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Proceedings of the National Academy of... Mar 2024The early-life environment can profoundly shape the trajectory of an animal's life, even years or decades later. One mechanism proposed to contribute to these early-life...
The early-life environment can profoundly shape the trajectory of an animal's life, even years or decades later. One mechanism proposed to contribute to these early-life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early-life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early-life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early-life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early-life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early-life effects on fitness-related traits.
Topics: Animals; DNA Methylation; Adverse Childhood Experiences; Nucleotide Motifs; Biological Assay; Papio
PubMed: 38442181
DOI: 10.1073/pnas.2309469121 -
Animal Cognition Mar 2024Chunking mechanisms are central to several cognitive processes. During the acquisition of visuo-motor sequences, it is commonly reported that these sequences are...
Chunking mechanisms are central to several cognitive processes. During the acquisition of visuo-motor sequences, it is commonly reported that these sequences are segmented into chunks leading to more fluid, rapid, and accurate performances. The question of a chunk's storage capacity has been often investigated but little is known about the dynamics of chunk size evolution relative to sequence length. In two experiments, we studied the dynamics and the evolution of a sequence's chunking pattern as a function of sequence length in a non-human primate species (Guinea baboons, Papio papio). Using an operant conditioning device, baboons had to point on a touch screen to a moving target. In Experiment 1, they had to produce repeatedly the same sequence of 4 movements during 2000 trials. In Experiment 2, the sequence was composed of 5 movements and was repeated 4000 times. For both lengths, baboons initially produced small chunks that became fewer and longer with practice. Moreover, the dynamics and the evolution of the chunking pattern varied as a function of sequence length. Finally, with extended practice (i.e., more than 2000 trials), we observed that the mean chunk size reached a plateau indicating that there are fundamental limits to chunking processes that also depend on sequence length. These data therefore provide new empirical evidence for understanding the general properties of chunking mechanisms in sequence learning.
PubMed: 38429566
DOI: 10.1007/s10071-024-01835-z -
Journal of Human Evolution Apr 2024Bipedal locomotion was a major functional change during hominin evolution, yet, our understanding of this gradual and complex process remains strongly debated. Based on...
Bipedal locomotion was a major functional change during hominin evolution, yet, our understanding of this gradual and complex process remains strongly debated. Based on fossil discoveries, it is possible to address functional hypotheses related to bipedal anatomy, however, motor control remains intangible with this approach. Using comparative models which occasionally walk bipedally has proved to be relevant to shed light on the evolutionary transition toward habitual bipedalism. Here, we explored the organization of the neuromuscular control using surface electromyography (sEMG) for six extrinsic muscles in two baboon individuals when they walk quadrupedally and bipedally on the ground. We compared their muscular coordination to five human subjects walking bipedally. We extracted muscle synergies from the sEMG envelopes using the non-negative matrix factorization algorithm which allows decomposing the sEMG data in the linear combination of two non-negative matrixes (muscle weight vectors and activation coefficients). We calculated different parameters to estimate the complexity of the sEMG signals, the duration of the activation of the synergies, and the generalizability of the muscle synergy model across species and walking conditions. We found that the motor control strategy is less complex in baboons when they walk bipedally, with an increased muscular activity and muscle coactivation. When comparing the baboon bipedal and quadrupedal pattern of walking to human bipedalism, we observed that the baboon bipedal pattern of walking is closer to human bipedalism for both baboons, although substantial differences remain. Overall, our findings show that the muscle activity of a non-adapted biped effectively fulfills the basic mechanical requirements (propulsion and balance) for walking bipedally, but substantial refinements are possible to optimize the efficiency of bipedal locomotion. In the evolutionary context of an expanding reliance on bipedal behaviors, even minor morphological alterations, reducing muscle coactivation, could have faced strong selection pressure, ultimately driving bipedal evolution in hominins.
Topics: Animals; Humans; Papio; Walking; Hominidae; Locomotion; Muscles; Biomechanical Phenomena
PubMed: 38401300
DOI: 10.1016/j.jhevol.2024.103513 -
Hormones and Behavior May 2024How female mammals adapt metabolically in response to environmental variation remains understudied in the wild, because direct measures of metabolic activity are...
How female mammals adapt metabolically in response to environmental variation remains understudied in the wild, because direct measures of metabolic activity are difficult to obtain in wild populations. However, recent advances in the non-invasive measurement of fecal thyroid hormones, triiodothyronine (T3), an important regulator of metabolism, provide an opportunity to understand how female baboons living in the harsh Amboseli ecosystem in southern Kenya adapt to environmental variability and escape strict reproductive seasonality. Specifically, we assessed how a female's activity budget, diet, and concentrations of fecal T3 metabolites (mT3) changed over the course of the year and between years. We then tested which of several environmental variables (season, rainfall, and temperature) and behavioral variables (female activity budget and diet) best predicted mT3 concentrations. Finally, we determined if two important reproductive events - onset of ovarian cycling and conception of an offspring - were preceded by changes in female mT3 concentrations. We found female baboons' mT3 concentrations varied markedly across the year and between years as a function of environmental conditions. Further, changes in a female's behavior and diet only partially mediated the metabolic response to the environment. Finally, mT3 concentrations increased in the weeks prior to menarche and cycling resumption, regardless of the month or season in which cycling started. This pattern indicates that metabolic activation may be an indicator of reproductive readiness in female baboons as their energy balance is restored.
