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Scientific Reports May 2024Reverse zoonotic respiratory diseases threaten great apes across Sub-Saharan Africa. Studies of wild chimpanzees have identified the causative agents of most respiratory...
Reverse zoonotic respiratory diseases threaten great apes across Sub-Saharan Africa. Studies of wild chimpanzees have identified the causative agents of most respiratory disease outbreaks as "common cold" paediatric human pathogens, but reverse zoonotic transmission pathways have remained unclear. Between May 2019 and August 2021, we conducted a prospective cohort study of 234 children aged 3-11 years in communities bordering Kibale National Park, Uganda, and 30 adults who were forest workers and regularly entered the park. We collected 2047 respiratory symptoms surveys to quantify clinical severity and simultaneously collected 1989 nasopharyngeal swabs approximately monthly for multiplex viral diagnostics. Throughout the course of the study, we also collected 445 faecal samples from 55 wild chimpanzees living nearby in Kibale in social groups that have experienced repeated, and sometimes lethal, epidemics of human-origin respiratory viral disease. We characterized respiratory pathogens in each cohort and examined statistical associations between PCR positivity for detected pathogens and potential risk factors. Children exhibited high incidence rates of respiratory infections, whereas incidence rates in adults were far lower. COVID-19 lockdown in 2020-2021 significantly decreased respiratory disease incidence in both people and chimpanzees. Human respiratory infections peaked in June and September, corresponding to when children returned to school. Rhinovirus, which caused a 2013 outbreak that killed 10% of chimpanzees in a Kibale community, was the most prevalent human pathogen throughout the study and the only pathogen present at each monthly sampling, even during COVID-19 lockdown. Rhinovirus was also most likely to be carried asymptomatically by adults. Although we did not detect human respiratory pathogens in the chimpanzees during the cohort study, we detected human metapneumovirus in two chimpanzees from a February 2023 outbreak that were genetically similar to viruses detected in study participants in 2019. Our data suggest that respiratory pathogens circulate in children and that adults become asymptomatically infected during high-transmission times of year. These asymptomatic adults may then unknowingly carry the pathogens into forest and infect chimpanzees. This conclusion, in turn, implies that intervention strategies based on respiratory symptoms in adults are unlikely to be effective for reducing reverse zoonotic transmission of respiratory viruses to chimpanzees.
Topics: Animals; Pan troglodytes; Humans; Child; Female; Male; Child, Preschool; Common Cold; Adult; Uganda; Prospective Studies; Zoonoses; COVID-19; Ape Diseases; Respiratory Tract Infections; Rhinovirus; SARS-CoV-2; Incidence
PubMed: 38714841
DOI: 10.1038/s41598-024-61236-7 -
BMC Genomic Data Jan 2024We tackle the problem of estimating species TMRCAs (Time to Most Recent Common Ancestor), given a genome sequence from each species and a large known phylogenetic tree...
BACKGROUND
We tackle the problem of estimating species TMRCAs (Time to Most Recent Common Ancestor), given a genome sequence from each species and a large known phylogenetic tree with a known structure (typically from one of the species). The number of transitions at each site from the first sequence to the other is assumed to be Poisson distributed, and only the parity of the number of transitions is observed. The detailed phylogenetic tree contains information about the transition rates in each site. We use this formulation to develop and analyze multiple estimators of the species' TMRCA. To test our methods, we use mtDNA substitution statistics from the well-established Phylotree as a baseline for data simulation such that the substitution rate per site mimics the real-world observed rates.
RESULTS
We evaluate our methods using simulated data and compare them to the Bayesian optimizing software BEAST2, showing that our proposed estimators are accurate for a wide range of TMRCAs and significantly outperform BEAST2. We then apply the proposed estimators on Neanderthal, Denisovan, and Chimpanzee mtDNA genomes to better estimate their TMRCA with modern humans and find that their TMRCA is substantially later, compared to values cited recently in the literature.
