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252 results for “chimpanzees”
Wild chimpanzees exhibit human-like aging of glucocorticoid regulation
<p><span>Cortisol, a key product of the stress response, has critical influences on degenerative aging in humans. In turn, cortisol production is affected by senescence of the hypothalamic-pituitary-adrenal (HPA) axis, leading to progressive dysregulation and increased cortisol exposure. These processes have been studied extensively in industrialized settings, but few comparative data are available from humans and closely-related species living in natural environments, where stressors are very different. Here, we examine age-related changes in urinary cortisol in a 20-year longitudinal study of wild chimpanzees (N = 59 adults) in the Kanyawara community of Kibale National Park, Uganda. We tested for three key features of HPA aging identified in many human studies: increased average levels, a blunted diurnal rhythm, and enhanced response to stressors. Using linear mixed models, we found that aging was associated with a blunting of the diurnal rhythm and a significant linear increase in cortisol, even after controlling for changes in dominance rank. These effects did not differ by sex. Aging did not increase sensitivity to energetic stress or social status. Female chimpanzees experienced their highest levels of cortisol during cycling (versus lactation), and this effect increased with age. Male chimpanzees experienced their highest levels when exposed to sexually-attractive females, but this effect was diminished by age. Our results indicate that chimpanzees share some key features of HPA aging with humans. These findings suggest that impairments of HPA regulation are intrinsic to the aging process in hominids and are neither side effects of extended human lifespan nor of atypical environments.</span></p>
Listening and watching: do camera traps or acoustic sensors more efficiently detect wild chimpanzees in an open habitat?
<p>1. With one million animal species at risk of extinction, there is an urgent need to regularly monitor threatened species. However, in practice this is challenging, especially with wide-ranging, elusive and cryptic species or those that occur at low density.<br> 2. Here we compare two non-invasive methods, passive acoustic monitoring (n=12) and camera trapping (n=53), to detect chimpanzees (Pan troglodytes) in a savanna-woodland mosaic habitat at the Issa Valley, Tanzania. With occupancy modelling we evaluate the efficacy of each method, using the estimated number of sampling days needed to establish chimpanzee absence with 95% probability, as our measure of efficacy.<br> 3. Passive acoustic monitoring was more efficient than camera trapping in detecting wild chimpanzees. Detectability varied over seasons, likely due to social and ecological factors that influence party size and vocalization rate. The acoustic method can infer chimpanzee absence with less than ten days of recordings in the field during the late dry season, the period of highest detectability, which was five times faster than the visual method.<br> 4. Synthesis and applications: Despite some technical limitations, we demonstrate that passive acoustic monitoring is a powerful tool for species monitoring. Its applicability in evaluating presence/absence, especially but not exclusively for loud call species, such as cetaceans, elephants, gibbons or chimpanzees provides a more efficient way of monitoring populations and inform conservation plans to mediate species-loss.</p>
Predicted genome-wide chromatin contact differences among 71 bonobos and chimpanzees
<p>This file contains predicted chromatin contact differences in HFF cells using Akita among pairs of 71 bonobos and chimpanzees at 4,420 ~ 1 Mb genomic windows in the panTro6 genome. Each entry corresponds to a pairwise comparison at a given window. Data per comparison includes the individual IDs in the pairwise comparison, lineages represented, chromosome, position, window ID, mean squared error, Spearman correlation, divergence (1 - Spearman correlation), and the number of nucleotide differences for the pair at the given window.</p>
Chimpanzee food processing video archive (Waibira community, Budongo Forest, Uganda)
<p>This is a video archive containing data (n = 474 videos) on food processing techniques and other behaviours used by the chimpanzees in the Waibira community, Budongo Forest, Uganda. Each video is labelled with data on date, location, individuals and behaviours present (including non-processing behaviours). </p> <p>Also included is the ethogram used to categorise processing behaviours as they are labelled in the archive, and 19 exemplar clips demonstrating some of these behaviours. This archive is intended to be used as a data ark for future interdisciplinary research. While the videos themselves cannot be made publicly accessible, those interested in collaborations may browse the available videos and contact the researchers to request access to specific videos. </p>
Data from: The origins of cognitive flexibility in chimpanzees
