives of humans, bonobos (Pan paniscus) and chimpanzees (Pan troglodytes), share many traits that are common in humans but rare in other mammals, including societies with high fission–fusion dynamics, male philopatry, female dispersal and extensive social bonding among unrelated individuals [1] . The major difference betw...

Significance Many animals, especially humans, carry out activities collectively because the benefits of doing so exceed those that can be achieved individually. But how can collective action evolve when individuals receive the benefits of cooperation regardless of whether they pay the costs of participation? Collective action may be especially diff...

Comparisons of MHC gene content and diversity among closely related species can provide insights into the evolutionary mechanisms shaping immune system variation. After chimpanzees and bonobos, gorillas are humans’ closest living relatives; but in contrast, relatively little is known about the structure and variation of gorilla MHC class I genes (G...

Objectives: Female bonobos (Pan paniscus) are characterized as highly affiliative and cooperative, but few studies have quantified the strength and stability of female intra-sexual relationships or explored how variation in social relationships influences cooperation. We measure female social preferences, identify causes of variation in preference...

Genetic capture-recapture (CR) estimates of population size have potential for aiding the conservation and management of rare or elusive animals. To date, few studies have explored the performance of genetic CR estimates by implementing them in a population of known size. We evaluated the accuracy and precision of genetic CR estimates by genotyping...

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. M...

Of chimpanzees and bonobos Modern non-African human genomes contain genomic remnants that suggest that there was interbreeding between ancient humans and archaic hominoid lineages. Now, de Manuel et al. show similar ancestral interbreeding between the ancestors of today's chimpanzees and bonobos (see the Perspective by Hoelzel). The study also prov...

Documenting inbreeding and its potential costs in wild populations is a complicated matter. Early infant death before genetic samples can be collected limits the ability of researchers to measure fitness costs, and pedigree information is necessary to accurately estimate relatedness between breeding individuals. Using data from 25 years of research...

Knowledge of kin relationships between members of wild animal populations has broad application in ecology and evolution research by allowing the investigation of dispersal dynamics, mating systems, inbreeding avoidance, kin recognition , and kin selection as well as aiding the management of endangered populations. However, the assessment of kinshi...

Table S1. Numbers of microsatellites (STRs) and single‐nucleotide polymorphisms (SNPs) with equal power for kinship analyses.

The ability to recognize kin has important impacts on fitness because it can allow for kin-biased affiliative behaviours and avoidance of mating with close kin. While the presence and effects of kin biases have been widely studied, less is known about the process by which animals recognize close kin. Here we investigate potential cues that white-fa...

Sexually selected infanticide is an important source of infant mortality in many mammalian species. In species with long-term male-female associations, females may benefit from male protection against infanticidal outsiders. We tested whether mountain gorilla (Gorilla beringei beringei) mothers in single and multi-male groups monitored by the Dian...

Confiscated and displaced mammals are often taken to sanctuaries, where the explicit goal may be reintroduction to the wild. By inadvertently collecting animals from different source populations, however, such efforts risk reintroducing individuals that have not been in genetic contact for significant periods of time. Using genetic analyses and 44...

In many social animals, individuals derive fitness benefits from close social bonds, which are often formed among kin of the philopatric sex. Hamadryas baboons, however, exhibit a hierarchical, multilevel social system where both sexes disperse from their natal one-male-unit (OMU). Although this would seem to hinder maintenance of kin ties, both se...

Model output for dyads containing non-dominant males. Model main effects and interaction terms for the outcome variables: proportion of point samples in close proximity; rate of female approaches to males; rate of females leaving males; percent time spent resting in contact; percent time spent grooming; and following rates, for dyads containing non...

Unlike most mammals, male orang-utans exhibit bimaturism, in that mature individuals express one of two distinct morphological forms. Socially subordinate, ‘unflanged’ males are comparable to females in their size and facial morphology, while socially dominant ‘flanged’ males exhibit extreme sexual dimorphism and secondary sexual characteristics, p...

As habitat degradation and fragmentation continue to impact wildlife populations around the world, it is critical to understand the behavioral flexibility of species in these environments. In Uganda, the mostly unprotected forest fragment landscape between the Budongo and Bugoma Forests is a potential corridor for chimpanzees, yet little is known a...

Genes encoded by the major histocompatibility complex (MHC) are crucial for the recognition and presentation of antigens to the immune system. In contrast to their closest relatives, chimpanzees and humans, much less is known about variation in gorillas at these loci. This study explored the exon 2 variation of -DPB1, -DQB1, and -DRB genes in 46 go...

As in other highly sexually dimorphic, group-living animals, reproduction in gorillas has been largely viewed as the outcome of competition among males. However, females may exert choice via dispersal decisions or choice of partner in multimale groups, and males may also mate selectively. Here, we examine the paternity of 79 wild mountain gorilla o...

Kin discrimination mechanisms are expected to evolve when they provide fitness benefits. To date, evidence for kin discrimination is mixed across taxa and mating systems even when it would apparently be beneficial. In animals with promiscuous mating systems, males were long believed to abstain from parenting behaviours partly because the costs of o...

Gorillas, like all non-human great apes, are endangered. Understanding the distribution of genetic diversity across their range is important because low diversity may arise in small populations through increased inbreeding, and, by reducing reproductive fitness, may lead to decreased chances of persistence of a given population. Previous studies fo...

Socioecological models predict that as resources become more sparsely distributed, primate populations will occur at lower densities and this demographic shift may have some effect on social structure. In savanna-woodland habitats, chimpanzees live at lower densities and in larger home ranges compared to forested habitats, presumably because of mor...

Population estimates using genetic capture-recapture methods from non-invasively collected wildlife samples are more accurate and precise than those obtained from traditional methods when detection and resampling rates are high. Recently, detection dogs have been increasingly used to find elusive species and their by-products. Here we compared the...

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),...

Dispersal and grouping patterns form the foundations of social interactions in group-living mammals and are the outcomes of a complex interplay between inbreeding avoidance, kin cooperation and competition, predation pressure and food resource distribution. In species where both sexes disperse, the potential for kin-biased associations would seem l...

Compared with other African apes, eastern gorillas (Gorilla beringei) have been little studied genetically. We used analysis of autosomal DNA genotypes obtained from non-invasively collected faecal samples to estimate the evolutionary histories of the two extant mountain gorilla populations and the closely related eastern lowland gorillas. Our resu...