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European Journal of Human Genetics :... Jun 2024There have been reports of examples of exclusive yin yang haplotypes, differing at every locus, but there has been no systematic search for them. Unphased whole genome...
There have been reports of examples of exclusive yin yang haplotypes, differing at every locus, but there has been no systematic search for them. Unphased whole genome sequence data for 2504 unrelated 1000 Genomes subjects was searched for chains of SNPs having global minor allele frequency (MAF) > =0.1 made up of at least 20 SNPs in complete linkage disequilibrium with each other and with no pair being separated by more than 9 other SNPs. The global distribution of these haplotypes was investigated, along with their ancestral origins and associations with genes and phenotypes. A number of previously unrecognised repeats were noted, flagged by all or most subjects being called as heterozygotes, and these were discarded. There were 5114 exclusive yin yang haplotypes each consisting of on average 34.8 SNPs, each spanning on average 15.7 kb and cumulatively covering 80 Mb. Although for some haplotypes the MAF varied markedly between populations the average global fixation index was similar to that for SNPs elsewhere in the genome and there was no evidence of enrichment for genes or gene ontologies. For all but 92 haplotypes there were partial forms present in the chimpanzee and/or Neanderthal genome, indicating that they had been formed in a gradual process but that intermediate haplotypes were now absent from modern humans. Exclusive yin yang haplotypes cover over 2% of the human genome. The mechanisms accounting for their formation and preservation are unclear. They may serve as useful markers of the dispersal of chromosomal regions through human history.
Topics: Humans; Haplotypes; Polymorphism, Single Nucleotide; Genome, Human; Yin-Yang; Animals; Linkage Disequilibrium; Gene Frequency; Pan troglodytes
PubMed: 37308599
DOI: 10.1038/s41431-023-01399-5 -
American Journal of Primatology Apr 2024Primate social organizations, or grouping patterns, vary significantly across species. Behavioral strategies that allow for flexibility in grouping patterns offer a...
Primate social organizations, or grouping patterns, vary significantly across species. Behavioral strategies that allow for flexibility in grouping patterns offer a means to reduce the costs of group living. Chimpanzees (Pan troglodytes) have a fission-fusion social system in which temporary subgroups ("parties") change in composition because of local socio-ecological conditions. Notably, western chimpanzees (P. t. verus) are described as showing a higher degree of bisexual bonding and association than eastern chimpanzees, and eastern female chimpanzees (P. t. schweinfurthii) are thought to be more solitary than western female chimpanzees. However, reported comparisons in sociality currently depend on a small number of study groups, particularly in western chimpanzees, and variation in methods. The inclusion of additional communities and direct comparison using the same methods are essential to assess whether reported subspecies differences in sociality hold in this behaviorally heterogeneous species. We explored whether sociality differs between two communities of chimpanzees using the same motion-triggered camera technology and definitions of social measures. We compare party size and composition (party type, sex ratio) between the western Gahtoy community in the Nimba Mountains (Guinea) and the eastern Waibira community in the Budongo Forest (Uganda). Once potential competition for resources such as food and mating opportunities were controlled for, subspecies did not substantially influence the number of individuals in a party. We found a higher sex-ratio, indicating more males in a party, in Waibira; this pattern was driven by a greater likelihood in Gahtoy to be in all-female parties. This finding is the opposite of what was expected for eastern chimpanzees, where female-only parties are predicted to be more common. Our results highlight the flexibility in chimpanzee sociality, and caution against subspecies level generalizations.
Topics: Male; Female; Animals; Pan troglodytes; Hominidae; Social Behavior; Uganda; Forests
PubMed: 38247391
DOI: 10.1002/ajp.23593 -
Journal of Human Evolution Mar 2024Since the initial discovery of Paranthropus robustus at the site of Kromdraai in 1938, the hypodigm of this species has been expanded by subsequent work at the...