<p>Cognitive flexibility is a core component of executive function, a suite of cognitive capacities that enables individuals to update their behavior in dynamic environments. Human executive functions are proposed to be enhanced compared to other species, but this inference is based primarily on neuroanatomical studies. To address this, we examined the nature and origins of cognitive flexibility in chimpanzees, our closest living relatives. Across three studies, we examined different components of cognitive flexibility using reversal learning tasks where individuals first learned one contingency and then had to shift responses when contingencies flipped. In Study 1, we tested n = 82 chimpanzees ranging from juvenility to adulthood on a spatial reversal task, to characterize the development of basic shifting skills. In Study 2, we tested how n = 24 chimpanzees use spatial versus arbitrary perceptual information to shift, a proposed difference between human and nonhuman cognition. In Study 3, we tested n = 40 chimpanzees on a probabilistic reversal task. We found an extended developmental trajectory for basic shifting and shifting in response to probabilistic feedback—chimpanzees did not reach mature performance until late in ontogeny. Additionally, females were faster to shift than males were. We also found that chimpanzees were much more successful when using spatial versus perceptual cues, and highly perseverative when faced with probabilistic versus consistent outcomes. These results identify both core features of chimpanzee cognitive flexibility that are shared with humans, as well as constraints on chimpanzee cognitive flexibility that may represent evolutionary changes in human cognitive development.</p>
Data from: Chimpanzee communities differ in their inter- and intrasexual social relationships
<p><span>Male and female human social bonding strategies are both culturally and genetically shaped. Chimpanzees, our phylogenetically joint closest living relatives, exhibit complex social structures and show impressive cultural diversity. Whether chimpanzee male and female bonding patterns are culturally shaped remains unclear. Studies of wild chimpanzees bonding across sex show that in some communities males show strong bonds with other males, whereas in others females form particularly strong intra-sex bonds. This suggests that there may be cultural variation in chimpanzee social bonding patterns, but excluding genetic or ecological explanations when comparing different wild populations is difficult. Here, we applied social network analysis to examine male and female social bonds in two neighbouring semi-wild chimpanzee groups of comparable ecological conditions and subspecies compositions, but that differ in demographic makeup. Results showed differences in bonding strategies across the two groups. While female-female proximity associations were significantly stronger in Group 1 (which had an even distribution of males and females) than Group 2 (which had a higher proportion of females than males), there were no such differences for male-male or male-female associations. Conversely, female-female grooming bonds were stronger in Group 2 than Group 1. We also found that, in line with captive studies but contrasting research with wild chimpanzees, maternal kinship strongly predicted proximity and grooming patterns across the groups. Our findings suggest that, as with humans, male and female chimpanzee social bonds are influenced by the specific social group they live in, rather than predisposed sex-based bonding strategies.</span></p>
Data from: Timbres of tolerance: Co-feeding tolerance in chimpanzees and bonobos is better explained by group-specific variation than species differences
<p><span>The human species exhibits a remarkable level of social tolerance which has propelled a plethora of behavioural expressions pivotal to our biological success. To date, the evolutionary origins of humans' "ultra-sociality" remain unclear, despite a substantial research focus on our closest living evolutionary relatives, the great apes. Bonobos are typically portrayed as more socially tolerant than chimpanzees and consequentially (sometimes) presented as a better model to study the evolutionary roots of human sociality. Yet, the current evidence supporting such a species-level categorization is equivocal. Here, we used validated group-level co-feeding tasks to test 16 independent <em>Pan </em>groups living in zoo (n=9) and sanctuary (n=7) settings, representing 225 individuals. We found that the expressions of social tolerance substantially overlapped between species, thus precluding categorical inference at the species level. Instead, marked differences were observed among groups, with some bonobo groups exhibiting higher social tolerance than chimpanzee groups, and vice versa. Interestingly, substantial intergroup variation was found within species living in the same environment, which attests to Pan's behavioural flexibility. We conclude that the pervasive dichotomy between the tolerant bonobo and the belligerent chimpanzee requires quantitative nuance, and that accurate phylogenetic tracing of (human) social behaviour necessitates estimations of intraspecific intergroup variation.</span></p>
Call combinations in chimpanzees: a social tool?
