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Scientific Reports Jan 2024Comparative perspectives are crucial in the study of human development, yet longitudinal comparisons of humans and other primates are still relatively uncommon. Here, we...
Comparative perspectives are crucial in the study of human development, yet longitudinal comparisons of humans and other primates are still relatively uncommon. Here, we combined theoretical frameworks from cross-cultural and comparative psychology, to study maternal style in 10 mother-infant pairs of German urban humans (Homo sapiens) and 10 mother-infant pairs of captive chimpanzees (Pan troglodytes), during the first year of infants' development. We conducted focal observations of different behaviours (i.e. nursing, carrying, body contact, touching, grooming, restraining, approaching, leaving, rejection, aggression, mutual gaze, object stimulation), during natural interactions. Analyses revealed a more distal maternal style in WEIRD humans than in captive chimpanzees, with different behaviours being generally more common in one of the two species throughout development. For other behaviours (i.e. nursing), developmental trajectories differed between WEIRD humans and captive chimpanzees, although differences generally decreased through infants' development. Overall, our study confirms functional approaches as a valid tool for comparative longitudinal studies.
Topics: Animals; Female; Infant; Humans; Pan troglodytes; Maternal Behavior; Mothers; Aggression; Child Development
PubMed: 38233560
DOI: 10.1038/s41598-024-51999-4 -
Frontiers in Immunology 2023The killer cell immunoglobulin-like receptors (KIR) play a pivotal role in modulating the NK cell responses, for instance, through interaction with major...
INTRODUCTION
The killer cell immunoglobulin-like receptors (KIR) play a pivotal role in modulating the NK cell responses, for instance, through interaction with major histocompatibility complex (MHC) class I molecules. Both gene systems map to different chromosomes but co-evolved during evolution. The human gene family is characterized by abundant allelic polymorphism and copy number variation. In contrast, our knowledge of the repertoire in chimpanzees is limited to 39 reported alleles, with no available population data. Only three genomic region configurations have been mapped, and seventeen additional ones were deduced by genotyping.
METHODS
Previously, we documented that the chimpanzee MHC class I repertoire has been skewed due to an ancient selective sweep. To understand the depth of the sweep, we set out to determine the full-length transcriptome - in our MHC characterized pedigreed West African chimpanzee cohort - using SMRT sequencing (PacBio). In addition, the genomic organization of 14 haplotypes was characterized by applying a Cas9-mediated enrichment approach in concert with long-read sequencing by Oxford Nanopore Technologies.
RESULTS
In the cohort, we discovered 35 undescribed and 15 already recorded alleles, and a novel hybrid gene. Some transcripts are subject to evolutionary conserved alternative splicing events. A detailed insight on the region dynamics (location and order of genes) was obtained, however, only five new region configurations were detected. The population data allowed to investigate the distribution of the MHC-C1 and C2-epitope specificity of the inhibitory lineage III KIR repertoire, and appears to be skewed towards C2.
DISCUSSION
Although the region is known to evolve fast, as observed in other primate species, our overall conclusion is that the genomic architecture and repertoire in West African chimpanzees exhibit only limited to moderate levels of variation. Hence, the ancient selective sweep that affected the chimpanzee MHC class I region may also have impacted the system.
Topics: Animals; Humans; Pan troglodytes; Haplotypes; Alleles; DNA Copy Number Variations; Hominidae; Histocompatibility Antigens Class I; Receptors, KIR; HLA Antigens; Primates; Killer Cells, Natural
PubMed: 38149259
DOI: 10.3389/fimmu.2023.1308316 -
Proceedings of the National Academy of... Jan 2024
Topics: Animals; Pan troglodytes; Pan paniscus; Eye-Tracking Technology; Emotions; Eye Movements
PubMed: 38147565
DOI: 10.1073/pnas.2319953121 -
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 -
Scientific Reports Feb 2024Partner choice promotes competition among individuals to be selected as a cooperative partner, a phenomenon referred to as competitive altruism. We explored whether...
Partner choice promotes competition among individuals to be selected as a cooperative partner, a phenomenon referred to as competitive altruism. We explored whether chimpanzees engage in competitive altruism in a triadic Ultimatum Game where two proposers can send offers simultaneously or consecutively to a responder who can only accept one of the two competing offers. In a dyadic control condition only one proposer at a time could send an offer to the responder. Chimpanzees increased their offers across trials in the competitive triadic, but not in the dyadic control condition. Chimpanzees also increased their offers after being rejected in previous triadic trials. Furthermore, we found that chimpanzees, under specific conditions, outcompete first proposers in triadic consecutive trials before the responder could choose which offer to accept by offering more than what is expected if they acted randomly or simply offered the smallest possible amount. These results suggest that competitive altruism in chimpanzees did not emerge just as a by-product of them trying to increase over previous losses. Chimpanzees might consider how others' interactions affect their outcomes and engage in strategies to maximize their chances of being selected as cooperative partners.
Topics: Animals; Humans; Altruism; Pan troglodytes; Games, Experimental; Acceptance and Commitment Therapy; Decision Making
PubMed: 38336923
DOI: 10.1038/s41598-024-53973-6 -
EBioMedicine Feb 2024Simian immunodeficiency viruses (SIV) have been jumping between non-human primates in West/Central Africa for thousands of years and yet, the HIV-1 epidemic only...
BACKGROUND
Simian immunodeficiency viruses (SIV) have been jumping between non-human primates in West/Central Africa for thousands of years and yet, the HIV-1 epidemic only originated from a primate lentivirus over 100 years ago.
METHODS
This study examined the replicative fitness, transmission, restriction, and cytopathogenicity of 22 primate lentiviruses in primary human lymphoid tissue and both primary human and chimpanzee peripheral blood mononuclear cells.
FINDINGS
Pairwise competitions revealed that SIV from chimpanzees (cpz) had the highest replicative fitness in human or chimpanzee peripheral blood mononuclear cells, even higher fitness than HIV-1 group M strains responsible for worldwide epidemic. The SIV strains belonging to the "HIV-2 lineage" (including SIVsmm, SIVmac, SIVagm) had the lowest replicative fitness. SIVcpz strains were less inhibited by human restriction factors than the "HIV-2 lineage" strains. SIVcpz efficiently replicated in human tonsillar tissue but did not deplete CD4+ T-cells, consistent with the slow or nonpathogenic disease observed in most chimpanzees. In contrast, HIV-1 isolates and SIV of the HIV-2 lineage were pathogenic to the human tonsillar tissue, almost independent of the level of virus replication.
INTERPRETATION
Of all primate lentiviruses, SIV from chimpanzees appears most capable of infecting and replicating in humans, establishing HIV-1. SIV from other Old World monkeys, e.g. the progenitor of HIV-2, replicate slowly in humans due in part to restriction factors. Nonetheless, many of these SIV strains were more pathogenic than SIVcpz. Either SIVcpz evolved into a more pathogenic virus while in humans or a rare SIVcpz, possibly extinct in chimpanzees, was pathogenic immediately following the jump into human.
FUNDING
Support for this study to E.J.A. was provided by the NIH/NIAID R01 AI49170 and CIHR project grant 385787. Infrastructure support was provided by the NIH CFAR AI36219 and Canadian CFI/Ontario ORF 36287. Efforts of J.A.B. and N.J.H. was provided by NIH AI099473 and for D.H.C., by VA and NIH AI AI080313.
Topics: Animals; Humans; Lentiviruses, Primate; Pan troglodytes; Simian Acquired Immunodeficiency Syndrome; Virulence; Leukocytes, Mononuclear; Simian Immunodeficiency Virus; Primates; HIV-1; Lymphoid Tissue; Ontario
PubMed: 38215691
DOI: 10.1016/j.ebiom.2023.104965 -
Frontiers in Genetics 2024Alport Syndrome (AS) is a genetic kidney disorder characterized by progressive hearing loss and atypical eye symptoms, resulting in a poor prognosis and lack of...
Alport Syndrome (AS) is a genetic kidney disorder characterized by progressive hearing loss and atypical eye symptoms, resulting in a poor prognosis and lack of effective targeted therapy. The primary mode of inheritance is X-linked dominant (XLAS) due to variants in the gene. This study revealed a previously unidentified alternative form of the gene, namely, the c.4822-10T>C variant, which was confirmed through experiments. To investigate the impact of a splicing variant on mRNA production, an minigene splicing assay was utilized. Additionally, molecular dynamics was employed to predict the ability of α5(IV) to form a triple helix. Results from the experiment revealed that the wild-type (WT) plasmid produced two distinct mRNA products simultaneously. Sequence analysis using the BLAST database revealed a 173-bp deletion in the mRNA sequence of the first product, indicating a potential similarity to the XM_016942897.2 transcript of . The second mRNA product of the WT plasmid contained the full sequence of exons 51, 52, and 53, as anticipated. Conversely, the mutant (MT) plasmid generated a single mRNA product with a 173-bp deletion in exon 52, leading to the identification of the mature mRNA expression as NM_033380.2: COL4A5: c.4822_4994del. In the context of nonsense-mediated mRNA decay (NMD), the deletion c.4822_4994 results in the production of a truncated protein, p.His1608*, that terminates prematurely. This truncated protein may disrupt the secondary structure of α5(IV) and potentially cause an abnormal conformation of α345(IV). This study examines the relationship between the variable splicing pattern in the NM_033380.2 transcript of the gene in XLAS patients and the presence of the gene splice variant c.4822-10T>C. Our findings indicate that the c.4822-10T>C splice variant leads to activation of nonsense-mediated mRNA degradation (NMD) and reduced mRNA expression, resulting in inadequate synthesis of the corresponding proteins. This aligns with the patient's immunofluorescence results showing negative α5(IV) chain presence at the glomerular basement membrane, bursa, and tubular basement membrane, confirming the pathogenic nature of c.4822-10T>C.
PubMed: 38818038
DOI: 10.3389/fgene.2024.1330525 -
ELife Feb 2024Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely...
Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell-type-specific -regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell-type, avoiding the potentially deleterious consequences of -acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. It has recently become possible to quantify human-specific -acting regulatory divergence by measuring allele-specific expression in human-chimpanzee hybrid cells-the product of fusing induced pluripotent stem (iPS) cells of each species . However, these -regulatory changes have only been explored in a limited number of cell types. Here, we quantify human-chimpanzee -regulatory divergence in gene expression and chromatin accessibility across six cell types, enabling the identification of highly cell-type-specific -regulatory changes. We find that cell-type-specific genes and regulatory elements evolve faster than those shared across cell types, suggesting an important role for genes with cell-type-specific expression in human evolution. Furthermore, we identify several instances of lineage-specific natural selection that may have played key roles in specific cell types, such as coordinated changes in the -regulation of dozens of genes involved in neuronal firing in motor neurons. Finally, using novel metrics and a machine learning model, we identify genetic variants that likely alter chromatin accessibility and transcription factor binding, leading to neuron-specific changes in the expression of the neurodevelopmentally important genes and . Overall, our results demonstrate that integrative analysis of -regulatory divergence in chromatin accessibility and gene expression across cell types is a promising approach to identify the specific genes and genetic variants that make us human.
Topics: Humans; Animals; Chromatin; Pan troglodytes; Hybrid Cells; Motor Neurons; Gene Expression
PubMed: 38358392
DOI: 10.7554/eLife.89594 -
Genes Jun 2024We identified five distinct full-length human mineralocorticoid receptor (MR) genes containing either 984 amino acids (MR-984) or 988 amino acids (MR-988), which can be... (Comparative Study)
Comparative Study
We identified five distinct full-length human mineralocorticoid receptor (MR) genes containing either 984 amino acids (MR-984) or 988 amino acids (MR-988), which can be distinguished by the presence or absence of Lys, Cys, Ser, and Trp (KCSW) in their DNA-binding domain (DBD) and mutations at codons 180 and 241 in their amino-terminal domain (NTD). Two human MR-KCSW genes contain either (Val-180, Val-241) or (Ile-180, Val-241) in their NTD, and three human MR-984 genes contain either (Ile-180, Ala-241), (Val-180, Val-241), or (Ile-180, Val-241). Human MR-KCSW with (Ile-180, Ala-241) has not been cloned. In contrast, chimpanzees contain four MRs: two MR-988s with KCSW in their DBD, or two MR-984s without KCSW in their DBD. Chimpanzee MRs only contain (Ile180, Val-241) in their NTD. A chimpanzee MR with either (Val-180, Val-241) or (Ile-180, Ala-241) in the NTD has not been cloned. Gorillas and orangutans each contain one MR-988 with KCSW in the DBD and one MR-984 without KCSW, and these MRs only contain (Ile-180, Val-241) in their NTD. A gorilla MR or orangutan MR with either (Val-180, Val-241) or (Ile-180, Ala-241) in the NTD has not been cloned. Together, these data suggest that human MRs with (Val-180, Val-241) or (Ile-180, Ala-241) in the NTD evolved after humans and chimpanzees diverged from their common ancestor. Considering the multiple functions in human development of the MR in kidney, brain, heart, skin, and lungs, as well as MR activity in interaction with the glucocorticoid receptor, we suggest that the evolution of human MRs that are absent in chimpanzees may have been important in the evolution of humans from chimpanzees. Investigation of the physiological responses to corticosteroids mediated by the MR in humans, chimpanzees, gorillas, and orangutans may provide insights into the evolution of humans and their closest relatives.
Topics: Animals; Receptors, Mineralocorticoid; Humans; Pan troglodytes; Evolution, Molecular; Gorilla gorilla; Phylogeny; Pongo; Amino Acid Sequence; Protein Domains
PubMed: 38927703
DOI: 10.3390/genes15060767 -
Communications Biology Jun 2024Although the gross morphology of the heart is conserved across mammals, subtle interspecific variations exist in the cardiac phenotype, which may reflect evolutionary...
Although the gross morphology of the heart is conserved across mammals, subtle interspecific variations exist in the cardiac phenotype, which may reflect evolutionary divergence among closely-related species. Here, we compare the left ventricle (LV) across all extant members of the Hominidae taxon, using 2D echocardiography, to gain insight into the evolution of the human heart. We present compelling evidence that the human LV has diverged away from a more trabeculated phenotype present in all other great apes, towards a ventricular wall with proportionally greater compact myocardium, which was corroborated by post-mortem chimpanzee (Pan troglodytes) hearts. Speckle-tracking echocardiographic analyses identified a negative curvilinear relationship between the degree of trabeculation and LV systolic twist, revealing lower rotational mechanics in the trabeculated non-human great ape LV. This divergent evolution of the human heart may have facilitated the augmentation of cardiac output to support the metabolic and thermoregulatory demands of the human ecological niche.
Topics: Animals; Humans; Heart Ventricles; Hominidae; Phenotype; Echocardiography; Biological Evolution; Pan troglodytes; Male; Female
PubMed: 38877299
DOI: 10.1038/s42003-024-06280-9