CONCLUSIONS
Our methods utilize the transition statistics from the entire known human mtDNA phylogenetic tree (Phylotree), eliminating the requirement to reconstruct a tree encompassing the specific sequences of interest. Moreover, they demonstrate notable improvement in both running speed and accuracy compared to BEAST2, particularly for earlier TMRCAs like the human-Chimpanzee split. Our results date the human - Neanderthal TMRCA to be [Formula: see text] years ago, considerably later than values cited in other recent studies.
Topics: Animals; Humans; Neanderthals; Phylogeny; Pan troglodytes; Bayes Theorem; Hominidae; DNA, Mitochondrial
PubMed: 38166646
DOI: 10.1186/s12863-023-01185-8 -
PLoS Biology Nov 2023Tactical warfare is considered a driver of the evolution of human cognition. One such tactic, considered unique to humans, is collective use of high elevation in...
Tactical warfare is considered a driver of the evolution of human cognition. One such tactic, considered unique to humans, is collective use of high elevation in territorial conflicts. This enables early detection of rivals and low-risk maneuvers, based on information gathered. Whether other animals use such tactics is unknown. With a unique dataset of 3 years of simultaneous behavioral and ranging data on 2 neighboring groups of western chimpanzees, from the Taï National Park, Côte d'Ivoire, we tested whether chimpanzees make decisions consistent with tactical use of topography to gain an advantage over rivals. We show that chimpanzees are more likely to use high hills when traveling to, rather than away from, the border where conflict typically takes place. Once on border hills, chimpanzees favor activities that facilitate information gathering about rivals. Upon leaving hills, movement decisions conformed with lowest risk engagement, indicating that higher elevation facilitates the detection of rivals presence or absence. Our results support the idea that elevation use facilitated rival information gathering and appropriate tactical maneuvers. Landscape use during territorial maneuvers in natural contexts suggests chimpanzees seek otherwise inaccessible information to adjust their behavior and points to the use of sophisticated cognitive abilities, commensurate with selection for cognition in species where individuals gain benefits from coordinated territorial defense. We advocate territorial contexts as a key paradigm for unpicking complex animal cognition.
Topics: Animals; Humans; Pan troglodytes; Cote d'Ivoire
PubMed: 37917608
DOI: 10.1371/journal.pbio.3002350 -
Royal Society Open Science Nov 2023The social complexity hypothesis for the evolution of communication posits that complex social environments require greater communication complexity for individuals to...
The social complexity hypothesis for the evolution of communication posits that complex social environments require greater communication complexity for individuals to effectively manage their relationships. We examined how different socially uncertain contexts, reflecting an increased level of social complexity, relate to variation in signalling within and between two species, which display varying levels of fission-fusion dynamics (sympatric-living chimpanzees and sooty mangabeys, Taï National Park, Ivory Coast). Combined signalling may improve message efficacy, notably when involving different perception channels, thus may increase in moments of high social uncertainty. We examined the probability of individuals to emit no signal, single or multisensory or combined (complex) signals, during social approaches which resulted in non-agonistic outcomes. In both species, individuals were more likely to use more combined and multisensory signals in post-conflict approaches with an opponent than in other contexts. The clearest impact of social uncertainty on signalling complexity was observed during chimpanzee fusions, where the likelihood of using complex signals tripled relative to other contexts. Overall, chimpanzees used more multisensory signals than mangabeys. Social uncertainty may shape detected species differences in variation in signalling complexity, thereby supporting the hypothesis that social complexity, particularly associated with high fission-fusion dynamics, promotes signalling complexity.
PubMed: 38034119
DOI: 10.1098/rsos.231073 -
Cognition May 2024The strength of human society can largely be attributed to the tendency to work together to achieve outcomes that are not possible alone. Effective social coordination...
