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Falcão BMR, Limeira CH, de Souza JG, Dos Santos Figuerêdo MB, de Andrade Morais D, Dos Santos Higino SS. Systematic review and meta-analysis on seroprevalence of leptospirosis in non-human primates worldwide. Res Vet Sci 2024; 178:105342. [PMID: 39146598 DOI: 10.1016/j.rvsc.2024.105342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/30/2024] [Indexed: 08/17/2024]
Abstract
Leptospirosis is a zoonotic disease whose transmission is linked to multiple factors involving the interface between animals, humans, and the environment. This disease is of great importance for public health, as it profoundly affects the health aspects of the population and animals. Considering the importance of non-human primates in this epidemiological chain, the objective of this research was to conduct a systematic literature review with meta-analysis, providing information on leptospirosis in non-human primates (NHPs) and an update on the infection situation in Brazil and other countries. Thus, a search was performed in five databases, initially finding 3332 studies, of which 32 met the eligibility criteria and were used for the systematic review. According to them, the most prevalent serogroup in non-human primates was Icterohaemorrhagiae, which is adapted to rodents as primary hosts. A wide distribution of the infection was found in the regions of both wild and captive animals. Through meta-analysis, the seroprevalence rate of leptospirosis in non-human primates was 27.21% (CI 17.97-38.95%). Cochran's Q test (p < 0.01) identified heterogeneity between studies, classified as high by the Higgins and Thompson test (I2 = 92.4%). Therefore, seroepidemiological and Leptospira isolation studies in non-human primates are important to investigate and monitor the suspected impact of these species as maintainers or transmitters of the pathogen to humans and other wild and domestic animals, in addition to demonstrating the need for standardization related to control and prevention measures.
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Affiliation(s)
- Brunna Muniz Rodrigues Falcão
- Postgraduate Program in Animal Science and Health, Federal University of Campina Grande, 58708-110 Patos, PB, Brazil
| | - Clécio Henrique Limeira
- Postgraduate Program in Animal Science and Health, Federal University of Campina Grande, 58708-110 Patos, PB, Brazil
| | - Joyce Galvão de Souza
- Postgraduate Program in Animal Science and Health, Federal University of Campina Grande, 58708-110 Patos, PB, Brazil
| | | | - Davidianne de Andrade Morais
- Postgraduate Program in Animal Science and Health, Federal University of Campina Grande, 58708-110 Patos, PB, Brazil
| | - Severino Silvano Dos Santos Higino
- Postgraduate Program in Animal Science and Health, Federal University of Campina Grande, 58708-110 Patos, PB, Brazil; Professor Program in Animal Science and Health, Federal University of Campina Grande, 58708-110, Patos, PB, Brazil.
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2
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Ramezanpour H, Giverin C, Kar K. Low-cost, portable, easy-to-use kiosks to facilitate home-cage testing of nonhuman primates during vision-based behavioral tasks. J Neurophysiol 2024; 132:666-677. [PMID: 39015072 DOI: 10.1152/jn.00397.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 06/12/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
Nonhuman primates (NHPs), especially rhesus macaques, have significantly contributed to our understanding of the neural computations underlying human vision. Besides the established homologies in the visual brain areas between these species and our ability to probe detailed neural mechanisms in monkeys at multiple scales, NHPs' ability to perform human-like visual behavior makes them an extremely appealing animal model of human vision. Traditionally, such behavioral studies have been conducted in controlled laboratory settings, offering experimenters tight control over variables like luminance, eye movements, and auditory interference. However, in-lab experiments have several constraints, including limited experimental time, the need for dedicated human experimenters, additional lab space requirements, invasive surgeries for headpost implants, and extra time and training for chairing and head restraints. To overcome these limitations, we propose adopting home-cage behavioral training and testing of NHPs, enabling the administration of many vision-based behavioral tasks simultaneously across multiple monkeys with reduced human personnel requirements, no NHP head restraint, and monkeys' unrestricted access to experiments. In this article, we present a portable, low-cost, easy-to-use kiosk system developed to conduct home-cage vision-based behavioral tasks in NHPs. We provide details of its operation and build to enable more open-source development of this technology. Furthermore, we present validation results using behavioral measurements performed in the lab and in NHP home cages, demonstrating the system's reliability and potential to enhance the efficiency and flexibility of NHP behavioral research.NEW & NOTEWORTHY Training nonhuman primates (NHPs) for vision-based behavioral tasks in a laboratory setting is a time-consuming process and comes with many limitations. To overcome these challenges, we have developed an affordable, open-source, wireless, touchscreen training system that can be placed in the NHPs' housing environment. This system enables NHPs to work at their own pace. It provides a platform to implement continuous behavioral training protocols without major experimenter intervention and eliminates the need for other standard practices like NHP chair training, collar placement, and head restraints. Hence, these kiosks ultimately contribute to animal welfare and therefore better-quality neuroscience in the long run. In addition, NHPs quickly learn complex behavioral tasks using this system, making it a promising tool for wireless electrophysiological research in naturalistic, unrestricted environments to probe the relation between brain and behavior.