Topics: Animals; Female; Seasons; Papio; Feces; Triiodothyronine; Thyroid Hormones; Diet; Reproduction; Environment; Kenya
PubMed: 38364455
DOI: 10.1016/j.yhbeh.2024.105505 -
Legal Medicine (Tokyo, Japan) May 2024Species specificity of commercial human DNA quantification kits and short tandem repeat (STR) profiling kits was examined using primate DNA samples. These samples...
Species specificity of commercial human DNA quantification kits and short tandem repeat (STR) profiling kits was examined using primate DNA samples. These samples comprised 33 individuals from eight primate species, each with gender and kinship data, including human (Homo sapiens), chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus) of Hominidae family, and Japanese macaque (Macaca fuscata), long-tailed macaque (Macaca fascicularis), hamadryas baboon (Papio hamadryas), and savannah monkey (Chlorocebus sp.) of Cercopithecidae family. The findings revealed varying levels of cross-species amplifications in all non-human DNA samples that correlated with their evolutionary proximity to humans, both kit types. Moreover, cross-species amplification, including female DNA samples, was observed in a Y-chromosomal STR profiling kit. Additionally, species specificity differed among the commercial kits examined. The cross-species amplification data presented in this study offer valuable assistance in interpreting the results of individual human identification in forensic cases involving non-human primates.
Topics: Animals; Humans; Species Specificity; Microsatellite Repeats; DNA; Female; Male; DNA Fingerprinting; Primates; Polymerase Chain Reaction; Forensic Genetics
PubMed: 38325235
DOI: 10.1016/j.legalmed.2023.102369 -
PLoS Computational Biology Jan 2024As part of a long-term research project aiming at generating a biomechanical model of a fossil human tongue from a carefully designed 3D Finite Element mesh of a living...
As part of a long-term research project aiming at generating a biomechanical model of a fossil human tongue from a carefully designed 3D Finite Element mesh of a living human tongue, we present a computer-based method that optimally registers 3D CT images of the head and neck of the living human into similar images of another primate. We quantitatively evaluate the method on a baboon. The method generates a geometric deformation field which is used to build up a 3D Finite Element mesh of the baboon tongue. In order to assess the method's ability to generate a realistic tongue from bony structure information alone, as would be the case for fossil humans, its performance is evaluated and compared under two conditions in which different anatomical information is available: (1) combined information from soft-tissue and bony structures; (2) information from bony structures alone. An Uncertainty Quantification method is used to evaluate the sensitivity of the transformation to two crucial parameters, namely the resolution of the transformation grid and the weight of a smoothness constraint applied to the transformation, and to determine the best possible meshes. In both conditions the baboon tongue morphology is realistically predicted, evidencing that bony structures alone provide enough relevant information to generate soft tissue.
Topics: Animals; Humans; Hominidae; Fossils; Skull; Tongue; Papio; Finite Element Analysis; Computer Simulation
PubMed: 38252664
DOI: 10.1371/journal.pcbi.1011808 -
Stem Cell Research Mar 2024Cross-species comparisons studying primate pluripotent stem cells and their derivatives are crucial to better understand the molecular and cellular mechanisms behind...
Cross-species comparisons studying primate pluripotent stem cells and their derivatives are crucial to better understand the molecular and cellular mechanisms behind human disease and development. Within this context, Baboons (Papio anubis) have emerged as a prominent primate model for such investigations. Herein, we reprogrammed skin fibroblasts of one male individual and generated two induced pluripotent stem cell (iPSC) lines, which exhibit the characteristic ESC-like morphology, demonstrated robust expression of key pluripotency factors and displayed multilineage differentiation potential. Notably, both iPSC lines can be cultured under feeder-free conditions in commercially available medium, enhancing their value for cross-species comparisons.
Topics: Animals; Male; Humans; Induced Pluripotent Stem Cells; Papio; Cell Line; Fibroblasts; Cell Differentiation
PubMed: 38246118
DOI: 10.1016/j.scr.2024.103316 -
International Journal of Radiation... 2024In a previous baboon-study, a total of 29 genes were identified for clinical outcome prediction of the hematologic, acute, radiation, syndrome (H-ARS) severity. Among...
PURPOSE
In a previous baboon-study, a total of 29 genes were identified for clinical outcome prediction of the hematologic, acute, radiation, syndrome (H-ARS) severity. Among them, four genes ( appeared promising and were validated in five leukemia patients. Within this study, we sought further in-vivo validation in a larger number of whole-body irradiated patients.