The strength of human society can largely be attributed to the tendency to work together to achieve outcomes that are not possible alone. Effective social coordination benefits from mentally representing a partner's actions. Specifically, humans optimize social coordination by forming internal action models adapted to joint rather than individual task demands. To what extent do humans share the cognitive mechanisms that support optimal human coordination and collaboration with other species? An ecologically inspired joint handover-to-retrieve task was systematically manipulated across several experiments to assess whether joint action planning in chimpanzees reflects similar patterns to humans. Chimpanzees' chosen handover locations shifted towards the location of the experimenter's free or unobstructed hand, suggesting they represent the constraints of the joint task even though their individual half of the task was unobstructed. These findings indicate that chimpanzees and humans may share common cognitive mechanisms or predispositions that support joint action.
Topics: Animals; Humans; Pan troglodytes; Behavior, Animal; Cooperative Behavior
PubMed: 38412760
DOI: 10.1016/j.cognition.2024.105747 -
PloS One 2024We investigated children's and non-human great apes' ability to anticipate others' choices from their evident food preferences-regardless of whether these preferences...
We investigated children's and non-human great apes' ability to anticipate others' choices from their evident food preferences-regardless of whether these preferences deviate or align with one's own. We assessed children from three culturally-diverse societies (Namibia, Germany, and Samoa; N = 71; age range = 5-11) and four non-human great ape species (chimpanzees (Pan troglodytes), bonobos (Pan paniscus), gorillas (Gorilla gorilla), and orangutans (Pongo abelii); N = 25; age range = 7-29) regarding their choices in a dyadic food-retrieval task. Across conditions, participants' preferences were either aligned (same preference condition) or opposed (opposite preference condition) to those of their competitors. Children across societies altered their choices based on their competitor's preferences, indicating a cross-culturally recurrent capacity to anticipate others' choices relying on preferences-based inferences. In contrast to human children, all non-human great apes chose according to their own preferences but independent of those of their competitors. In sum, these results suggest that the tendency to anticipate others' choices based on their food preferences is cross-culturally robust and, among the great apes, most likely specific to humans.
Topics: Animals; Humans; Hominidae; Gorilla gorilla; Pan troglodytes; Pongo abelii; Pongo pygmaeus; Pan paniscus
PubMed: 38232055
DOI: 10.1371/journal.pone.0295221 -
Royal Society Open Science Jan 2024Inbreeding (reproduction between relatives) often decreases the fitness of offspring and is thus expected to lead to the evolution of inbreeding avoidance strategies....
Inbreeding (reproduction between relatives) often decreases the fitness of offspring and is thus expected to lead to the evolution of inbreeding avoidance strategies. Chimpanzees () are expected to avoid inbreeding as they are long-lived, invest heavily in offspring and may encounter adult, opposite sex kin frequently, especially in populations where both males and females commonly remain in the group in which they were born (bisexual philopatry). However, it is unclear whether substantial bisexual philopatry has been a feature of chimpanzees' evolutionary history or whether it is a result of recent anthropogenic interference, as the only groups for which it has been documented are significantly impacted by human encroachment and experience notable rates of potentially unsustainable inbreeding. Here we use 14 years of observational data and a large genomic dataset of 256 481 loci sequenced from 459 individuals to document dispersal and inbreeding dynamics in an eastern chimpanzee () community with low levels of anthropogenic disturbance. We document the first case of substantial bisexual philopatry in a relatively undisturbed chimpanzee community and show that, despite an increased inbreeding risk incurred by females who do not disperse before reaching reproductive age, natal females were still able to avoid producing inbred offspring.
PubMed: 38234436
DOI: 10.1098/rsos.230967 -
Comparative Biochemistry and... 2024Ecometabolomics could be implemented as a powerful tool in molecular ecology studies, but it is necessary to know the baseline of certain metabolites and understand how...