<p><span>A growing body of evidence suggests the capacity for animals to combine calls into larger communicative structures is more common than previously assumed. Despite its cross-taxa prevalence, little is known regarding the evolutionary pressures driving such combinatorial abilities. One dominant hypothesis posits that social complexity and vocal complexity are linked, with changes in social structuring (e.g. group size) driving the emergence of ever-more complex vocal abilities, such as call sequencing. In this paper, we tested this hypothesis through investigating combinatoriality in the vocal system of the highly social chimpanzee. Specifically, we predicted combinatoriality to be more common in socially-driven contexts and in females and lower-ranked males (socially challenging contexts and socially challenged individuals respectively). Firstly, through applying methods from computational linguistics (i.e. collocation analyses), we built an objective repertoire of combinatorial structures in this species. Second, we investigated what potential factors influenced call combination production. We show that combinatoriality is predominant in i) social contexts vs. non-social contexts, ii) females vs. males and iii) negatively correlates with male rank. Together, these results suggest one function of combinatoriality in chimpanzees may be to help individuals navigate their dynamic social world. More generally, we argue these findings provide support for the hypothesised link between social and vocal complexity and can provide insight into the evolution of our own highly combinatorial communication system, language.</span></p>
Mielke & Carvalho 2022 Chimpanzee play sequences are structured hierarchically as games - Data
<p>Data and scripts for the 2022 manuscript 'Chimpanzee play sequences are structured hierarchically as games' - preprint here: </p> <p>https://doi.org/10.1101/2022.06.14.496075</p> <p>Dataset and scripts generated on 20/09/2022. For potential changes and all information see:</p> <p>https://github.com/AlexMielke1988/Mielke-Carvalho_Chimpanzee-Play</p>
Inter-Community Interactions in Chimpanzees
<p>Panel discussion on inter-community interactions in chimpanzees of Budongo Forest</p>
De novo assembly of chimpanzee ONT reads
<p><em>De novo</em> assembly of a western chimpanzee genome (Pan troglodytes verus) from LCL cell line (AG18359), generated with Oxford Nanopore Technologies (ONT) reads basecalled with Guppy v5.0.11 and assembled with Shasta software v0.7.0 for Linux. Nanopore raw reads were originally published in PMID: 32143403.</p>
Data from: Age-related physiological dysregulation progresses slowly in semi-free-ranging chimpanzees
<p>Lifestyle has widespread effects on human health and aging. Prior results from chimpanzees, one of the closest evolutionary relatives of humans, indicate that these lifestyle effects may also be shared with other species, as semi-free-ranging chimpanzees fed a naturalistic diet show healthier values in several specific health biomarkers, compared with their sedentary, captive counterparts. Here, we examined how lifestyle factors associated with different environments affect rates of physiological aging in closely related chimpanzees (<em>Pan troglodytes</em>). We compared physiological dysregulation, an index of biological aging, in semi-free-ranging chimpanzees in an African sanctuary versus captive chimpanzees in US laboratories. If the rate of aging is accelerated by a high-calorie diet and sedentism, we predicted greater age-related dysregulation in the laboratory populations. Conversely, if the costs of a wild lifestyle accelerate aging, then semi-free-ranging chimpanzees at the sanctuary, whose environment better approximates the wild, should show greater age-related dysregulation. We further tested whether dysregulation differed based on sex or body system, as in humans. We found that semi-free-ranging chimpanzees showed lower overall dysregulation, as well as lower age-related change in dysregulation, than laboratory chimpanzees. Males experienced lower dysregulation in both contexts, and the two populations exhibited distinct aging patterns based on the body system. Our results support the conclusion that naturalistic living conditions result in healthier aging in chimpanzees. These data provide support for the proposal that lifestyle effects on human health and aging are conserved from deeper into our evolutionary history.</p>
Data: Social tolerance and role model diversity increase tool use learning opportunities across chimpanzees ontogeny.
Open the record for dataset details and reuse information.
