Pan Troglodytes Schweinfurthii Research Articles

Hunting of mammals by central chimpanzees (Pan troglodytes troglodytes) in the Loango National Park, Gabon

The predation and consumption of animals are common behaviours in chimpanzees across tropical Africa. To date, however, relatively little is known concerning the hunting behaviour of central chimpanzees (Pan troglodytes troglodytes). Here, we provide the first direct observations of hunting behaviour by individuals of the newly habituated Rekambo community in the Loango National Park, Gabon. Over a period of 23 months (May 2017 to March 2019), we observed a total of 61 predation attempts on eight mammal species, including four monkey species. The two most frequently hunted species were two monkey species (Cercocebus torquatus,Cercopithecus nictitans), which are not hunted at other long-term field sites. The majority of predation events observed involved parties of an average of eight individuals, mainly adult males, with hunting success being higher with increasing numbers of participants. Hunting occurred all year round, but hunting rates increased in the dry season, the period of high fruit availability in the Loango National Park. These results are in line with the nutrient surplus hypothesis which explains seasonal variation in hunting behaviour in several populations of eastern chimpanzees (Pan troglodytes schweinfurthii: e.g., Mahale, Tanzania; Ngogo, Uganda). Finally, with a hunting frequency of 2.65 hunts per month, the Rekambo community had higher hunting rates than other sites (Bossou, Republic of Guinea; Kahuzi-Biega, Democratic Republic of Congo; Budongo, Uganda) where red colobus monkeys are also absent. We discuss these results and compare them to patterns at other long-term sites.

Mountain Biodiversity Is Central to Sustainable Development in Mountains and Beyond

Rich biological diversity in mountains provides ample benefits to people locally and beyond. However, mountain biodiversity is decreasing rapidly, often as a result of geographically distant demands. We can achieve the transition to sustainable development only by accounting for the drivers and benefits of mountain biodiversity from a local to global level.

Urine as a high-quality source of host genomic DNA from wild populations.

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, for many species, it is impossible legally, ethically or logistically to obtain tissue samples of quality sufficient for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (faeces, urine, dentin and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbours significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as faeces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.

Demography, life-history trade-offs, and the gastrointestinal virome of wild chimpanzees.

In humans, senescence increases susceptibility to viral infection. However, comparative data on viral infection in free-living non-human primates-even in our closest living relatives, chimpanzees and bonobos (Pan troglodytes and P. paniscus)-are relatively scarce, thereby constraining an evolutionary understanding of age-related patterns of viral infection. We investigated a population of wild eastern chimpanzees (P. t. schweinfurthii), using metagenomics to characterize viromes (full viral communities) in the faeces of 42 sexually mature chimpanzees (22 males, 20 females) from the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We identified 12 viruses from at least four viral families possessing genomes of both single-stranded RNA and single-stranded DNA. Faecal viromes of both sexes varied with chimpanzee age, but viral richness increased with age only in males. This effect was largely due to three viruses, salivirus, porprismacovirus and chimpanzee stool-associated RNA virus (chisavirus), which occurred most frequently in samples from older males. This finding is consistent with the hypothesis that selection on males for early-life reproduction compromises investment in somatic maintenance, which has delayed consequences for health later in life, in this case reflected in viral infection and/or shedding. Faecal viromes are therefore useful for studying processes related to the divergent reproductive strategies of males and females, ageing, and sex differences in longevity. This article is part of the theme issue 'Evolution of the primate ageing process'.

