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BMC Genomic Data Jan 2024We tackle the problem of estimating species TMRCAs (Time to Most Recent Common Ancestor), given a genome sequence from each species and a large known phylogenetic tree...
BACKGROUND
We tackle the problem of estimating species TMRCAs (Time to Most Recent Common Ancestor), given a genome sequence from each species and a large known phylogenetic tree with a known structure (typically from one of the species). The number of transitions at each site from the first sequence to the other is assumed to be Poisson distributed, and only the parity of the number of transitions is observed. The detailed phylogenetic tree contains information about the transition rates in each site. We use this formulation to develop and analyze multiple estimators of the species' TMRCA. To test our methods, we use mtDNA substitution statistics from the well-established Phylotree as a baseline for data simulation such that the substitution rate per site mimics the real-world observed rates.
RESULTS
We evaluate our methods using simulated data and compare them to the Bayesian optimizing software BEAST2, showing that our proposed estimators are accurate for a wide range of TMRCAs and significantly outperform BEAST2. We then apply the proposed estimators on Neanderthal, Denisovan, and Chimpanzee mtDNA genomes to better estimate their TMRCA with modern humans and find that their TMRCA is substantially later, compared to values cited recently in the literature.
CONCLUSIONS
Our methods utilize the transition statistics from the entire known human mtDNA phylogenetic tree (Phylotree), eliminating the requirement to reconstruct a tree encompassing the specific sequences of interest. Moreover, they demonstrate notable improvement in both running speed and accuracy compared to BEAST2, particularly for earlier TMRCAs like the human-Chimpanzee split. Our results date the human - Neanderthal TMRCA to be [Formula: see text] years ago, considerably later than values cited in other recent studies.
Topics: Animals; Humans; Neanderthals; Phylogeny; Pan troglodytes; Bayes Theorem; Hominidae; DNA, Mitochondrial
PubMed: 38166646
DOI: 10.1186/s12863-023-01185-8 -
Genome Biology and Evolution Jan 2024The human brain utilizes ∼20% of all of the body's metabolic resources, while chimpanzee brains use <10%. Although previous work shows significant differences in...
The human brain utilizes ∼20% of all of the body's metabolic resources, while chimpanzee brains use <10%. Although previous work shows significant differences in metabolic gene expression between the brains of primates, we have yet to fully resolve the contribution of distinct brain cell types. To investigate cell type-specific interspecies differences in brain gene expression, we conducted RNA-seq on neural progenitor cells, neurons, and astrocytes generated from induced pluripotent stem cells from humans and chimpanzees. Interspecies differential expression analyses revealed that twice as many genes exhibit differential expression in astrocytes (12.2% of all genes expressed) than neurons (5.8%). Pathway enrichment analyses determined that astrocytes, rather than neurons, diverged in expression of glucose and lactate transmembrane transport, as well as pyruvate processing and oxidative phosphorylation. These findings suggest that astrocytes may have contributed significantly to the evolution of greater brain glucose metabolism with proximity to humans.
Topics: Animals; Humans; Astrocytes; Pan troglodytes; Neurons; Brain; Gene Expression
PubMed: 38159045
DOI: 10.1093/gbe/evad239 -
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 -
Scientific Reports Dec 2023Although once regarded as a unique human feature, tool-use is widespread in the animal kingdom. Some of the most proficient tool-users are our closest living relatives,...
Although once regarded as a unique human feature, tool-use is widespread in the animal kingdom. Some of the most proficient tool-users are our closest living relatives, chimpanzees. These repertoires however consist primarily of tool use, rather than tool manufacture (for later use). Furthermore, most populations of chimpanzees use organic materials, such as sticks and leaves, rather than stones as tools. This distinction may be partly ecological, but it is also important as chimpanzees are often used as models for the evolution of human material culture, the oldest traces of which consist of manufactured sharp stone tools (so-called "flakes"). Thus, examining the conditions (if any) under which chimpanzees may develop flake manufacture and use can provide insight into the drivers of these behaviours in our own lineage. Previous studies on non-human apes' ability to make and use flakes focused on enculturated apes, giving them full demonstrations of the behaviour immediately, without providing social information on the task in a stepwise manner. Here we tested naïve, captive chimpanzees (N = 4; three potentially enculturated and one unenculturated subject) in a social learning experimental paradigm to investigate whether enculturated and/or unenculturated chimpanzees would develop flake making and use after social information of various degrees (including a human demonstration) was provided in a scaffolded manner. Even though social learning opportunities were provided, neither the unenculturated subject nor any of the potentially enculturated subjects made or used flakes, in stark contrast to previous studies with enculturated apes. These data suggest that flake manufacture and use is outside of our tested group of captive chimpanzees' individual and social learning repertoires. It also suggests that high levels of enculturation alongside human demonstrations (and/or training) may be required before captive chimpanzees can develop this behaviour.