Since the initial discovery of Paranthropus robustus at the site of Kromdraai in 1938, the hypodigm of this species has been expanded by subsequent work at the localities of Swartkrans and Drimolen, with a few fossils also known from Cooper's D, Gondolin and Sterkfontein Member 5. Beginning in 2014, systematic excavations at Kromdraai uncovered a large and previously unknown fossiliferous area, shedding light on Units O and P in the earliest part of the site's stratigraphic sequence. The aim of this paper is to provide detailed descriptions and illustrations of 30 P. robustus craniodental specimens recovered between 2014 and 2017 within the Unit P deposits at Kromdraai. This new sample predates all prior conspecific specimens found at this site (including the holotype of P. robustus from Kromdraai, TM 1517). Its basic dental morphology dimensions and cranial features are compared in a preliminary analysis with other P. robustus samples. The P. robustus sample from Kromdraai Unit P documents previously unknown portions of the P. robustus juvenile cranium. The new dental and cranial remains aid in the exploration of potential morphological distinctions between site-specific P. robustus samples and are compared favorably in size and morphology with the small P. robustus specimens from Drimolen (e.g., DNH 7). These findings do not support the hypothesis that the specimens from Drimolen belong to a different taxonomic group. Instead, they reinforce the presence of a significant degree of sexual dimorphism within P. robustus. The Kromdraai Unit P specimens also contribute to the biodemographic profile of P. robustus. The notable prevalence of infants (i.e., juvenile individuals before the emergence of their first permanent molars) mirrors the natural mortality profiles observed in wild chimpanzees. This suggests a closer resemblance in the processes of accumulation in Kromdraai Unit P and Drimolen than at Swartkrans.
Topics: Humans; Animals; Fossils; Hominidae; South Africa; Molar; Pan troglodytes
PubMed: 38382132
DOI: 10.1016/j.jhevol.2023.103481 -
Primates; Journal of Primatology Nov 2023Many anthropogenic-driven changes, such as hunting, have clear and immediate negative impacts on wild primate populations, but others, like climate change, may take...
Many anthropogenic-driven changes, such as hunting, have clear and immediate negative impacts on wild primate populations, but others, like climate change, may take generations to become evident. Thus, informed conservation plans will require decades of population monitoring. Here, we expand the duration of monitoring of the diurnal primates at Ngogo in Kibale National Park, Uganda, from 32.9 to 47 years. Over the 3531 censuses that covered 15,340 km, we encountered 2767 primate groups. Correlation analyses using blocks of 25 census walks indicate that encounters with groups of black and white colobus, blue monkeys, and baboons neither increased nor decreased significantly over time, while encounters with groups of redtail monkeys and chimpanzees marginally increased. Encounters with mangabeys and L'Hoesti monkeys increased significantly, while red colobus encounters dramatically decreased. Detailed studies of specific groups at Ngogo document changes in abundances that were not always well represented in the censuses because these groups expanded into areas away from the transect, such as nearby regenerating forest. For example, the chimpanzee population increased steadily over the last 2 + decades but this increase is not revealed by our census data because the chimpanzees expanded, mainly to the west of the transect. This highlights that extrapolating population trends to large areas based on censuses at single locations should be done with extreme caution, as forests change over time and space, and primates adapt to these changes in several ways.
Topics: Animals; Pan troglodytes; Uganda; Parks, Recreational; Population Dynamics; Primates; Colobus; Papio
PubMed: 37656336
DOI: 10.1007/s10329-023-01087-4 -
Biological Reviews of the Cambridge... Apr 2024Empathy is a complex, multi-dimensional capacity that facilitates the sharing and understanding of others' emotions. As our closest living relatives, bonobos (Pan...
Empathy is a complex, multi-dimensional capacity that facilitates the sharing and understanding of others' emotions. As our closest living relatives, bonobos (Pan paniscus) and chimpanzees (P. troglodytes) provide an opportunity to explore the origins of hominin social cognition, including empathy. Despite certain assumptions that bonobos and chimpanzees may differ empathically, these species appear to overlap considerably in certain socio-emotional responses related to empathy. However, few studies have systematically tested for species variation in Pan empathic or socio-emotional tendencies. To address this, we synthesise the growing literature on Pan empathy to inform our understanding of the selection pressures that may underlie the evolution of hominin empathy, and its expression in our last common ancestor. As bonobos and chimpanzees show overlaps in their expression of complex socio-emotional phenomena such as empathy, we propose that group comparisons may be as or more meaningful than species comparisons when it comes to understanding the evolutionary pressures for such behaviour. Furthermore, key differences, such as how humans and Pan communicate, appear to distinguish how we experience empathy compared to our closest living relatives.
PubMed: 38597291
DOI: 10.1111/brv.13080 -
PNAS Nexus Feb 2024For highly visual species like primates, facial and bodily emotion expressions play a crucial role in emotion perception. However, most research focuses on facial...