The Relationship Between Tool Use and Prey Availability in Chimpanzees (Pan troglodytes schweinfurthii) of Northern Democratic Republic of Congo

A key feature of human behavioral diversity is that it can be constrained by cultural preference (“cultural override”); that is, population-specific preferences can override resource availability. Here we investigate whether a similar phenomenon can be found in one of our closest relatives, as well as the potential impacts of ecological differences on feeding behavior. Our study subjects were different subpopulations of Eastern chimpanzees (Pan troglodytes schweinfurthii) occupying two very different habitats, moist tropical lowland forests vs. moist tropical forest–savanna mosaic on opposite sides of a major river. Given differences in encounter rates of different kinds of tool sites on both sides of the Uele River, we predicted that these subpopulations would differ in their likelihood of using tools to prey on two insect species despite similar availability. In surveys conducted over a 9-year period at 19 different survey regions in northern Democratic Republic of Congo (10 in lowland forest and 9 in mosaic), we collected and analyzed data on chimpanzee tool-assisted exploitation of insects. To determine the availability of insect species eaten by the chimpanzees, we counted insects and their mounds on transects and recces at 12 of these sites. For stick tools used to harvest epigaeic Dorylus and ponerine ants, we evaluated seasonal, geographical, and prey-availability factors that might influence their occurrence, using nest encounter rate as a proxy to control for chimpanzee abundance. Across the 19 survey regions spanning both sides of the Uele, we found little difference in the availability of epigaeic Dorylus and ponerine ants. Despite this, tool encounter rates for epigaeic Dorylus, but not ponerine, ants were significantly higher in the mosaic to the north of the Uele. Furthermore, we found no evidence for termite fishing anywhere, despite the availability of Macrotermes mounds throughout the region and the fact that chimpanzees at a number of other study sites use tools to harvest these termites. Instead, the chimpanzees of this region used a novel percussive technique to harvest two other types of termites, Cubitermes sp. and Thoracotermes macrothorax. This mismatch between prey availability and predation is consistent with cultural override, but given the different habitats on the two sides of the Uele River, we cannot fully rule out the influence of ecological factors. Comparing our findings with those of similar studies of other chimpanzee populations promises to contribute to our understanding of the evolution of behavioral diversity in humans and our closest cousins.

Variation in Intergroup Relationships Among Species and Among and Within Local Populations of African Apes

Although many animals typically defend key resources from conspecifics during encounters, tolerant encounters also occur frequently in some primate species. For example, African apes and humans (Homininae) show large variation in terms of agonistic and affiliative intergroup relationships, and local human communities are formed via a network of affiliative relationships among groups. To understand this variation and its evolution, we need to examine the variation between species, between populations, and within populations. In the genus Pan, both eastern and western chimpanzees commonly express aggressive intergroup relationships, whereas intergroup relationships in bonobos are generally affiliative. In the genus Gorilla, although the proportions of groups with multiple males differ, all subspecies show large overlap of home ranges and both aggressive and affiliative intergroup interactions. Differences in intergroup relationships among local populations of the same (sub)species are limited in both Pan and Gorilla. In contrast, intergroup relationships vary within the same local populations in bonobos, with female dispersal among groups seemingly contributing to the affiliative relationships. Such tendencies in bonobos seem to resemble those in local human communities, where intergroup relationships differ for different combinations of groups and female dispersal among groups plays an important role in affiliative relationships. Intergroup relationships within the same local populations also vary from affiliative to aggressive in all subspecies of gorillas, and kin relations between leading males play important roles in affiliative relationships. Studies of variation in intergroup relationships, the contributions of males and females to such variation, and the genetic structure of local populations might increase our understanding of the evolutionary process underpinning local communities in Homininae.

A comparison of fecal sampling and direct feeding observations for quantifying the diet of a frugivorous primate.

Both observational and indirect evidence are widely used to determine the diets of wild animals. Direct observations are often assumed to provide the most comprehensive reflection of diet, but many wild animals are logistically challenging to observe. Despite the regular use of observational and indirect methods for inferring diet in wild animals, they have rarely been compared in detail for the same study population. Over 12 months this study assessed the congruence of methods in estimating the diet of a montane community of eastern chimpanzees Pan troglodytes schweinfurthii in Nyungwe National Park, Rwanda using observational scan samples and macroscopic fecal inspection. The assessment of the number of food species consumed each month was comparable between methods, but the estimation of the composition of items in the diet differed significantly. Most notably, the fecal samples significantly underestimated the consumption of flowers, and certain fruit species, which based on direct behavioral observations were seasonally consumed at very high rates. Conversely, direct observations underestimated the consumption of leaves and pith in comparison to results present in the fecal samples. These results suggest that combining methods where possible is most useful for accurate monitoring of dietary trends, particularly for species that experience significant seasonal shifts in their diet.