Topics: Animals; Humans; Pan troglodytes; Learning; Behavior, Animal; Social Behavior; Social Learning
PubMed: 38123639
DOI: 10.1038/s41598-023-49780-0 -
Primates; Journal of Primatology Mar 2024In human speech, the close back rounded vowel /u/ (the vowel in "boot") is articulated with the tongue arched toward the dorsal boundary of the hard palate, with the...
In human speech, the close back rounded vowel /u/ (the vowel in "boot") is articulated with the tongue arched toward the dorsal boundary of the hard palate, with the pharyngeal cavity open. Acoustic and perceptual properties of chimpanzee (Pan troglodytes) hoo's are similar to those of the human vowel /u/. However, the vocal tract morphology of chimpanzees likely limits their phonetic capabilities, so that it is unlikely, or even impossible, that their articulation is comparable to that of a human. To determine how qualities of the vowel /u/ may be achieved given the chimpanzee vocal tract, we calculated transfer functions of the vocal tract area for tube models of vocal tract configurations in which vocal tract length, length and area of a laryngeal air sac simulacrum, length of lip protrusion, and area of lip opening were systematically varied. The method described is principally acoustic; we make no claim as to the actual shape of the chimpanzee vocal tract during call production. Nonetheless, we demonstrate that it may be possible to achieve the acoustic and perceptual qualities of back vowels without a reconfigured human vocal tract. The results, while tentative, suggest that the production of hoo's by chimpanzees, while achieving comparable vowel-like qualities to the human /u/, may involve articulatory gestures that are beyond the range of the human articulators. The purpose of this study was to (1) stimulate further simulation research on great ape articulation, and (2) show that apparently vowel-like phenomena in nature are not necessarily indicative of evolutionary continuity per se.
Topics: Animals; Humans; Pan troglodytes; Speech Acoustics; Speech; Phonetics; Tongue
PubMed: 38110671
DOI: 10.1007/s10329-023-01107-3 -
Proceedings of the National Academy of... Dec 2023Recognition and memory of familiar conspecifics provides the foundation for complex sociality and is vital to navigating an unpredictable social world [Tibbetts and...
Recognition and memory of familiar conspecifics provides the foundation for complex sociality and is vital to navigating an unpredictable social world [Tibbetts and Dale, , 529-537 (2007)]. Human social memory incorporates content about interactions and relationships and can last for decades [Sherry and Schacter, , 439-454 (1987)]. Long-term social memory likely played a key role throughout human evolution, as our ancestors increasingly built relationships that operated across distant space and time [Malone ., , 1251-1277 (2012)]. Although individual recognition is widespread among animals and sometimes lasts for years, little is known about social memory in nonhuman apes and the shared evolutionary foundations of human social memory. In a preferential-looking eye-tracking task, we presented chimpanzees and bonobos ( = 26) with side-by-side images of a previous groupmate and a conspecific stranger of the same sex. Apes' attention was biased toward former groupmates, indicating long-term memory for past social partners. The strength of biases toward former groupmates was not impacted by the duration apart, and our results suggest that recognition may persist for at least 26 y beyond separation. We also found significant but weak evidence that, like humans, apes may remember the quality or content of these past relationships: apes' looking biases were stronger for individuals with whom they had more positive histories of social interaction. Long-lasting social memory likely provided key foundations for the evolution of human culture and sociality as they extended across time, space, and group boundaries.
Topics: Animals; Humans; Pan troglodytes; Pan paniscus; Hominidae; Social Behavior; Recognition, Psychology
PubMed: 38109542
DOI: 10.1073/pnas.2304903120 -
Personality Neuroscience 2023Autism spectrum disorder (ASD) is a developmental disorder characterized by stereotypies or repetitive behaviors and impairments in social behavior and...
