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Primates; Journal of Primatology Nov 2023Intercommunity (lethal) aggression is a familiar component of the behavioural repertoire of many forest-dwelling chimpanzee (Pan troglodytes) communities. However, until...
Intercommunity (lethal) aggression is a familiar component of the behavioural repertoire of many forest-dwelling chimpanzee (Pan troglodytes) communities. However, until now, the absence of intercommunity attacks - including killings - in communities that live in open, mosaic environments has supported hypotheses of reduced resource competition in drier habitats, and informed referential models of early hominin social dynamics in a similar habitat. In June 2020, we observed the first instance of intercommunity lethal aggression, a male-committed infanticide, by the Issa chimpanzee community, which live in a savannah-mosaic habitat in the Issa Valley, western Tanzania. The carcass was recovered by researchers after it was abandoned by the attackers. Here, we give a detailed account of the events leading up to and including the infanticide, and contextualise our observations with what has been described for other chimpanzee communities. Notably, in contrast to the majority of reported intercommunity infanticides, the infant male victim was castrated (and not cannibalised), making this the youngest reported castration. This observation of intercommunity aggression disproves its hypothesised absence in savannah-dwelling chimpanzees, which by extension, has implications for early hominin evolution. We suggest that the near absence of observations of intercommunity aggression in savannah chimpanzee communities is most likely due to the lack of long-term study communities, and in some cases geographic isolation. We hypothesise that food-rich areas within a habitat with otherwise widely distributed food sources may select for intense intercommunity aggression despite the low population density characteristic of savannah communities. Anecdotes such as this add to the comparative database available on intercommunity killings in chimpanzee society, improving our ability to draw inferences about their evolutionary significance.
Topics: Male; Animals; Pan troglodytes; Tanzania; Aggression; Hominidae; Ecosystem
PubMed: 37615802
DOI: 10.1007/s10329-023-01085-6 -
BioRxiv : the Preprint Server For... Aug 2023Many traits, intrinsic and extrinsic to an organism, contribute to interindividual variation in immunity in wild habitats. The vertebrate includes genes encoding...
Many traits, intrinsic and extrinsic to an organism, contribute to interindividual variation in immunity in wild habitats. The vertebrate includes genes encoding antigen-presenting molecules that are highly variable, and that variation often predicts susceptibility/resistance to and recovery from pathogen infection. I compare variation at two long-term chimpanzee research sites, Kibale National Park in Uganda and Gombe National Park in Tanzania. Using decades of respiratory health data available for these chimpanzees, I test hypotheses associated with maintenance of diversity at loci, including heterozygote, divergent allele, and rare allele advantage hypotheses, and predictions for unique function of in great apes. I found, despite confirmation of recent shared ancestry between Kibale and Gombe chimpanzees, including an overlapping allele repertoire and similar MHC-B phenotype compositions, chimpanzees from the two research sites experienced differences in the occurrence of respiratory signs and had different associations of diversity with signs of respiratory illness. Kibale chimpanzees with heterozygous genotypes and different peptide-binding supertypes were observed less often with respiratory signs than those homozygous or possessing the same supertypes, but this same association was not observed among Gombe chimpanzees. Gombe chimpanzees with specific MHC-B phenotypes that enable engagement of Natural Killer (NK) cells were observed more often with respiratory signs than chimpanzees with other phenotypes, but this was not observed at Kanyawara. This study emphasizes local adaptation in shaping genetic and phenotypic traits in different infectious disease contexts, even among close genetic relatives of the same subspecies, and highlights utility for continued and simultaneous tracking of host immune genes and specific pathogens in wild species.
PubMed: 37577711
DOI: 10.1101/2023.08.02.551731 -
Nature Ecology & Evolution Sep 2023Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and...
Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.
Topics: Animals; Humans; Gorilla gorilla; Pan paniscus; Bayes Theorem; Hominidae; Pan troglodytes; Neanderthals
PubMed: 37500909
DOI: 10.1038/s41559-023-02145-2 -
Nature Aug 2023Human-specific genomic changes contribute to the unique functionalities of the human brain. The cellular heterogeneity of the human brain and the complex regulation of...
Human-specific genomic changes contribute to the unique functionalities of the human brain. The cellular heterogeneity of the human brain and the complex regulation of gene expression highlight the need to characterize human-specific molecular features at cellular resolution. Here we analysed single-nucleus RNA-sequencing and single-nucleus assay for transposase-accessible chromatin with sequencing datasets for human, chimpanzee and rhesus macaque brain tissue from posterior cingulate cortex. We show a human-specific increase of oligodendrocyte progenitor cells and a decrease of mature oligodendrocytes across cortical tissues. Human-specific regulatory changes were accelerated in oligodendrocyte progenitor cells, and we highlight key biological pathways that may be associated with the proportional changes. We also identify human-specific regulatory changes in neuronal subtypes, which reveal human-specific upregulation of FOXP2 in only two of the neuronal subtypes. We additionally identify hundreds of new human accelerated genomic regions associated with human-specific chromatin accessibility changes. Our data also reveal that FOS::JUN and FOX motifs are enriched in the human-specifically accessible chromatin regions of excitatory neuronal subtypes. Together, our results reveal several new mechanisms underlying the evolutionary innovation of human brain at cell-type resolution.