Ecometabolomics could be implemented as a powerful tool in molecular ecology studies, but it is necessary to know the baseline of certain metabolites and understand how different traits could affect the metabolome of the animals. Therefore, the main objective of this study was to provide values for the nutritional metabolome profile of different diet groups and animal species, as well as to study the differences in the metabolomic profile due to the effect of diet type and species. To achieve this goal, blood samples were taken from healthy animals (n = 43) of different species: lion (Panthera leo), jaguar (Panthera onca), chimpanzee (Pan troglodytes), bison (Bison bison), gazelle (Gazella cuvieri) and fallow deer (Dama dama), and with different types of diet (carnivore, herbivore and omnivore). Each blood sample was analysed to determine nutritional metabolites. The main results this study provides are the nutritional metabolic profile of these animals based on the type of diet and the animal species. A significant effect of the dietary type was found on nutritional metabolite levels, with those metabolites related to protein metabolism (total protein and creatine) being higher in carnivores. There is also an effect of the species on nutritional metabolites, observing a metabolome differentiation between lion and jaguar. In the case of herbivores, bison showed higher levels of uric acid and cholesterol, and lower urea levels than gazelle and fallow deer. More molecular ecology studies are needed to further the knowledge of the metabolism of these animals.
Topics: Animals; Herbivory; Deer; Lions; Bison; Antelopes; Diet; Metabolome; Panthera
PubMed: 38452851
DOI: 10.1016/j.cbpb.2024.110965 -
Emerging Infectious Diseases Mar 2024Despite zoonotic potential, data are lacking on enteric infection diversity in wild apes. We employed a novel molecular diagnostic platform to detect enteric infections...
Despite zoonotic potential, data are lacking on enteric infection diversity in wild apes. We employed a novel molecular diagnostic platform to detect enteric infections in wild chimpanzees and gorillas. Prevalent Cryptosporidium parvum, adenovirus, and diarrheagenic Escherichia coli across divergent sites and species demonstrates potential widespread circulation among apes in Africa.
Topics: Animals; Gorilla gorilla; Pan troglodytes; Cameroon; Tanzania; Cryptosporidiosis; Cryptosporidium; Escherichia coli
PubMed: 38407249
DOI: 10.3201/eid3003.230318 -
Scientific Reports Nov 2023The utilization of mechanical ventilation is of utmost importance in the management of individuals afflicted with severe pulmonary conditions. During periods of a...
The utilization of mechanical ventilation is of utmost importance in the management of individuals afflicted with severe pulmonary conditions. During periods of a pandemic, it becomes imperative to build ventilators that possess the capability to autonomously adapt parameters over the course of treatment. In order to fulfil this requirement, a research investigation was undertaken with the aim of forecasting the magnitude of pressure applied on the patient by the ventilator. The aforementioned forecast was derived from a comprehensive analysis of many variables, including the ventilator's characteristics and the patient's medical state. This analysis was conducted utilizing a sophisticated computational model referred to as Long Short-Term Memory (LSTM). To enhance the predictive accuracy of the LSTM model, the researchers utilized the Chimp Optimization method (ChoA) method. The integration of LSTM and ChoA led to the development of the LSTM-ChoA model, which successfully tackled the issue of hyperparameter selection for the LSTM model. The experimental results revealed that the LSTM-ChoA model exhibited superior performance compared to alternative optimization algorithms, namely whale grey wolf optimizer (GWO), optimization algorithm (WOA), and particle swarm optimization (PSO). Additionally, the LSTM-ChoA model outperformed regression models, including K-nearest neighbor (KNN) Regressor, Random and Forest (RF) Regressor, and Support Vector Machine (SVM) Regressor, in accurately predicting ventilator pressure. The findings indicate that the suggested predictive model, LSTM-ChoA, demonstrates a reduced mean square error (MSE) value. Specifically, when comparing ChoA with GWO, the MSE fell by around 14.8%. Furthermore, when comparing ChoA with PSO and WOA, the MSE decreased by approximately 60%. Additionally, the analysis of variance (ANOVA) findings revealed that the p-value for the LSTM-ChoA model was 0.000, which is less than the predetermined significance level of 0.05. This indicates that the results of the LSTM-ChoA model are statistically significant.
Topics: Humans; Animals; Ventilators, Mechanical; Algorithms; Respiration, Artificial; Random Forest; Analysis of Variance; Cetacea; Pan troglodytes
PubMed: 38017008
DOI: 10.1038/s41598-023-47837-8