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Genome Biology and Evolution Nov 2023Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and...
Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been studied in great apes; however, the diversity of splicing variants remains unexplored. Here, we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this data set resulted in several findings. First, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Second, our results suggest that BPY2 transcripts and proteins originate from separate genomic regions in bonobo versus human, which is possibly facilitated by acquiring new promoters. Third, our analysis indicates that the PRY gene family, having the highest representation of noncoding transcripts, has been undergoing pseudogenization. Fourth, we have not detected signatures of selection in the five YAG families shared among great apes, even though we identified many species-specific protein-coding transcripts. Fifth, we predicted consensus disorder regions across most gene families and species, which could be used for future investigations of male infertility. Overall, our work illuminates the YAG isoform landscape and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.
Topics: Animals; Male; Humans; Pan paniscus; Hominidae; Y Chromosome; Pan troglodytes; Protein Isoforms
PubMed: 37967251
DOI: 10.1093/gbe/evad205 -
Genes Dec 2023Comparative analyses of MHC gene diversity and evolution across different species could offer valuable insights into the evolution of MHC genes. Intra- and inter-species...
Comparative analyses of MHC gene diversity and evolution across different species could offer valuable insights into the evolution of MHC genes. Intra- and inter-species sequence diversity and conservation of 12 classical major histocompatibility complex (MHC) class I genes from cattle, chimpanzees, pigs, and humans was analyzed using 20 representative allelic groups for each gene. The combined analysis of paralogous loci for each species revealed that intra-locus amino-acid sequence variations in the peptide-binding region (PBR) of MHC I genes did not differ significantly between species, ranging from 8.44% for to 10.75% for BoLA class I genes. In contrast, intraspecies differences in the non-PBRs of these paralogous genes were more pronounced, varying from 4.59% for to 16.89% for . Interestingly, the Shannon diversity index and rate of nonsynonymous substitutions for PBR were significantly higher in and BoLA than those in and . Analysis of peptide-binding pockets across all analyzed MHC class I genes of the four species indicated that pockets A and E showed the lowest and highest diversity, respectively. The estimated divergence times suggest that primate and artiodactyl MHC class I genes diverged 60.41 Mya, and BoLA and genes diverged 35.34 Mya. These results offer new insights into the conservation and diversity of MHC class I genes in various mammalian species.
Topics: Humans; Animals; Cattle; Swine; Pan troglodytes; Genes, MHC Class I; Hominidae; Histocompatibility Antigens Class I; HLA Antigens; Primates; Genetic Variation; Peptides; Mammals
PubMed: 38275589
DOI: 10.3390/genes15010007 -
Scientific Data May 2024Human and non-human primates have strikingly similar genomes, but they strongly differ in many brain-based processes (e.g., behaviour and cognition). While the functions...
Human and non-human primates have strikingly similar genomes, but they strongly differ in many brain-based processes (e.g., behaviour and cognition). While the functions of protein-coding genes have been extensively studied, rather little is known about the role of non-coding RNAs such as long non-coding RNAs (lncRNAs). Here, we predicted lncRNAs and analysed their expression pattern across different brain regions of human and non-human primates (chimpanzee, gorilla, and gibbon). Our analysis identified shared orthologous and non-orthologous lncRNAs, showing striking differences in the genomic features. Differential expression analysis of the shared orthologous lncRNAs from humans and chimpanzees revealed distinct expression patterns in subcortical regions (striatum, hippocampus) and neocortical areas while retaining a homogeneous expression in the cerebellum. Co-expression analysis of lncRNAs and protein-coding genes revealed massive proportions of co-expressed pairs in neocortical regions of humans compared to chimpanzees. Network analysis of co-expressed pairs revealed the distinctive role of the hub-acting orthologous lncRNAs in a region- and species-specific manner. Overall, our study provides novel insight into lncRNA driven gene regulatory landscape, neural regulation, brain evolution, and constitutes a resource for primate's brain lncRNAs.
Topics: Animals; Humans; Brain; Gorilla gorilla; Hylobates; Pan troglodytes; Primates; RNA, Long Noncoding; Species Specificity
PubMed: 38806530
DOI: 10.1038/s41597-024-03380-3 -
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 -
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 -
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 -
Scientific Reports Oct 2023Detailed observations of animal reactions to a collapsed individual in wild are rare but essential to debates about the perception of death by nonhuman animals,...
Detailed observations of animal reactions to a collapsed individual in wild are rare but essential to debates about the perception of death by nonhuman animals, including chimpanzees. A male juvenile chimpanzee named Volta, a member of the M group in the Mahale Mountains National Park, fell from a tall tree and was temporarily incapacitated, suffering a severe concussion and nasal bone fracture. However, Volta showed signs of gradual recovery. We compared the behavior of other chimpanzees towards Volta with the previous reports on the behavior towards collapsed or recently dead group members. We found that behaviors towards Volta were similar to those observed towards collapsed or dead members. These included other-regarding behaviors and aggressive behaviors, and notably, licking of Volta's blood, which has not been previously reported. Adult males tended to be in close proximity to Volta for longer periods than adult females. The social situation with adult males including alpha male, surrounding Volta likely influenced the behavior of other individuals. Exploring the state of recovery of the injured individual, by closely approaching, directing various behaviors, and observing the reactions of the victim, and demonstrate tolerance and consideration towards the victim.
Topics: Humans; Male; Animals; Female; Pan troglodytes; Behavior, Animal; Aggression; Accidents; Social Behavior; Tanzania
PubMed: 37794020
DOI: 10.1038/s41598-023-43229-0 -
Magnetic Resonance Imaging Jul 2024Field-to-susceptibility inversion in quantitative susceptibility mapping (QSM) is ill-posed and needs numerical stabilization through either regularization or...
PURPOSE
Field-to-susceptibility inversion in quantitative susceptibility mapping (QSM) is ill-posed and needs numerical stabilization through either regularization or oversampling by acquiring data at three or more object orientations. Calculation Of Susceptibility through Multiple Orientations Sampling (COSMOS) is an established oversampling approach and regarded as QSM gold standard. It achieves a well-conditioned inverse problem, requiring rotations by 0°, 60° and 120° in the yz-plane. However, this is impractical in vivo, where head rotations are typically restricted to a range of ±25°. Non-ideal sampling degrades the conditioning with residual streaking artifacts whose mitigation needs further regularization. Moreover, susceptibility anisotropy in white matter is not considered in the COSMOS model, which may introduce additional bias. The current work presents a thorough investigation of these effects in primate brain.
METHODS
Gradient-recalled echo (GRE) data of an entire fixed chimpanzee brain were acquired at 7 T (350 μm resolution, 10 orientations) including ideal COSMOS sampling and realistic rotations in vivo. Comparisons of the results included ideal COSMOS, in-vivo feasible acquisitions with 3-8 orientations and single-orientation iLSQR QSM.
RESULTS
In-vivo feasible and optimal COSMOS yielded high-quality susceptibility maps with increased SNR resulting from averaging multiple acquisitions. COSMOS reconstructions from non-ideal rotations about a single axis required additional L2-regularization to mitigate residual streaking artifacts.
CONCLUSION
In view of unconsidered anisotropy effects, added complexity of the reconstruction, and the general challenge of multi-orientation acquisitions, advantages of sub-optimal COSMOS schemes over regularized single-orientation QSM appear limited in in-vivo settings.
Topics: Anisotropy; Brain; Animals; Algorithms; Magnetic Resonance Imaging; Image Processing, Computer-Assisted; Artifacts; Pan troglodytes; Brain Mapping; White Matter; Nonlinear Dynamics; Reproducibility of Results
PubMed: 38631534
DOI: 10.1016/j.mri.2024.04.020 -
Nature Communications Jan 2024Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the...
Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.
Topics: Animals; Hominidae; Gastrointestinal Microbiome; Microbiota; Pan troglodytes; Pan paniscus
PubMed: 38182626
DOI: 10.1038/s41467-023-44636-7