For highly visual species like primates, facial and bodily emotion expressions play a crucial role in emotion perception. However, most research focuses on facial expressions, while the perception of bodily cues is still poorly understood. Using a novel comparative priming eye-tracking design, we examined whether our close primate relatives, the chimpanzees (), and humans infer emotions from bodily cues through subsequent perceptual integration with facial expressions. In experiment 1, we primed chimpanzees with videos of bodily movements of unfamiliar conspecifics engaged in social activities of opposite valence ( and ) against neutral control scenes to examine attentional bias toward succeeding congruent or incongruent facial expressions. In experiment 2, we assessed the same attentional bias in humans yet using stimuli showing unfamiliar humans. In experiment 3, humans watched the chimpanzee stimuli of experiment 1, to examine cross-species emotion perception. Chimpanzees exhibited a persistent attention bias but did not associate bodily with congruent facial cues. In contrast, humans prioritized conspecifics' congruent facial expressions (matching bodily scenes) over incongruent ones (mismatching). Nevertheless, humans exhibited no congruency effect when viewing chimpanzee stimuli, suggesting difficulty in cross-species emotion perception. These results highlight differences in emotion perception, with humans being greatly affected by fearful and playful bodily cues and chimpanzees being strongly drawn toward fearful expressions, regardless of the preceding bodily priming cue. These data advance our understanding of the evolution of emotion signaling and the presence of distinct perceptual patterns in hominids.
PubMed: 38344008
DOI: 10.1093/pnasnexus/pgae012 -
Primates; Journal of Primatology Jan 2024Like humans, chimpanzees (Pan troglodytes) are well known for their vertebrate and invertebrate hunting, but they rarely scavenge. In contrast, while hunting and meat...
Like humans, chimpanzees (Pan troglodytes) are well known for their vertebrate and invertebrate hunting, but they rarely scavenge. In contrast, while hunting and meat consumption became increasingly important during the evolution of the genus Homo, scavenging meat and marrow from carcasses of large mammals was also likely to be an important component of their subsistence strategies. Here, we describe a confrontational scavenging interaction between an adult male chimpanzee from the Issa Valley and a crowned eagle (Stephanoaetus coronatus), which resulted in the chimpanzee capturing and consuming the carcass of a juvenile bushbuck (Tragelaphus scriptus). We describe the interaction and contextualize this with previous scavenging observations from chimpanzees.
Topics: Humans; Male; Animals; Pan troglodytes; Tanzania; Hominidae; Vertebrates; Environment; Eagles; Mammals
PubMed: 37903999
DOI: 10.1007/s10329-023-01099-0 -
Journal of Virology Mar 2024Macrophages are important target cells for diverse viruses and thus represent a valuable system for studying virus biology. Isolation of primary human macrophages is...
UNLABELLED
Macrophages are important target cells for diverse viruses and thus represent a valuable system for studying virus biology. Isolation of primary human macrophages is done by culture of dissociated tissues or from differentiated blood monocytes, but these methods are both time consuming and result in low numbers of recovered macrophages. Here, we explore whether macrophages derived from human induced pluripotent stem cells (iPSCs)-which proliferate indefinitely and potentially provide unlimited starting material-could serve as a faithful model system for studying virus biology. Human iPSC-derived monocytes were differentiated into macrophages and then infected with HIV-1, dengue virus, or influenza virus as model human viruses. We show that iPSC-derived macrophages support the replication of these viruses with kinetics and phenotypes similar to human blood monocyte-derived macrophages. These iPSC-derived macrophages were virtually indistinguishable from human blood monocyte-derived macrophages based on surface marker expression (flow cytometry), transcriptomics (RNA sequencing), and chromatin accessibility profiling. iPSC lines were additionally generated from non-human primate (chimpanzee) fibroblasts. When challenged with dengue virus, human and chimpanzee iPSC-derived macrophages show differential susceptibility to infection, thus providing a valuable resource for studying the species-tropism of viruses. We also show that blood- and iPSC-derived macrophages both restrict influenza virus at a late stage of the virus lifecycle. Collectively, our results substantiate iPSC-derived macrophages as an alternative to blood monocyte-derived macrophages for the study of virus biology.
IMPORTANCE
Macrophages have complex relationships with viruses: while macrophages aid in the removal of pathogenic viruses from the body, macrophages are also manipulated by some viruses to serve as vessels for viral replication, dissemination, and long-term persistence. Here, we show that iPSC-derived macrophages are an excellent model that can be exploited in virology.