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Affiliation(s)
- Hamidreza Ramezanpour
- Department of Biology, York University Toronto, Ontario, Canada
- Centre for Vision Research, York University, Toronto, Ontario, Canada
| | - Christopher Giverin
- Department of Biology, York University Toronto, Ontario, Canada
- Vision: Science to Applications (VISTA), York University, Toronto, Ontario, Canada
| | - Kohitij Kar
- Department of Biology, York University Toronto, Ontario, Canada
- Centre for Vision Research, York University, Toronto, Ontario, Canada
- Vision: Science to Applications (VISTA), York University, Toronto, Ontario, Canada
- Centre for Integrated and Applied Neuroscience (CIAN), York University, Toronto, Ontario, Canada
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3
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Caldon M, Mutti G, Mondanaro A, Imai H, Shotake T, Oteo Garcia G, Belay G, Morata J, Trotta JR, Montinaro F, Gippoliti S, Capelli C. Gelada genomes highlight events of gene flow, hybridisation and local adaptation that track past climatic changes. Mol Ecol 2024:e17514. [PMID: 39206888 DOI: 10.1111/mec.17514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/28/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Theropithecus gelada, the last surviving species of this genus, occupy a unique and highly specialised ecological niche in the Ethiopian highlands. A subdivision into three geographically defined populations (Northern, Central and Southern) has been tentatively proposed for this species on the basis of genetic analyses, but genomic data have been investigated only for two of these groups (Northern and Central). Here we combined newly generated whole genome sequences of individuals sampled from the population living south of the East Africa Great Rift Valley with available data from the other two gelada populations to reconstruct the evolutionary history of the species. Integrating genomic and paleoclimatic data we found that gene-flow across populations and with Papio species tracked past climate changes. The isolation and climatic conditions experienced by Southern geladas during the Holocene shaped local diversity and generated diet-related genomic signatures.
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Affiliation(s)
- Matteo Caldon
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giacomo Mutti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Hiroo Imai
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
| | | | - Gonzalo Oteo Garcia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jordi Morata
- Centre Nacional d'Anàlisi Genòmica, Barcelona, Spain
| | | | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, Bari, Italy
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Spartaco Gippoliti
- IUCN/SSC Primate Specialist Group, Rome, Italy
- Società Italiana per la Storia Della Fauna "G. Altobello", Rome, Italy
| | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Department of Biology, University of Oxford, Oxford, UK
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4
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Vargas-Pinilla P, S Oliveira Fam B, Medina Tavares G, Lima T, Landau L, Paré P, de Cássia Aleixo Tostes R, Pissinatti A, Falótico T, Costa-Neto C, Maestri R, Bortolini MC. From molecular variations to behavioral adaptations: Unveiling adaptive epistasis in primate oxytocin system. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 184:e24947. [PMID: 38783700 DOI: 10.1002/ajpa.24947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
OBJECTIVE Our primary objective was to investigate the variability of oxytocin (OT) and the GAMEN binding motif within the LNPEP oxytocinase in primates. MATERIALS AND METHODS We sequenced the LNPEP segment encompassing the GAMEN motif in 34 Platyrrhini species, with 21 of them also sequenced for the OT gene. Our dataset was supplemented with primate sequences of LNPEP, OT, and the oxytocin receptor (OTR) sourced from public databases. Evolutionary analysis and coevolution predictions were made followed by the macroevolution analysis of relevant amino acids associated with phenotypic traits, such as mating systems, parental care, and litter size. To account for phylogenetic structure, we utilized two distinct statistical tests. Additionally, we calculated binding energies focusing on the interaction between Callithtrix jacchus VAMEN and Pro8OT. RESULTS We identified two novel motifs (AAMEN and VAMEN), challenging the current knowledge of motif conservation in placental mammals. Coevolution analysis demonstrated a correlation between GAMEN, AAMEN, and VAMEN and their corresponding OTs and OTRs. Callithrix jacchus exhibited a higher binding energy between VAMEN and Pro8OT than orthologous molecules found in humans (GAMEN and Leu8OT). DISCUSSION The coevolution of AAMEN and VAMEN with their corresponding OTs and OTRs suggests a functional relationship that could have contributed to specific reproductive and adaptive behaviors, including paternal care, social monogamy, and twin births, prominent traits in Cebidae species, such as marmosets and tamarins. Our findings underscore the coevolution of taxon-specific amino acids among the three studied molecules, shedding light on the oxytocinergic system as an adaptive epistatic repertoire in primates.