Autism spectrum disorder (ASD) is a developmental disorder characterized by stereotypies or repetitive behaviors and impairments in social behavior and socio-communicative skills. One hallmark phenotype of ASD is poor joint attention skills compared to neurotypical controls. In addition, individuals with ASD have lower scores on several of the Big 5 personality dimensions, including Extraversion. Here, we examine these traits in a nonhuman primate model (chimpanzees; ) to further understand the relationship between personality and joint attention skills, as well as the genetic and neural systems that contribute to these phenotypes. We used archival data including receptive joint attention (RJA) performance, personality based on caretaker ratings, and magnetic resonance images from 189 chimpanzees. We found that, like humans, chimpanzees who performed worse on the RJA task had lower Extraversion scores. We also found that joint attention skills and several personality dimensions, including Extraversion, were significantly heritable. There was also a borderline significant genetic correlation between RJA and Extraversion. A conjunction analysis examining gray matter volume showed that there were five main brain regions associated with both higher levels of Extraversion and social cognition. These regions included the right posterior middle and superior temporal gyrus, bilateral inferior frontal gyrus, left inferior frontal sulcus, and left superior frontal sulcus, all regions within the social brain network. Altogether, these findings provide further evidence that chimpanzees serve as an excellent model for understanding the mechanisms underlying social impairment related to ASD. Future research should further examine the relationship between social cognition, personality, genetics, and neuroanatomy and function in nonhuman primate models.
PubMed: 38107781
DOI: 10.1017/pen.2023.8 -
ELife Dec 2023Because of their close relationship with humans, non-human apes (chimpanzees, bonobos, gorillas, orangutans, and gibbons, including siamangs) are of great scientific...
Because of their close relationship with humans, non-human apes (chimpanzees, bonobos, gorillas, orangutans, and gibbons, including siamangs) are of great scientific interest. The goal of understanding their complex behavior would be greatly advanced by the ability to perform video-based pose tracking. Tracking, however, requires high-quality annotated datasets of ape photographs. Here we present , a new public dataset of 71,868 photographs, annotated with 16 body landmarks of six ape species in naturalistic contexts. We show that a standard deep net (HRNet-W48) trained on ape photos can reliably track out-of-sample ape photos better than networks trained on monkeys (specifically, the dataset) and on humans () can. This trained network can track apes almost as well as the other networks can track their respective taxa, and models trained without one of the six ape species can track the held-out species better than the monkey and human models can. Ultimately, the results of our analyses highlight the importance of large, specialized databases for animal tracking systems and confirm the utility of our new ape database.
Topics: Animals; Hominidae; Gorilla gorilla; Pan troglodytes; Haplorhini; Pan paniscus; Hylobates
PubMed: 38078902
DOI: 10.7554/eLife.86873 -
Journal of Human Evolution Jan 2024Recent Plio-Pleistocene hominin findings have revealed the complexity of human evolutionary history and the difficulties involved in its interpretation. Moreover, the...
Recent Plio-Pleistocene hominin findings have revealed the complexity of human evolutionary history and the difficulties involved in its interpretation. Moreover, the study of hominin long bone remains is particularly problematic, since it commonly depends on the analysis of fragmentary skeletal elements that in many cases are merely represented by small diaphyseal portions and appear in an isolated fashion in the fossil record. Nevertheless, the study of the postcranial skeleton is particularly important to ascertain locomotor patterns. Here we report on the discovery of a robust hominin femoral fragment (OH 84) at the site of Amin Mturi Korongo dated to 1.84 Ma (Olduvai Bed I). External anatomy and internal bone structure of OH 84 were analyzed and compared with previously published data for modern humans and chimpanzees, as well as for Australopithecus, Paranthropus and Homo specimens ranging from the Late Pliocene to Late Pleistocene. Biomechanical analyses based on transverse cross-sections and the comparison of OH 84 with another robust Olduvai specimen (OH 80) suggest that OH 84 might be tentatively allocated to Paranthropus boisei. More importantly, the identification of a unique combination of traits in OH 84 could indicate both terrestrial bipedalism and an arboreal component in the locomotor repertoire of this individual. If interpreted correctly, OH 84 could thus add to the already mounting evidence of substantial locomotor diversity among Early Pleistocene hominins. Likewise, our results also highlight the difficulties in accurately interpreting the link between form and function in the human fossil record based on fragmentary remains, and ultimately in distinguishing between coeval hominin groups due to the heterogeneous pattern of inter- and intraspecific morphological variability detected among fossil femora.
Topics: Animals; Humans; Hominidae; Femur; Pan troglodytes; Biological Evolution; Fossils; Africa, Eastern
PubMed: 38071888
DOI: 10.1016/j.jhevol.2023.103469