The impact of genetic adaptation on chimpanzee subspecies differentiation.

Chimpanzees, humans' closest relatives, are in danger of extinction. Aside from direct human impacts such as hunting and habitat destruction, a key threat is transmissible disease. As humans continue to encroach upon their habitats, which shrink in size and grow in density, the risk of inter-population and cross-species viral transmission increases, a point dramatically made in the reverse with the global HIV/AIDS pandemic. Inhabiting central Africa, the four subspecies of chimpanzees differ in demographic history and geographical range, and are likely differentially adapted to their particular local environments. To quantitatively explore genetic adaptation, we investigated the genic enrichment for SNPs highly differentiated between chimpanzee subspecies. Previous analyses of such patterns in human populations exhibited limited evidence of adaptation. In contrast, chimpanzees show evidence of recent positive selection, with differences among subspecies. Specifically, we observe strong evidence of recent selection in eastern chimpanzees, with highly differentiated SNPs being uniquely enriched in genic sites in a way that is expected under recent adaptation but not under neutral evolution or background selection. These sites are enriched for genes involved in immune responses to pathogens, and for genes inferred to differentiate the immune response to infection by simian immunodeficiency virus (SIV) in natural vs. non-natural host species. Conversely, central chimpanzees exhibit an enrichment of signatures of positive selection only at cytokine receptors, due to selective sweeps in CCR3, CCR9 and CXCR6 -paralogs of CCR5 and CXCR4, the two major receptors utilized by HIV to enter human cells. Thus, our results suggest that positive selection has contributed to the genetic and phenotypic differentiation of chimpanzee subspecies, and that viruses likely play a predominate role in this differentiation, with SIV being a likely selective agent. Interestingly, our results suggest that SIV has elicited distinctive adaptive responses in these two chimpanzee subspecies.

Differences in MHC-B diversity and KIR epitopes in two populations of wild chimpanzees

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 MHC variation can have effects on the immune functionality of individuals; hence, comparisons of MHC diversity among closely related phylogenetic taxa may give insight into the factors responsible for the shaping of its diversity. The four geographically separated chimpanzee subspecies differ in their overall genetic diversity, have different population histories, and are confronted with different pathogens in their natural habitat, all of which may affect MHC class I DNA sequence diversity. Here, we compare the MHC-B exon two DNA sequence diversity from 24 wild western and 46 wild eastern chimpanzees using necropsy and noninvasively collected fecal samples, respectively. We found a higher MHC-B exon two nucleotide diversity, in our western than eastern chimpanzees. The inclusion of previously published MHC-B exon two data from other western and eastern chimpanzees supported this finding. In addition, our results confirm and extend the finding of a very low C1 epitope frequency at eastern chimpanzee MHC-B molecules, which likely affects the ability of these molecules to interact with NK cells. While the understanding of the differing pathogen environments encountered by disparate populations of a species is a challenging endeavor, these findings highlight the potential for these pathogens to selectively shape immune system variation.

Camera traps provide a robust alternative to direct observations for constructing social networks of wild chimpanzees

Social network analysis provides valuable opportunities to quantify the nature of social relationships in animal societies including aspects of group structure, dynamics and behaviour transmission. Remote monitoring approaches such as camera trapping offer rich data sets from groups and species that are difficult to observe, yet the robustness of these data for constructing social networks remains unexplored. Here we compared networks of party association based on camera traps with those based on direct observations over the same 9-month sampling period in a group of habituated western chimpanzees, Pan troglodytes verus. Networks based on camera traps and direct observations were both stable with sufficient sampling, and had very similar structures, patterns of sex assortment and individual network positions. However, camera trap data led to lower estimates of group density and dyadic association strengths, and slightly higher modularity, illustrating the limitations raised by differences in data collection methods for network comparisons. We then constructed a social network using camera trap data from unhabituated eastern chimpanzees, P.t. schweinfurthii, demonstrating the feasibility of this approach in the absence of extensive prior knowledge of the study subjects. Further, differences between the eastern and western chimpanzee social networks followed expected patterns based on recognized social differences, illustrating the promise of this approach for detecting within-species social variation. Although long-term behavioural observations will continue to provide rich data for many species, camera traps offer a powerful alternative to gain information on social group dynamics in elusive or unhabituated animals, as well as to conduct systematic multisite comparative studies.