Connectional asymmetry of the inferior parietal lobule shapes hemispheric specialization in humans, chimpanzees, and rhesus macaques
<p>The inferior parietal lobule (IPL) is one of the most expanded cortical regions in humans relative to other primates. It is also among the most structurally and functionally asymmetric regions in the human cerebral cortex. Whether the structural and connectional asymmetries of IPL subdivisions differ across primate species and how this relates to functional asymmetries remain unclear. We identified IPL subregions that exhibited positive allometric in both hemispheres, scaling across rhesus macaque monkeys, chimpanzees, and humans. The patterns of IPL subregions asymmetry were similar in chimpanzees and humans, but no IPL asymmetries were evident in macaques. Among the comparative sample of primates, humans showed the most widespread asymmetric connections in the frontal, parietal, and temporal cortices, constituting leftward asymmetric networks that may provide an anatomical basis for language and tool use. Unique human asymmetric connectivity between the IPL and primary motor cortex might be related to handedness. These findings suggest that structural and connectional asymmetries may underlie hemispheric specialization of the human brain.</p>
Data from: CHIIMP: an automated high-throughput microsatellite genotyping approach reveals greater allelic diversity in wild chimpanzees
Short tandem repeats (STRs), also known as microsatellites, are commonly used to non-invasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping non-habituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
Data from: Does tolerance allow bonobos to outperform chimpanzees on a cooperative task? A conceptual replication of Hare et al., 2007
<p><span>Across various taxa, social tolerance is thought to facilitate cooperation, and many species are treated as having species-specific patterns of social tolerance. Yet studies that assess wild and captive bonobos and chimpanzees result in contrasting findings. By replicating a cornerstone experimental study on tolerance and cooperation in bonobos and chimpanzees (Hare et al., 2007</span><span> <em>Cur. Biol</em>. </span><span>17</span><span>, 619–623</span><span>), we aim to understand whether current discrepant findings may result from noise, methodological differences, or behavioural variability. We tested bonobos and chimpanzees housed at the same facility in a co-feeding and cooperation task. Food was placed on dishes located on both ends or in the middle of a platform. In the co-feeding task, the tray was simply made available to the ape duos, whereas in the cooperation task the apes had to simultaneously pull at both ends of a rope attached to the platform to retrieve the food. In contrast to the published findings, b</span><span>onobos and chimpanzees co-fed to a similar degree, indicating a similar level of tolerance. However, bonobos cooperated more than chimpanzees when the food was monopolizable, which replicates the original study. Our findings call into question the interpretation that at the species level bonobos cooperate to a higher degree because they are inherently more tolerant.</span></p>
Chimpanzee and Human Gray Matter Masks
<p>Gray matter (GM) mask for human and chimpanzee structural T1-weighted magnetic resonance imaging (MRI) scans </p> <p>The human mask was created using the GM tissue segment map from the CAT12 (Computational Anatomy Toolbox) tissue probability map (TPM) and shooting template. Using a probability threshold of 0.2 voxels within both segment maps were included in the mask. Finally, single voxels that did not touch any other voxel were removed during clean up. </p> <p>The chimpanzee GM mask was created using the chimpanzee TPM (Vickery et al., 2020) provided with CAT12.7+ at a GM probability threshold of 0.3.</p> <p>The human GM mask is provided at a resolution of 1.5mm and 3mm while the chimpanzee GM mask at a resolution of 1mm and 2mm. We also provide a cortex GM mask containing the cerebral cortex and basal ganglia for both species with the cerebellum and brain stem removed. Cerebellum and brain stem are removed using the chimpanzee Davi130 parcellation (Vickery et al., 2020) in chimpanzees and for human the parcellation registered to MNI space.</p> <p><strong>Version 2:</strong> A new human cortex and sub-cortex GM mask created from the 1.5mm "CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz" mask by using the Schaefer 1000 parcellation (Scaefer et al., 2018) for the cortex mask and Tian sub-cortex atlas (Tian et al., 2020) for the sub-cortex mask. A shell script "cortex_subcortex_mask.sh" outlines the steps taken to create the GM mask.</p>
Data from: Observational approaches to chimpanzee behavior in an African sanctuary: implications for research, welfare, and capacity-building
<p>Research in African ape sanctuaries has emerged as an important context for our understanding of comparative cognition and behavior. While much of this work has focused on experimental studies of cognition, these animals semi-free-range in forest habitats and therefore can also provide important information about the behavior of primates in socioecologically-relevant naturalistic contexts. In this 'New Approaches' article, we describe a project where we implemented a synthetic program of observational data collection at Ngamba Island Chimpanzee Sanctuary in Uganda, directly modeled after long-term data collection protocols at the Kibale Chimpanzee Project in Uganda, a wild chimpanzee field site. The foundation for this project was a strong partnership between sanctuary staff, field site staff, and external researchers. We describe how we developed a data-collection protocol through discussion and collaboration among these groups, and trained sanctuary caregivers to collect novel observational data using these protocols. We use these data as a case study to examine: (1) how behavioral observations in sanctuaries can inform primate welfare and care practices, such as by understanding aggression within the group; (2) how matched observational protocols across sites can inform our understanding of primate behavior across different contexts, including sex differences in social relationships; and (3) how more robust collaborations between foreign researchers and local partners can support capacity-building in primate range countries, along with mentoring and training students more broadly.</p>
Chimpanzee Adenovirus and Self-Amplifying mRNA Prime-Boost Prophylactic Vaccines Against SARS-CoV-2 in Healthy Adults
ClinicalTrials.gov study NCT04776317. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Ebola Sudan Chimpanzee Adenovirus Vector Vaccine in Healthy Adults
ClinicalTrials.gov study NCT04041570. IPD Sharing: NO. Countries: 1. Publications: 6.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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