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Affiliation(s)
- Pedro Vargas-Pinilla
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Farmacologia, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Bibiana S Oliveira Fam
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Gustavo Medina Tavares
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thaynara Lima
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luane Landau
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Pâmela Paré
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Tiago Falótico
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazil
| | - Cláudio Costa-Neto
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Renan Maestri
- Laboratório de Ecomorfologia e Macroevolução, Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maria Cátira Bortolini
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Twyman H, Heywood I, Barros M, Zeredo J, Mundy NI, Santangelo AM. Evolution of threat response-related polymorphisms at the SLC6A4 locus in callitrichid primates. Biol Lett 2024; 20:20240024. [PMID: 39013428 PMCID: PMC11251774 DOI: 10.1098/rsbl.2024.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/03/2024] [Accepted: 06/09/2024] [Indexed: 07/18/2024] Open
Abstract
Variation in an upstream repetitive region at the SLC6A4 locus, which encodes the serotonin transporter, is associated with anxiety-related behaviour in a few primate species, including humans and rhesus macaques, and has been suggested to be related to ecological adaptability among macaques. In this study, we investigate evolution of SLC6A4 polymorphisms associated with anxiety-related behaviour in common marmosets (Callithrix jacchus). Assaying variation in the SLC6A4 repeat region across 14 species in eight genera of callitrichid primates (marmosets and tamarins), we find large interspecific variation in the number of repeats present (24-43). The black tufted-ear marmoset (C. penicillata) has sequence polymorphisms similar to those found in the common marmoset, which is its sister species, and no other species has intraspecific variation at these sites. We conclude that, similar to humans and macaques, the functional polymorphism at SLC6A4 in common marmosets has a recent evolutionary origin, and that the anxiety-related allele is evolutionarily derived. Common/black tufted-ear marmosets and rhesus/bonnet macaques share high ecological adaptability and behavioural flexibility that we propose may be related to the maintenance of the polymorphism.
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Affiliation(s)
- Hanlu Twyman
- Department of Zoology, Downing Street, CambridgeCB2 3EJ, UK
| | - India Heywood
- Department of Zoology, Downing Street, CambridgeCB2 3EJ, UK
| | - Marília Barros
- Departamento de Farmácia, Universidade de Brasília, Campus Universitário - Asa Norte, Brasília, Brazil
| | - Jorge Zeredo
- Graduate Program in Health Sciences and Technologies, Universidade de Brasília, Campus Ceilândia – Ceilândia Sul, Brasília, DFCEP 72.220-275, Brazil
| | | | - Andrea M. Santangelo
- MRC Cognition and Brain Sciences Unit, University of Cambridge, 15 Chaucer Road, CambridgeCB2 7EF, UK
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6
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Hou M, Akhtar MS, Hayashi M, Ashino R, Matsumoto-Oda A, Hayakawa T, Ishida T, Melin AD, Imai H, Kawamura S. Reduction of bitter taste receptor gene family in folivorous colobine primates relative to omnivorous cercopithecine primates. Primates 2024; 65:311-331. [PMID: 38605281 PMCID: PMC11219393 DOI: 10.1007/s10329-024-01124-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/26/2024] [Indexed: 04/13/2024]
Abstract