Intra-community infanticide in wild, eastern chimpanzees: a 24-year review

Infanticide is well documented in chimpanzees and various hypotheses have been proposed to explain this behavior. However, since infanticide by chimpanzees is relatively rare, it has thus far not been possible to thoroughly test these hypotheses. Here we present an analysis of the largest dataset of infanticides from a single community of chimpanzees, a full record of all intra-community infanticides and failed attempts at infanticide over a 24-year period for the Sonso community of chimpanzees in the Budongo Forest, Uganda. We use these data to test four hypotheses for this behavior: the sexual selection hypothesis, male mating competition, resource competition, and meat acquisition. Our dataset consisted of 33 attacks on 30 victims, 11 of which were ‘definite’ infanticides, four of which ‘almost certain’, and nine were ‘suspected’, while nine were ‘attempted’ infanticides. The majority of attacks where the perpetrators were known (23) had only male attackers and victims were disproportionately young (two-thirds of victims with known ages were under 1 week old). Our data best support the sexual selection hypothesis for infanticide. Cannibalism was infrequent and partial, suggesting meat acquisition was a by-product of infanticide, and there was no evidence to suggest that infanticide was part of a male strategy to eliminate future competitors. Infanticide by females was rare, but we suggest sexual selection, operating through intra-sexual competition, may also be responsible for infanticide by females.

Chimpanzee feeding ecology and fallback food use in the montane forest of Nyungwe National Park, Rwanda.

Almost all primates experience seasonal fluctuations in the availability of key food sources. However, the degree to which this fluctuation impacts foraging behavior varies considerably. Eastern chimpanzees (Pan troglodytes schweinfurthii) in Nyungwe National Park, Rwanda, live in a montane forest environment characterized by lower primary productivity and resource diversity than low-elevation forests. Little is known about chimpanzee feeding ecology in montane forests, and research to date predominantly relies on indirect methods such as fecal analyses. This study is the first to use mostly observational data to examine how seasonal food availability impacts the feeding ecology of montane forest chimpanzees. We examine seasonal changes in chimpanzee diet and fallback foods (FBFs) using instantaneous scan samples and fecal analyses, supported by inspection of feeding remains. Chimpanzee fruit abundance peaked during the major dry season, with a consequent change in chimpanzee diet reflecting the abundance and diversity of key fruit species. Terrestrial herbaceous vegetation was consumed throughout the year and is defined as a "filler" FBF. In contrast to studies conducted in lower-elevation chimpanzee sites, figs (especially Ficus lutea) were preferred resources, flowers were consumed at seasonally high rates and the proportion of non-fig fruits in the diet were relatively low in the current study. These divergences likely result from the comparatively low environmental diversity and productivity in higher-elevation environments.

Factors affecting species richness and distribution spatially and temporally within a protected area using multi‐season occupancy models