Topics: Animals; Humans; Cell Nucleus; Chromatin; Datasets as Topic; Evolution, Molecular; Genome, Human; Genomics; Gyrus Cinguli; Macaca mulatta; Neurons; Oligodendroglia; Pan troglodytes; Single-Cell Gene Expression Analysis; Stem Cells; Transposases; Chromatin Assembly and Disassembly
PubMed: 37468639
DOI: 10.1038/s41586-023-06338-4 -
Journal of Biomechanics Aug 2023Motion analysis, as applied to evolutionary biomechanics, has experienced its own evolution over the last 50 years. Here we review how an ever-increasing fossil record,... (Review)
Review
Motion analysis, as applied to evolutionary biomechanics, has experienced its own evolution over the last 50 years. Here we review how an ever-increasing fossil record, together with continuing advancements in biomechanics techniques, have shaped our understanding of the origin of upright bipedal walking. The original, and long-established hypothesis held by Lamarck (1809), Darwin (1859) and Keith (1934), amongst others, maintained that bipedality originated in an arboreal context. However, the first field studies of gorilla and chimpanzees from the 1960's, highlighted their so-called 'knucklewalking' quadrupedalism, leading scientists to assume, semi-automatically, that knucklewalking must have been the precursor to bipedality. It would not be until the discovery of skeletons of early human relatives Australopithecus afarensis and Australopithecus prometheus, and the inclusion of methods of analysis from computer science, biomechanics, sports science and medicine, that the knucklewalking hypothesis would be most robustly challenged. Their short, but human-like lower limbs and human-like hand indicated that knucklewalking was not part of our ancestral locomotor repertoire. Rather, most current research in evolutionary biomechanics agrees it was a combination of climbing and bipedalism, both in an arboreal context, which facilitated upright, terrestrial, bipedal walking over short distances.
Topics: Animals; Humans; Biomechanical Phenomena; Walking; Pan troglodytes; Biological Evolution; Locomotion
PubMed: 37451208
DOI: 10.1016/j.jbiomech.2023.111701 -
ELife Jul 2023Inflammasomes are cytosolic innate immune complexes that assemble upon detection of diverse pathogen-associated cues and play a critical role in host defense and...
Inflammasomes are cytosolic innate immune complexes that assemble upon detection of diverse pathogen-associated cues and play a critical role in host defense and inflammatory pathogenesis. Here, we find that the human inflammasome-forming sensor CARD8 senses HIV-1 infection via site-specific cleavage of the CARD8 N-terminus by the HIV protease (HIV-1). HIV-1 cleavage of CARD8 induces pyroptotic cell death and the release of pro-inflammatory cytokines from infected cells, processes regulated by Toll-like receptor stimulation prior to viral infection. In acutely infected cells, CARD8 senses the activity of both de novo translated HIV-1 and packaged HIV-1 that is released from the incoming virion. Moreover, our evolutionary analyses reveal that the HIV-1 cleavage site in human CARD8 arose after the divergence of chimpanzees and humans. Although chimpanzee CARD8 does not recognize proteases from HIV or simian immunodeficiency viruses from chimpanzees (SIVcpz), SIVcpz does cleave human CARD8, suggesting that SIVcpz was poised to activate the human CARD8 inflammasome prior to its cross-species transmission into humans. Our findings suggest a unique role for CARD8 inflammasome activation in response to lentiviral infection of humans.
Topics: Animals; Humans; Inflammasomes; HIV-1; Pan troglodytes; HIV Infections; Simian Immunodeficiency Virus; Apoptosis Regulatory Proteins; Neoplasm Proteins; CARD Signaling Adaptor Proteins
PubMed: 37417868
DOI: 10.7554/eLife.84108 -
Communications Biology Jul 2023Identifying the evolutionary origins of human speech remains a topic of intense scientific interest. Here we describe a unique feature of adult human neuroanatomy...
Identifying the evolutionary origins of human speech remains a topic of intense scientific interest. Here we describe a unique feature of adult human neuroanatomy compared to chimpanzees and other primates that may provide an explanation of changes that occurred to enable the capacity for speech. That feature is the Prefrontal extent of the Frontal Operculum (PFOp) region, which is located in the ventrolateral prefrontal cortex, adjacent and ventromedial to the classical Broca's area. We also show that, in chimpanzees, individuals with the most human-like PFOp, particularly in the left hemisphere, have greater oro-facial and vocal motor control abilities. This critical discovery, when combined with recent paleontological evidence, suggests that the PFOp is a recently evolved feature of human cortical structure (perhaps limited to the genus Homo) that emerged in response to increasing selection for cognitive and motor functions evident in modern speech abilities.
Topics: Adult; Animals; Humans; Speech; Pan troglodytes; Frontal Lobe; Primates; Voice
PubMed: 37407769
DOI: 10.1038/s42003-023-05066-9 -
Scientific Reports Jul 2023Humans are adept at extracting affective information from vocalizations of humans and other animals. However, the extent to which human recognition of vocal affective...
Humans are adept at extracting affective information from vocalizations of humans and other animals. However, the extent to which human recognition of vocal affective cues of other species is due to cross-taxa similarities in acoustic parameters or the phylogenetic closeness between species is currently unclear. To address this, we first analyzed acoustic variation in 96 affective vocalizations, taken from agonistic and affiliative contexts, of humans and three other primates-rhesus macaques (Macaca mulatta), chimpanzees and bonobos (Pan troglodytes and Pan paniscus). Acoustic analyses revealed that agonistic chimpanzee and bonobo vocalizations were similarly distant from agonistic human voices, but chimpanzee affiliative vocalizations were significantly closer to human affiliative vocalizations, than those of bonobos, indicating a potential derived vocal evolution in the bonobo lineage. Second, we asked 68 human participants to categorize and also discriminate vocalizations based on their presumed affective content. Results showed that participants reliably categorized human and chimpanzee vocalizations according to affective content, but not bonobo threat vocalizations nor any macaque vocalizations. Participants discriminated all species calls above chance level except for threat calls by bonobos and macaques. Our results highlight the importance of both phylogenetic and acoustic parameter level explanations in cross-species affective perception, drawing a more complex picture to the origin of vocal emotions.
Topics: Animals; Humans; Phylogeny; Pan troglodytes; Macaca mulatta; Cues; Pan paniscus; Acoustics
PubMed: 37407601
DOI: 10.1038/s41598-023-37558-3 -
PloS One 2023Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed...
Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed apes. However, many important primate pathogens, including known zoonoses, are shed in saliva and transmitted via oral fluids. Using metagenomic methods, we identified viruses in saliva samples from 46 wild-born, sanctuary-housed chimpanzees at two African sanctuaries in Republic of Congo and Uganda. In total, we identified 20 viruses. All but one, an unclassified CRESS DNA virus, are classified in five families: Circoviridae, Herpesviridae, Papillomaviridae, Picobirnaviridae, and Retroviridae. Overall, viral prevalence ranged from 4.2% to 87.5%. Many of these viruses are ubiquitous in primates and known to replicate in the oral cavity (simian foamy viruses, Retroviridae; a cytomegalovirus and lymphocryptovirus; Herpesviridae; and alpha and gamma papillomaviruses, Papillomaviridae). None of the viruses identified have been shown to cause disease in chimpanzees or, to our knowledge, in humans. These data suggest that the risk of zoonotic viral disease from chimpanzee oral fluids in sanctuaries may be lower than commonly assumed.
Topics: Animals; Humans; Pan troglodytes; Saliva; Congo; Uganda; Zoonoses; Retroviridae
PubMed: 37384730
DOI: 10.1371/journal.pone.0288007 -
Scientific Reports Jun 2023The carbohydrate fraction of most mammalian milks contains a variety of oligosaccharides that encompass a range of structures and monosaccharide compositions. Human milk...
The carbohydrate fraction of most mammalian milks contains a variety of oligosaccharides that encompass a range of structures and monosaccharide compositions. Human milk oligosaccharides have received considerable attention due to their biological roles in neonatal gut microbiota, immunomodulation, and brain development. However, a major challenge in understanding the biology of milk oligosaccharides across other mammals is that reports span more than 5 decades of publications with varying data reporting methods. In the present study, publications on milk oligosaccharide profiles were identified and harmonized into a standardized format to create a comprehensive, machine-readable database of milk oligosaccharides across mammalian species. The resulting database, MilkOligoDB, includes 3193 entries for 783 unique oligosaccharide structures from the milk of 77 different species harvested from 113 publications. Cross-species and cross-publication comparisons of milk oligosaccharide profiles reveal common structural motifs within mammalian orders. Of the species studied, only chimpanzees, bonobos, and Asian elephants share the specific combination of fucosylation, sialylation, and core structures that are characteristic of human milk oligosaccharides. However, agriculturally important species do produce diverse oligosaccharides that may be valuable for human supplementation. Overall, MilkOligoDB facilitates cross-species and cross-publication comparisons of milk oligosaccharide profiles and the generation of new data-driven hypotheses for future research.
Topics: Infant, Newborn; Animals; Humans; Milk; Milk, Human; Mammals; Elephants; Oligosaccharides; Monosaccharides; Pan troglodytes
PubMed: 37365203
DOI: 10.1038/s41598-023-36866-y