Bitter taste perception is important in preventing animals from ingesting potentially toxic compounds. Whole-genome assembly (WGA) data have revealed that bitter taste receptor genes (TAS2Rs) comprise a multigene family with dozens of intact and disrupted genes in primates. However, publicly available WGA data are often incomplete, especially for multigene families. In this study, we employed a targeted capture (TC) approach specifically probing TAS2Rs for ten species of cercopithecid primates with diverse diets, including eight omnivorous cercopithecine species and two folivorous colobine species. We designed RNA probes for all TAS2Rs that we modeled to be intact in the common ancestor of cercopithecids ("ancestral-cercopithecid TAS2R gene set"). The TC was followed by short-read and high-depth massive-parallel sequencing. TC retrieved more intact TAS2R genes than found in WGA databases. We confirmed a large number of gene "births" at the common ancestor of cercopithecids and found that the colobine common ancestor and the cercopithecine common ancestor had contrasting trajectories: four gene "deaths" and three gene births, respectively. The number of intact TAS2R genes was markedly reduced in colobines (25-28 detected via TC and 20-26 detected via WGA analysis) as compared with cercopithecines (27-36 via TC and 19-30 via WGA). Birth or death events occurred at almost every phylogenetic-tree branch, making the composition of intact genes variable among species. These results show that evolutionary change in intact TAS2R genes is a complex process, refute a simple general prediction that herbivory favors more TAS2R genes, and have implications for understanding dietary adaptations and the evolution of detoxification abilities.
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Affiliation(s)
- Min Hou
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Muhammad Shoaib Akhtar
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Masahiro Hayashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Ryuichi Ashino
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Akiko Matsumoto-Oda
- Graduate School of Tourism Sciences, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Japan Monkey Centre, Inuyama, Aichi, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Alberta, Canada
| | - Hiroo Imai
- Molecular Biology Section, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Kyoto, Aichi, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience BLDG Room 502, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
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7
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Minami T, Furuichi T. Examining infantile facial features and their influence on caretaking behaviors in free-ranging Japanese macaques (Macaca fuscata). PLoS One 2024; 19:e0302412. [PMID: 38900785 PMCID: PMC11189181 DOI: 10.1371/journal.pone.0302412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/03/2024] [Indexed: 06/22/2024] Open
Abstract
Facial features of immature individuals play a pivotal role in eliciting caretaking behaviors in humans. It has been posited that non-human animals share particular infantile facial features with humans, which can elicit caregivers' attention and caretaking behaviors. Nevertheless, the empirical examination of this hypothesis is extremely limited. In this study, we investigated infantile facial features in Japanese macaques (Macaca fuscata), their developmental processes, and their correlation with caretaking and infant behaviors, based on 470 facial photographs from one free-ranging group. We measured the size of facial parts and evaluated these features using non-contact procedures with the animals. The results indicated that, although some partial species differences were observed, the infantile facial features in Japanese macaques were broadly consistent with those previously observed in humans and great apes. Furthermore, half of the infant subjects displayed non-linear developmental trajectories of infantile faces, similar to those suggested in humans. However, unlike previous studies in humans, infantile faces were not significantly associated with maternal or non-maternal caretaking behaviors, nor were their developmental changes correlated with infant behavioral development. These findings indicate that while many aspects of infantile facial features are shared among particular primates, humans may have evolved a uniquely elevated preference for selecting such features among the primate lineage.