AbstractExploring trends in species richness and the distribution of individual species over time as well as the factors affecting these trends informs conservation priorities in protecting species and ecosystems as a whole. We used data from 41 park‐wide line transect surveys in 2009 and 2014 and multi‐season occupancy models with multi‐species data to explore trends in species richness and distribution of individual species and factors affecting these trends in Nyungwe National Park (NNP), Rwanda. Mammalian species richness and the distributional range of 5 of the 7 species increased between 2009 and 2014 in NNP. The probability of colonization of a species into a new area in 2014, where it was not present in 2009, was highest in sites with a lower probability of poaching activity, close to tourist trails, and at lower elevations. The probability of colonization with no poaching activity was about 50% but dropped to about 10% with a 100% chance of poaching activity. Duiker species had the largest increase in distribution during the study, while there was a decrease in the distribution of the eastern chimpanzee and blue monkey. Our results suggest that increased patrols could be implemented in areas of the park with low species richness and areas with a low probability of occurrence for species of conservation concern to combat poaching activity and thus increase the probability of a species moving into a new area. Our use of a single multi‐season model for multiple species explicitly accounts for imperfect detection and species‐specific identities, while allowing for inferences to be made about rarely detected species by sharing covariates with common species. These results can be used to improve conservation planning in NNP for species management and ranger patrol protocols, and our modelling framework is broadly applicable to any protected area with presence/absence species field data.

Food mechanical properties and isotopic signatures in forest versus savannah dwelling eastern chimpanzees

Chimpanzees are traditionally described as ripe fruit specialists with large incisors but relatively small postcanine teeth, adhering to a somewhat narrow dietary niche. Field observations and isotopic analyses suggest that environmental conditions greatly affect habitat resource utilisation by chimpanzee populations. Here we combine measures of dietary mechanics with stable isotope signatures from eastern chimpanzees living in tropical forest (Ngogo, Uganda) and savannah woodland (Issa Valley, Tanzania). We show that foods at Issa can present a considerable mechanical challenge, most saliently in the external tissues of savannah woodland plants compared to their tropical forest equivalents. This pattern is concurrent with different isotopic signatures between sites. These findings demonstrate that chimpanzee foods in some habitats are mechanically more demanding than previously thought, elucidating the broader evolutionary constraints acting on chimpanzee dental morphology. Similarly, these data can help clarify the dietary mechanical landscape of extinct hominins often overlooked by broad C3/C4 isotopic categories.

Shifting through the forest: home range, movement patterns, and diet of the eastern chimpanzee (Pan troglodytes schweinfurthii) in Nyungwe National Park, Rwanda.

Populations of the endangered eastern chimpanzee (Pan troglodytes schweinfurthii) are declining throughout their range. Although Nyungwe National Park (NNP) harbors the largest remaining eastern chimpanzee population in Rwanda, we know little about their space use and dietary patterns. We studied home range, movement, and diet of two communities of chimpanzees in NNP using daily tracking data (6:00 am to 6:00 pm) collected from 2000 to 2015. One community, Mayebe, resided in the forest center, and the other community, Cyamudongo, inhabited a forest fragment located about 10 km from the main forest. Home range estimated with the 95% kernel density estimation (KDE) method was 21 km2 for the Mayebe community and 4 km2 for the Cyamudongo community. Chimpanzee home range sizes were smaller during the dry versus wet season and varied monthly throughout the year. The Mayebe community had an average hourly step length of 75 ± SE 5 m with a daily movement range of 987 ± SE 71 m, while the Cyamudongo community had a shorter hourly step length of 52 ± SE 3 m with a daily movement range of 651 ± SE 71 m. Both chimpanzee communities fed primarily on Ficus spp. Other important dietary items included fruits of Symphonia globulifera, Syzygium guineense, and Chrysophyllum gorungosanum for the Mayebe community and Trilepisium madagascariense for the Cyamudongo community. Food choice varied monthly and seasonally for each chimpanzee community. Our study provides the first estimates of home range size and movement parameters for chimpanzees in Rwanda and documents their food habits and seasonal variations therein. We also identified the 50% core home range for each chimpanzee community and suggest this area as the focus of management actions. These results could help park management reduce threats to chimpanzees and other sympatric species by improving the efficiency of ranger patrols.