Topics: Animals; Humans; Cell Differentiation; HIV-1; Induced Pluripotent Stem Cells; Macrophages; Orthomyxoviridae; Pan troglodytes; Dengue Virus; Fibroblasts; Monocytes; Virus Replication; Flow Cytometry; Gene Expression Profiling; Chromatin Assembly and Disassembly; Viral Tropism; Models, Biological; Virology; Biomarkers
PubMed: 38323811
DOI: 10.1128/jvi.01563-23 -
Scientific Reports Oct 2023HLA and disease studies by using single allele statistics have been fruitless during the last 40 years for explaining association pathogenesis of the associated...
HLA and disease studies by using single allele statistics have been fruitless during the last 40 years for explaining association pathogenesis of the associated diseases.Other approaches are necessary to untangle this puzzle. We aim to revisit complement alleleism in humans and primates for both studying MHC and disease association to complotypes and extended MHC haplotypes in order to also explain the positive directional selection of maintaining immune response genes (complement, MHC adaptive and MHC non-specific genes) that keeps these three type of genes together in a short chromosome stretch (MHC) for million years. These genes may be linked to conjointly avoid microbes attack and autoimmunity. In the present paper, it is obtained a new Bf chimpanzee allele, provisionaly named Patr-Bf*A:01,that differs from other Bf alleles by having CTG at eleventh codon of exon 2 in order to start the newly suggested methodology and explain functional and evolutionary MHC obscure aspects. Exons 1 to 6 of Ba fragment of Bf gene were obtained from chimpanzee. This new chimpanzee Factor B allele (Patr-Bf*A:01) is to be identical to a infrequent human Bf allele (SNP rs641153); it stresses the strong evolutive pressure upon certain alleles that are trans specific. It also may apply to MHC extended haplotipes which may conjointly act to start an adequate immune response. It is the first time that a complement MHC class III allele is described to undergo trans species evolution,in contrast to class I and class II alleles which had already been reported . Allelism of complement factors are again proposed for studying MHC complement genes, complotypes, and extended MHC haplotypes which may be more informative that single MHC marker studies.
Topics: Male; Animals; Humans; Alleles; Pan troglodytes; Major Histocompatibility Complex; Hominidae; Histocompatibility Antigens; Complement Factor B; Chromosomes
PubMed: 37794053
DOI: 10.1038/s41598-023-42016-1 -
PloS One 2023The Underwater Acoustic Sensor Network (UASN) is a large network in which the vicinity of a transmitting node is made up of numerous operational sensor nodes. The...
The Underwater Acoustic Sensor Network (UASN) is a large network in which the vicinity of a transmitting node is made up of numerous operational sensor nodes. The communication process may be substantially disrupted due to the underwater acoustic channel's time-varying and space-varying features. As a result, the underwater acoustic communication system faces the problems of reducing interference and enhancing communication effectiveness and quality through adaptive modulation. To overcome this issue, this paper intends to propose a model for optimal path selection and secured data transmission in UASN via Long Short-Term Memory (LSTM) based energy prediction. The proposed model of transmitting the secured data in UASN through the optimal path involves two major phases. Initially, the nodes are selected under the consideration of constraints like energy, distance and link quality in terms of throughput. Moreover, the energy is predicted with the aid of LSTM and the optimal path is selected with the proposed hybrid optimization algorithm termed as Pelican Updated Chimp Optimization Algorithm (PUCOA), which is the combination of two algorithms including the Pelican Optimization Algorithm (POA) and Chimp Optimization Algorithm (COA). Further, the data is transmitted via the optimal path securely by encrypting the data with the proposed improved blowfish algorithm (IBFA). At last, the developed LSTM+PUCOA model is validated with standard benchmark models and it proves that the performance of the proposed LSTM+PUCOA model attains 90.85% of accuracy, 92.78% of precision, 91.78% of specificity, 89.79% of sensitivity, 7.21% of FPR, 89.76% of F1 score, 89.77% of MCC, 10.20% of FNR, 92.45% of NPV, and 10.22% of FDR for Learning percentage 70.
Topics: Humans; Animals; Physical Phenomena; Acoustics; Algorithms; Benchmarking; Pan troglodytes
PubMed: 37669288
DOI: 10.1371/journal.pone.0289306