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Affiliation(s)
- Toshiki Minami
- Graduate School of Education, Kyoto University, Kyoto, Kyoto, Japan
| | - Takeshi Furuichi
- Wildlife Research Center, Kyoto University, Inuyama, Aichi, Japan
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Khani S, Topel H, Kardinal R, Tavanez AR, Josephrajan A, Larsen BDM, Gaudry MJ, Leyendecker P, Egedal NM, Güller AS, Stanic N, Ruppert PMM, Gaziano I, Hansmeier NR, Schmidt E, Klemm P, Vagliano LM, Stahl R, Duthie F, Krause JH, Bici A, Engelhard CA, Gohlke S, Frommolt P, Gnad T, Rada-Iglesias A, Pradas-Juni M, Schulz TJ, Wunderlich FT, Pfeifer A, Bartelt A, Jastroch M, Wachten D, Kornfeld JW. Cold-induced expression of a truncated adenylyl cyclase 3 acts as rheostat to brown fat function. Nat Metab 2024; 6:1053-1075. [PMID: 38684889 DOI: 10.1038/s42255-024-01033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/25/2024] [Indexed: 05/02/2024]
Abstract
Promoting brown adipose tissue (BAT) activity innovatively targets obesity and metabolic disease. While thermogenic activation of BAT is well understood, the rheostatic regulation of BAT to avoid excessive energy dissipation remains ill-defined. Here, we demonstrate that adenylyl cyclase 3 (AC3) is key for BAT function. We identified a cold-inducible promoter that generates a 5' truncated AC3 mRNA isoform (Adcy3-at), whose expression is driven by a cold-induced, truncated isoform of PPARGC1A (PPARGC1A-AT). Male mice lacking Adcy3-at display increased energy expenditure and are resistant to obesity and ensuing metabolic imbalances. Mouse and human AC3-AT are retained in the endoplasmic reticulum, unable to translocate to the plasma membrane and lack enzymatic activity. AC3-AT interacts with AC3 and sequesters it in the endoplasmic reticulum, reducing the pool of adenylyl cyclases available for G-protein-mediated cAMP synthesis. Thus, AC3-AT acts as a cold-induced rheostat in BAT, limiting adverse consequences of cAMP activity during chronic BAT activation.
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Affiliation(s)
- Sajjad Khani
- Institute for Genetics, University of Cologne, Cologne, Germany
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Hande Topel
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Ronja Kardinal
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ana Rita Tavanez
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Ajeetha Josephrajan
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | | | - Michael James Gaudry
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Philipp Leyendecker
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Nadia Meincke Egedal
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Aylin Seren Güller
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Natasa Stanic
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark
| | - Phillip M M Ruppert
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | | | - Elena Schmidt
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Paul Klemm
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Lara-Marie Vagliano
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Rainer Stahl
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Fraser Duthie
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jens-Henning Krause
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ana Bici
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
| | - Christoph Andreas Engelhard
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Centre for Physical Activity Research, Department of Infectious Diseases, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Gohlke
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Peter Frommolt
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Gnad
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Marta Pradas-Juni
- Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Copenhagen, Denmark
| | - Tim Julius Schulz
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | | | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, Bonn, Germany
| | - Alexander Bartelt
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Molecular Metabolism and Sabri Ülker Center for Metabolic Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Jastroch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Dagmar Wachten
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany.
| | - Jan-Wilhelm Kornfeld
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
- Novo Nordisk Foundation Center for Adipocyte Signaling (Adiposign), University of Southern Denmark, Odense, Denmark.
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Feng P, Wang H, Liang X, Dong X, Liang Q, Shu F, Zhou Q. Relationships between Bitter Taste Receptor Gene Evolution, Diet, and Gene Repertoire in Primates. Genome Biol Evol 2024; 16:evae104. [PMID: 38748818 PMCID: PMC11135642 DOI: 10.1093/gbe/evae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
Bitter taste perception plays a critical role in deterring animals from consuming harmful and toxic substances. To characterize the evolution of primate Tas2r, test the generality of Tas2r duplication in Cercopithecidae species, and examine whether dietary preferences have shaped the Tas2r repertoire of primate species, we identified Tas2r in the genomes of 35 primate species, including 16 Cercopithecidae, 6 Hominidae, 4 Cebidae, 3 Lemuridae, and 6 other species. The results showed that the total number of primate Tas2r ranged from 27 to 51, concentrating on 2 to 4 scaffolds of each species. Closely related genes were tandemly duplicated in the same scaffold. Phylogenetic construction revealed that Tas2r can be divided into 21 clades, including anthropoid-, Strepsirrhini-, and Cercopithecidae-specific Tas2r duplications. Phylogenetically independent contrast analysis revealed that the number of intact Tas2r significantly correlated with feeding preferences. Altogether, our data support diet as a driver of primate Tas2r evolution, and Cercopithecidae species have developed some specific Tas2r duplication during evolution. These results are probably because most Cercopithecidae species feed on plants containing many toxins, and it is necessary to develop specialized Tas2r to protect them from poisoning.
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Affiliation(s)
- Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China
| | - Hui Wang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China
| | - Xinyue Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China
| | - Xiaoyan Dong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China
| | - Qiufang Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China
| | - Fanglan Shu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China
| | - Qihai Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People’s Republic of China, Guangxi Normal University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China
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10
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Reda HG, Frost SR, Simons EA, Quade J, Simpson SW. Description and taxonomic assessment of fossil Cercopithecidae from the Pliocene Galili Formation (Ethiopia). J Hum Evol 2024; 190:103508. [PMID: 38599140 DOI: 10.1016/j.jhevol.2024.103508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 04/12/2024]
Abstract
The Mount Galili Formation in the Afar region, Ethiopia, samples a critical time in hominin evolution, 4.4 to 3.8 Ma, documenting the last appearance of Ardipithecus and the origin of Australopithecus. This period is also important in the evolution of cercopithecids, especially the origin of Theropithecus in general and Theropithecus oswaldi lineage in particular. Galili has provided a total of 655 cercopithecid specimens that include crania, mandibles, isolated teeth and postcrania. All the fossils were recovered from the Lasdanan (5.3-4.43 Ma), Dhidinley (4.43-3.9 Ma) and Shabeley Laag (∼3.92-3.8 Ma) Members. Here, we described and analyzed 362 fossils employing both qualitative and quantitative methods. Descriptions of the material were supplemented with dental metrics and cranial shape analysis using three-dimensional geometric morphometrics. Results indicate the presence of at least six cercopithecid taxa: Theropithecus oswaldi serengetensis (n = 28), Theropithecus sp. (n = 2), three non-Theropithecus papionin groups (n = 134) and one colobine-size group (n = 58). The T. o. serengetensis represents the earliest form of the lineage, documented from ∼3.9 Ma Galili sediments. The three Galili papionins include a smaller taxon, a medium-sized taxon comparable to Pliopapio alemui and a large papionin overlapping in size with Soromandrillus, Gorgopithecus and Dinopithecus. The majority of Galili colobines have closest affinities to Kuseracolobus aramisi and some overlap with other taxa. Papionins dominate the Galili cercopithecid collection, although colobines are still fairly common (approximately 25% of the sample). Thus, Galili sample is like Kanapoi (4.2-4.1 Ma) and Gona (5.2-3.9 Ma) localities but distinct from Aramis, suggesting paleoecological similarity to the former sites. On the other hand, Theropithecus is less abundant at Galili than geologically younger Hadar (3.4-3.2 Ma) and Woranso-Mille (3.8-3.6 Ma) sites. Whether this difference is due to sampling, time or landscape variation requires further investigation.
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Affiliation(s)
- Hailay G Reda
- Department of Anthropology, University of Oregon, Eugene, OR, 97403-1218, USA.
| | - Stephen R Frost
- Department of Anthropology, University of Oregon, Eugene, OR, 97403-1218, USA
| | - Evan A Simons
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd, L470, Portland, OR, 97239, USA
| | - Jay Quade
- Department of Geosciences, University of Arizona, 1040 E. 4th Street, Tucson, AZ, 85721, USA
| | - Scott W Simpson
- Department of Anatomy, Case Western Reserve University, Cleveland, OH, 44106-4930, USA; Laboratory of Physical Anthropology, Cleveland Museum of Natural History, Cleveland, OH, 44106, USA
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11
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Sartorius AM, Rokicki J, Birkeland S, Bettella F, Barth C, de Lange AMG, Haram M, Shadrin A, Winterton A, Steen NE, Schwarz E, Stein DJ, Andreassen OA, van der Meer D, Westlye LT, Theofanopoulou C, Quintana DS. An evolutionary timeline of the oxytocin signaling pathway. Commun Biol 2024; 7:471. [PMID: 38632466 PMCID: PMC11024182 DOI: 10.1038/s42003-024-06094-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Oxytocin is a neuropeptide associated with both psychological and somatic processes like parturition and social bonding. Although oxytocin homologs have been identified in many species, the evolutionary timeline of the entire oxytocin signaling gene pathway has yet to be described. Using protein sequence similarity searches, microsynteny, and phylostratigraphy, we assigned the genes supporting the oxytocin pathway to different phylostrata based on when we found they likely arose in evolution. We show that the majority (64%) of genes in the pathway are 'modern'. Most of the modern genes evolved around the emergence of vertebrates or jawed vertebrates (540 - 530 million years ago, 'mya'), including OXTR, OXT and CD38. Of those, 45% were under positive selection at some point during vertebrate evolution. We also found that 18% of the genes in the oxytocin pathway are 'ancient', meaning their emergence dates back to cellular organisms and opisthokonta (3500-1100 mya). The remaining genes (18%) that evolved after ancient and before modern genes were classified as 'medium-aged'. Functional analyses revealed that, in humans, medium-aged oxytocin pathway genes are highly expressed in contractile organs, while modern genes in the oxytocin pathway are primarily expressed in the brain and muscle tissue.
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Affiliation(s)
- Alina M Sartorius
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Jaroslav Rokicki
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Centre of Research and Education in Forensic Psychiatry, Oslo University Hospital, Oslo, Norway
| | - Siri Birkeland
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Francesco Bettella
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Claudia Barth
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Ann-Marie G de Lange
- Department of Psychology, University of Oslo, Oslo, Norway
- Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Marit Haram
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Department of Mental Health and Suicide, Norwegian Institute of Public Health, Oslo, Norway
| | - Alexey Shadrin
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Adriano Winterton
- Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway
| | - Nils Eiel Steen
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Emanuel Schwarz
- Hector Institute for Artificial Intelligence in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Dan J Stein
- SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Dennis van der Meer
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Lars T Westlye
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Daniel S Quintana
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Department of Psychology, University of Oslo, Oslo, Norway.
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway.
- NevSom, Department of Rare Disorders, Oslo University Hospital, Oslo, Norway.
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12
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Henriques C, Lopes MM, Silva AC, Lobo DD, Badin RA, Hantraye P, Pereira de Almeida L, Nobre RJ. Viral-based animal models in polyglutamine disorders. Brain 2024; 147:1166-1189. [PMID: 38284949 DOI: 10.1093/brain/awae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/26/2023] [Accepted: 12/30/2023] [Indexed: 01/30/2024] Open
Abstract
Polyglutamine disorders are a complex group of incurable neurodegenerative disorders caused by an abnormal expansion in the trinucleotide cytosine-adenine-guanine tract of the affected gene. To better understand these disorders, our dependence on animal models persists, primarily relying on transgenic models. In an effort to complement and deepen our knowledge, researchers have also developed animal models of polyglutamine disorders employing viral vectors. Viral vectors have been extensively used to deliver genes to the brain, not only for therapeutic purposes but also for the development of animal models, given their remarkable flexibility. In a time- and cost-effective manner, it is possible to use different transgenes, at varying doses, in diverse targeted tissues, at different ages, and in different species, to recreate polyglutamine pathology. This paper aims to showcase the utility of viral vectors in disease modelling, share essential considerations for developing animal models with viral vectors, and provide a comprehensive review of existing viral-based animal models for polyglutamine disorders.
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Affiliation(s)
- Carina Henriques
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Miguel M Lopes
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (III), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Ana C Silva
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (III), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Diana D Lobo
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (III), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Romina Aron Badin
- CEA, DRF, Institute of Biology François Jacob, Molecular Imaging Research Center (MIRCen), 92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, Université Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), 92265 Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA, DRF, Institute of Biology François Jacob, Molecular Imaging Research Center (MIRCen), 92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, Université Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), 92265 Fontenay-aux-Roses, France
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Rui Jorge Nobre
- Center for Neuroscience and Cell Biology (CNC), Gene and Stem Cell Therapies for the Brain Group, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, 3004-504 Coimbra, Portugal
- ViraVector-Viral Vector for Gene Transfer Core Facility, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research (III), University of Coimbra, 3030-789 Coimbra, Portugal
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13
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Houzelstein D, Eozenou C, Lagos CF, Elzaiat M, Bignon-Topalovic J, Gonzalez I, Laville V, Schlick L, Wankanit S, Madon P, Kirtane J, Athalye A, Buonocore F, Bigou S, Conway GS, Bohl D, Achermann JC, Bashamboo A, McElreavey K. A conserved NR5A1-responsive enhancer regulates SRY in testis-determination. Nat Commun 2024; 15:2796. [PMID: 38555298 PMCID: PMC10981742 DOI: 10.1038/s41467-024-47162-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 03/21/2024] [Indexed: 04/02/2024] Open
Abstract
The Y-linked SRY gene initiates mammalian testis-determination. However, how the expression of SRY is regulated remains elusive. Here, we demonstrate that a conserved steroidogenic factor-1 (SF-1)/NR5A1 binding enhancer is required for appropriate SRY expression to initiate testis-determination in humans. Comparative sequence analysis of SRY 5' regions in mammals identified an evolutionary conserved SF-1/NR5A1-binding motif within a 250 bp region of open chromatin located 5 kilobases upstream of the SRY transcription start site. Genomic analysis of 46,XY individuals with disrupted testis-determination, including a large multigenerational family, identified unique single-base substitutions of highly conserved residues within the SF-1/NR5A1-binding element. In silico modelling and in vitro assays demonstrate the enhancer properties of the NR5A1 motif. Deletion of this hemizygous element by genome-editing, in a novel in vitro cellular model recapitulating human Sertoli cell formation, resulted in a significant reduction in expression of SRY. Therefore, human NR5A1 acts as a regulatory switch between testis and ovary development by upregulating SRY expression, a role that may predate the eutherian radiation. We show that disruption of an enhancer can phenocopy variants in the coding regions of SRY that cause human testis dysgenesis. Since disease causing variants in enhancers are currently rare, the regulation of gene expression in testis-determination offers a paradigm to define enhancer activity in a key developmental process.