MATERIAL AND METHODS
Peripheral blood was drawn from 10 leukemia patients before and up to 3 days during a fractionated (2 Gy/day) total-body irradiation (TBI) with 2-12Gy. After RNA-isolation, gene expression (GE) was evaluated on 31 genes widely used in biodosimetry and H-ARS prediction employing qRT-PCR. A customized low-density-array (LDA) allowed simultanously analyzing all genes, the 96-well format further examined the four most promising genes. Fold-changes (FC) in GE relative to pre-irradiation were calculated.
RESULTS
Five patients suffering from acute-lymphoblastic-leukemia (ALL) respectively non-Hodgkin-lymphoma (NHL) revealed sufficient RNA-amounts and corresponding lymphocyte and neutrophile counts for running qRT-PCR, while acute-myeloid-leukemia (AML) and one myelofibrosis patient could not supply enough RNA. Generally, 1-2µg total RNA was isolated, whereas up to 10-fold differences in RNA-quantities (associated suppressed GE-changes) were identified among pre-exposure and exposure samples. From 31 genes, 23 were expressed in at least one of the pre-exposure samples. Relative to pre-exposure, the number of expressed genes could halve at 48 and 72h after irradiation. Using the LDA, 13 genes were validated in human samples. The four most promising genes (vid. sup.) were either undetermined or too close to pre-exposure. However, they were measured using the more sensitive 96-well format, except which wasn´t detectable. As in previous studies, an opposite regulation in GE for in leukemia patients (up-regulated) relative to baboons (down-regulated) was reconfirmed. Radiation-induced GE-changes of (up-regulated) and (down-regulated) behaved similarly in both species. Hence, 16 out of 23 genes of two species showed GE-changes in the same direction, and up-regulated as in human studies were revalidated.
CONCLUSION
Identified genes for H-ARS severity prediction, previously detected in baboons, were validated in ALL but not in AML patients. Limitations related to leukemia type, associated reduced RNA amounts, suppressed GE changes, and methodological challenges must be considered as factors negatively affecting the total number of validated genes. Based on that, we propose additional controls including blood cell counts and preferably fluorescence-based RNA quantity measurements for selecting promising samples and using a more sensitive 96-well format for candidate genes with low baseline copy numbers.
Topics: Humans; Animals; RNA; Whole-Body Irradiation; Blood Cell Count; Papio; Leukemia, Myeloid, Acute
PubMed: 38227483
DOI: 10.1080/09553002.2023.2295295 -
Communications Biology Jan 2024Shared-decision making is beneficial for the maintenance of group-living. However, little is known about whether consensus decision-making follows similar processes...
Shared-decision making is beneficial for the maintenance of group-living. However, little is known about whether consensus decision-making follows similar processes across different species. Addressing this question requires robust quantification of how individuals move relative to each other. Here we use high-resolution GPS-tracking of two vulturine guineafowl (Acryllium vulturinum) groups to test the predictions from a classic theoretical model of collective motion. We show that, in both groups, all individuals can successfully initiate directional movements, although males are more likely to be followed than females. When multiple group members initiate simultaneously, follower decisions depend on directional agreement, with followers compromising directions if the difference between them is small or choosing the majority direction if the difference is large. By aligning with model predictions and replicating the findings of a previous field study on olive baboons (Papio anubis), our results suggest that a common process governs collective decision-making in moving animal groups.
Topics: Humans; Male; Animals; Female; Movement; Motion
PubMed: 38218910
DOI: 10.1038/s42003-024-05782-w -
Scientific Reports Jan 2024Although male and female mammals differ in biological traits and functional needs, the contribution of this sexual dimorphism to variations in gut bacteria and fungi...
Although male and female mammals differ in biological traits and functional needs, the contribution of this sexual dimorphism to variations in gut bacteria and fungi (gut microbiota) in relation to habitat type has not been fully examined. To understand whether the combination of sex and habitat affects gut microbiota variation, we analyzed 40 fecal samples of wild yellow baboons (Papio cynocephalus) living in contrasting habitat types (intact, well-protected vs. fragmented, less protected forests) in the Udzungwa Mountains of Tanzania. Sex determination was performed using the marker genes SRY (Sex-determining Region Y) and DDX3X-DDX3Y (DEAD-Box Helicase 3). Samples were attributed to 34 individuals (19 females and 15 males) belonging to five social groups. Combining the results of sex determination with two amplicon sequencing datasets on bacterial (V1-V3 region of the 16S rRNA gene) and fungal (ITS2) gut communities, we found that overall, baboon females had a significantly higher gut bacterial richness compared to males. Beta diversity estimates indicated that bacterial composition was significantly different between males and females, and this was true for individuals from both well- and less protected forests. Our results highlight the combined role of sex and habitat type in shaping variation in gut microbial communities in wild non-human primates.
Topics: Female; Male; Animals; Papio cynocephalus; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Genes, sry; Forests; Papio; Mammals
PubMed: 38195759
DOI: 10.1038/s41598-023-50126-z