Morphological Identification of Hair Recovered from Feces for Detection of Cannibalism in Eastern Chimpanzees

Chimpanzees (Pan troglodytes) are primarily frugivorous but consume a variable amount of meat from a variety of organisms, including other chimpanzees. Cannibalism is rare, usually follows lethal aggression, and does not occur following natural deaths. While chimpanzee cannibalism has been documented at multiple sites, many instances of this behavior go unrecorded. Identification of chimpanzee remains in feces, however, can provide indirect evidence of cannibalism. Hair, in particular, typically passes through the gastrointestinal tract undamaged and is commonly used for purposes of identification in wildlife forensics. Here we test the hypothesis that eastern chimpanzee (Pan troglodytes schweinfurthii) guard hair morphology can be reliably distinguished from the hairs of their most common prey species. Methods and results are presented in the context of a case study involving a suspected chimpanzee infanticide from Gombe, Tanzania. We find that chimpanzee guard hair morphology is unique among tested mammals and that the presence of abundant chimpanzee hair in feces is likely the result of cannibalism and not incidental ingestion from grooming or other means. Accordingly, morphological analysis of guard hairs from feces is a promising, cost-effective tool for the determination of cannibalistic acts in chimpanzees.

Selection in the Introgressed Regions of the Chimpanzee Genome.

During the demographic history of the Pan clade, there has been gene-flow between species, likely >200,000 years ago. Bonobo haplotypes in three subspecies of chimpanzee have been identified to be segregating in modern-day chimpanzee populations, suggesting that these haplotypes, with increased differentiation, may be a target of natural selection. Here, we investigate signatures of adaptive introgression within the bonobo-like haplotypes in chimpanzees using site frequency spectrum-based tests. We find evidence for subspecies-specific adaptations in introgressed regions involved with male reproduction in central chimpanzees, the immune system in eastern chimpanzees, female reproduction and the nervous system in Nigeria-Cameroon chimpanzees. Furthermore, our results indicate signatures of balancing selection in some of the putatively introgressed regions. This might be the product of long-term balancing selection resulting in a similar genomic signature as introgression, or possibly balancing selection acting on alleles reintroduced through gene flow.

Personality in the chimpanzees of Gombe National Park

Researchers increasingly view animal personality traits as products of natural selection. We present data that describe the personalities of 128 eastern chimpanzees (Pan troglodytes schweinfurthii) currently living in or who lived their lives in the Kasekela and Mitumba communities of Gombe National Park, Tanzania. We obtained ratings on 24 items from an established, reliable, well-validated questionnaire used to study personality in captive chimpanzee populations. Ratings were made by former and present Tanzanian field assistants who followed individual chimpanzees for years and collected detailed behavioral observations. Interrater reliabilities across items ranged from acceptable to good, but the personality dimensions they formed were not as interpretable as those from captive samples. However, the personality dimensions corresponded to ratings of 24 Kasekela chimpanzees on a different questionnaire in 1973 that assessed some similar traits. These correlations established the repeatability and construct validity of the present ratings, indicating that the present data can facilitate historical and prospective studies that will lead to better understanding of the evolution of personality in chimpanzees and other primates.

Limited evidence for third-party affiliation during development in wild chimpanzees (Pan troglodytes schweinfurthii).

Examining the ontogeny of conflict-mitigating behaviours in our closest living relatives is an important component of understanding the evolutionary origins of cooperation in our species. In this study, we used 26 years of data to investigate the emergence of third-party affiliation (TPA), defined as affiliative contact given to recipients of aggression by uninvolved bystanders (regardless of initiation), in wild immature eastern chimpanzees (Pan troglodytes schweinfurthii) of Gombe National Park, Tanzania. We also characterized TPA by mothers in the same dataset as an adult benchmark for interpreting immature TPA patterns. In summary, we found that immatures did not express TPA as measured by grooming between the ages of 1.5 and 12.0 years, and that there was limited evidence that immatures expressed TPA via play. We also found that mothers did express TPA to offspring, although mothers did not show TPA towards non-offspring. Cases of TPA by mothers to other adults were too few to analyse separately. These results contrast with findings from captive studies which found that chimpanzees as young as 6 years of age demonstrated TPA. We argue that within-species variation in the expression of TPA, both in immatures and adulthood, provides evidence that the conflict management behaviours of young chimpanzees may be heavily influenced by social, ecological and demographic factors.

Whole mitochondrial genome capture from faecal samples and museum-preserved specimens.

Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms.