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PLoS Genetics Feb 2024Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we...
Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as rooted three-leaved trees, each with a topology and two coalescent events happening in discretized time intervals within the phylogeny. Posterior decoding of the hidden Markov model can be used to infer the ancestral recombination graph for the alignment and details on demographic changes within a branch. Since TRAILS performs posterior decoding at the base-pair level, genome-wide scans based on the posterior probabilities can be devised to detect deviations from neutrality. Using TRAILS on a human-chimp-gorilla-orangutan alignment, we recover speciation parameters and extract information about the topology and coalescent times at high resolution.
Topics: Animals; Humans; Genetic Speciation; Hominidae; Pan troglodytes; Phylogeny; Genetics, Population; Models, Genetic
PubMed: 38330138
DOI: 10.1371/journal.pgen.1010836 -
American Journal of Biological... Mar 2024Differences between adult humans and great apes in cervical vertebral morphology are well documented, but the ontogeny of this variation is still largely unexplored....
OBJECTIVES
Differences between adult humans and great apes in cervical vertebral morphology are well documented, but the ontogeny of this variation is still largely unexplored. This study examines patterns of growth in functionally relevant features of C1, C2, C4, and C6 in extant humans and apes to understand the development of their disparate morphologies.
MATERIALS AND METHODS
Linear and angular measurements were taken from 530 cervical vertebrae representing 146 individual humans, chimpanzees, gorillas, and orangutans. Specimens were divided into three age-categories based on dental eruption: juvenile, adolescent, and adult. Inter- and intraspecific comparisons were evaluated using resampling methods.
RESULTS
Of the eighteen variables examined here, seven distinguish humans from apes at the adult stage. Human-ape differences in features related to atlantoaxial joint function tend to be established by the juvenile stage, whereas differences in features related to the nuchal musculature and movement of the subaxial elements do not fully emerge until adolescence or later. The orientation of the odontoid process-often cited as a feature that distinguishes humans from apes-is similar in adult humans and adult chimpanzees, but the developmental patterns are distinct, with human adultlike morphology being achieved much earlier.
DISCUSSION
The biomechanical consequences of the variation observed here is poorly understood. Whether the differences in growth patterns represent functional links to cranial development or postural changes, or both, requires additional investigation. Determining when humanlike ontogenetic patterns evolved in hominins may provide insight into the functional basis driving the morphological divergence between extant humans and apes.
Topics: Animals; Humans; Adolescent; Pan troglodytes; Hominidae; Gorilla gorilla; Pongo; Cervical Vertebrae; Pongo pygmaeus
PubMed: 37283367
DOI: 10.1002/ajpa.24788 -
American Journal of Biological... Jan 2024Studying rib torsion is crucial for understanding the evolution of the hominid ribcage. Interestingly, there are variables of the rib cross section that could be...
OBJECTIVES
Studying rib torsion is crucial for understanding the evolution of the hominid ribcage. Interestingly, there are variables of the rib cross section that could be associated with rib torsion and, consequently, with the morphology of the thorax. The aim of this research is to conduct a comparative study of the shape and mineralized tissues of the rib cross section in different hominids to test for significant differences and, if possible, associate them to different thoracic morphotypes.
MATERIALS AND METHODS
The sample consists of the rib cross sections at the midshaft taken from 10 Homo sapiens and 10 Pan troglodytes adult individuals, as well as from A. africanus Sts 14. The shape of these rib cross sections was quantified using geometric morphometrics, while the mineralized tissues were evaluated using the compartmentalization index. Subsequently, covariation between both parameters was tested by a Spearman's ρ test, a permutation test and a linear regression.
RESULTS
Generally, P. troglodytes individuals exhibit rib cross sections that are rounder and more mineralized compared to those of H. sapiens. However, the covariation between both parameters was only observed in typical ribs (levels 3-10). Although covariation was not found in the rib cross sections of Sts 14, their parameters are closer to P. troglodytes.
DISCUSSION
On the one hand, the differences observed in the rib cross sections between H. sapiens and P. troglodytes might be related to different degrees of rib torsion and, consequently, to different thoracic 3D configurations. These findings can be functionally explained by considering their distinct modes of breathing and locomotion. On the other hand, although the rib cross sections belonging to Sts 14 are more similar to those of P. troglodytes, previous publications determined that their overall morphology is closer to modern humans. This discrepancy could reflect a diversity of post-cranial adaptations in Australopithecus.
Topics: Adult; Animals; Humans; Pan troglodytes; Hominidae; Thorax; Ribs; Skull
PubMed: 37724468
DOI: 10.1002/ajpa.24844 -
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 -
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 -
American Journal of Physiology. Heart... Mar 2024Atherosclerosis is the leading cause of death worldwide, and the predominant risk factors are advanced age and high-circulating low-density lipoprotein cholesterol... (Review)
Review
Atherosclerosis is the leading cause of death worldwide, and the predominant risk factors are advanced age and high-circulating low-density lipoprotein cholesterol (LDL-C). However, the findings of atherosclerosis in relatively young mummified remains and a lack of atherosclerosis in chimpanzees despite high LDL-C call into question the role of traditional cardiovascular risk factors. The inflammatory theory of atherosclerosis may explain the discrepancies between traditional risk factors and observed phenomena in current literature. Following the divergence from chimpanzees several millennia ago, loss of function mutations in immune regulatory genes and changes in gene expression have resulted in an overactive human immune system. The ubiquity of atherosclerosis in the modern era may reflect a selective pressure that enhanced the innate immune response at the cost of atherogenesis and other chronic disease states. Evidence provided from the fields of genetics, evolutionary biology, and paleoanthropology demonstrates a sort of circular dependency between inflammation, immune system functioning, and evolution at both a species and cellular level. More recently, the role of proinflammatory stimuli, somatic mutations, and the gene-environment effect appear to be underappreciated elements in the development and progression of atherosclerosis. Neurobiological stress, metabolic syndrome, and traditional cardiovascular risk factors may instead function as intermediary links between inflammation and atherosclerosis. Therefore, considering evolution as a mechanistic process and atherosclerosis as part of the inertia of evolution, greater insight into future preventative and therapeutic interventions for atherosclerosis can be gained by examining the past.
Topics: Animals; Humans; Pan troglodytes; Body Remains; Cholesterol, LDL; Atherosclerosis; Inflammation
PubMed: 38305751
DOI: 10.1152/ajpheart.00744.2023 -
Anatomical Record (Hoboken, N.J. : 2007) Dec 2023The evolution of human pelvic form is primarily studied using disarticulated osteological material of living and fossil primates that need rearticulation to approximate...
The evolution of human pelvic form is primarily studied using disarticulated osteological material of living and fossil primates that need rearticulation to approximate anatomical position. To test whether this technique introduces errors that impact biological signals, virtual rearticulations of the pelvis in anatomical position from computed tomography scans were compared with rearticulated models from the same individuals for one female and one male of Homo sapiens, Pan troglodytes, Macaca mulatta, Lepilemur mustelinus, Galago senegalensis, and Nycticebus pygmaeus. "Cadaveric" pelvic bones were first analyzed in anatomical position, then the three bones were segmented individually, intentionally scattered, and "rearticulated" to test for rearticulation error. Three-dimensional landmarks and linear measurements were used to characterize the overall pelvis shape. Cadaveric and rearticulated pelves were not identical, but inter-specific and intra-specific shape differences were higher than the landmarking error in the cadaveric individuals and the landmarking/rearticulation error in the rearticulated pelves, demonstrating that the biological signal is stronger than the noise introduced by landmarking and rearticulation. The rearticulation process, however, underestimates the medio-lateral pelvic measurements in species with a substantial pubic gap (e.g., G. senegalensis, N. pygmaeus) possibly because the greater contribution of soft tissue to the pelvic girdle introduces higher uncertainty during rearticulation. Nevertheless, this discrepancy affects only the caudal-most part of the pelvis. This study demonstrates that the rearticulation of pelvic bones does not substantially affect the biological signal in comparative 3D morphological studies but suggests that anatomically connected pelves of species with wide pubic gaps should be preferentially included in these studies.
PubMed: 38112056
DOI: 10.1002/ar.25366 -
Journal of Comparative Psychology... Aug 2023In this essay, the author explores the question of why distractions sometimes aid self-control. In a study with chimpanzees, Evans and Beran (2007) used two conditions...
In this essay, the author explores the question of why distractions sometimes aid self-control. In a study with chimpanzees, Evans and Beran (2007) used two conditions with toys to address the possibility raised by Mueller et al. (2023) about toys as distractors. In the first, the accumulating rewards were within reach, and so chimpanzees had to inhibit taking rewards if more were to accumulate. The second condition was essential to this issue, as in that case toys also were available, but the delayed reward was out of reach (i.e., the chimpanzees were forced to wait to get the delayed reward). Because these trial types were intermixed, an explanation of the toys' effectiveness through conditioned association with the delayed reward would predict that the chimpanzees should have engaged the toys equally often in both conditions. However, three of four chimpanzees engaged the toys more when the accumulating reward was within reach compared to when it was not. Evans and Beran suggested that engagement with distractors in that study occurred when it was functionally effective in aiding delayed gratification, not solely as a result of toys being associated with delayed rewards, and thus was a cognitively controlled decision by the chimpanzees. The results of Evans and Beran (2007) have yet to be replicated in any other primate species. But, Mueller et al. (2023) noted that a study with a parrot (Koepke et al., 2015) showed that the parrot would use distractors and even move the smaller, sooner reward away from itself, perhaps matching the self-distraction techniques of children who hide their faces or talk to themselves. Thus, it remains to be determined whether those behaviors also can be explained by learned associations with reward or whether they reflect attention-based explanations. Mueller et al. (2023) have provided a creative experiment and a compelling argument that more careful analysis is needed of exactly what happens when an animal (or child) engages distractors and shows improved self-control, so that we can understand what role past reinforcement history may play and what possible attentional strategies or other cognitive strategies are at work in different self-control tasks. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
Topics: Animals; Columbidae; Pan troglodytes; Learning; Parrots; Self-Control
PubMed: 37639231
DOI: 10.1037/com0000363 -
Science (New York, N.Y.) Oct 2023Among mammals, post-reproductive life spans are currently documented only in humans and a few species of toothed whales. Here we show that a post-reproductive life span...
Among mammals, post-reproductive life spans are currently documented only in humans and a few species of toothed whales. Here we show that a post-reproductive life span exists among wild chimpanzees in the Ngogo community of Kibale National Park, Uganda. Post-reproductive representation was 0.195, indicating that a female who reached adulthood could expect to live about one-fifth of her adult life in a post-reproductive state, around half as long as human hunter-gatherers. Post-reproductive females exhibited hormonal signatures of menopause, including sharply increasing gonadotropins after age 50. We discuss whether post-reproductive life spans in wild chimpanzees occur only rarely, as a short-term response to favorable ecological conditions, or instead are an evolved species-typical trait as well as the implications of these alternatives for our understanding of the evolution of post-reproductive life spans.
Topics: Animals; Female; Humans; Demography; Longevity; Menopause; Pan troglodytes; Uganda; Gonadotropins; Fertility; Gonadal Steroid Hormones
PubMed: 37883540
DOI: 10.1126/science.add5473 -
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