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Affiliation(s)
- Denis Houzelstein
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France.
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France.
| | - Caroline Eozenou
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
- Institut Cochin, Université Paris Cité, INSERM, CNRS, Paris, France
| | - Carlos F Lagos
- Chemical Biology & Drug Discovery Lab, Escuela de Química y Farmacia, Facultad de Medicina y Ciencia, Universidad San Sebastián, Campus Los Leones, Lota 2465 Providencia, 7510157, Santiago, Chile
- Centro Ciencia & Vida, Fundación Ciencia & Vida, Av. del Valle Norte 725, Huechuraba, 8580702, Santiago, Chile
| | - Maëva Elzaiat
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
| | - Joelle Bignon-Topalovic
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
| | - Inma Gonzalez
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
- Institut Pasteur, Université Paris Cité, Epigenomics, Proliferation, and the Identity of Cells Unit, F-75015, Paris, France
| | - Vincent Laville
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
- Institut Pasteur, Université Paris Cité, Stem Cells and Development Unit, F-75015, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France
| | - Laurène Schlick
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
| | - Somboon Wankanit
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Prochi Madon
- Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, Mumbai, India
| | - Jyotsna Kirtane
- Department of Pediatric Surgery, Jaslok Hospital and Research Centre, Mumbai, India
| | - Arundhati Athalye
- Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, Mumbai, India
| | - Federica Buonocore
- Genetics and Genomic Medicine Research & Teaching Department, UCL GOS Institute of Child Health, University College London, London, United Kingdom
| | - Stéphanie Bigou
- ICV-iPS core facility, Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Gerard S Conway
- Institute for Women's Health, University College London, London, United Kingdom
| | - Delphine Bohl
- ICV-iPS core facility, Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - John C Achermann
- Genetics and Genomic Medicine Research & Teaching Department, UCL GOS Institute of Child Health, University College London, London, United Kingdom
| | - Anu Bashamboo
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
| | - Ken McElreavey
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France.
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France.
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14
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Warren CJ, Barbachano-Guerrero A, Bauer VL, Stabell AC, Dirasantha O, Yang Q, Sawyer SL. Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.13.566830. [PMID: 38014262 PMCID: PMC10680607 DOI: 10.1101/2023.11.13.566830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Simian immunodeficiency viruses (SIVs) comprise a large group of primate lentiviruses that endemically infect African monkeys. HIV-1 spilled over to humans from this viral reservoir, but the spillover did not occur directly from monkeys to humans. Instead, a key event was the introduction of SIVs into great apes, which then set the stage for infection of humans. Here, we investigate the role of the lentiviral entry receptor, CD4, in this key and fateful event in the history of SIV/HIV emergence. First, we reconstructed and tested ancient forms of CD4 at two important nodes in ape speciation, both prior to the infection of chimpanzees and gorillas with these viruses. These ancestral CD4s fully supported entry of diverse SIV isolates related to the viruses that made this initial jump to apes. In stark contrast, modern chimpanzee and gorilla CD4 orthologs are more resistant to these viruses. To investigate how this resistance in CD4 was gained, we acquired CD4 gene sequences from 32 gorilla individuals of two species, and identified alleles that encode 8 unique CD4 protein variants. Functional testing of these identified variant-specific differences in susceptibility to virus entry. By engineering single point mutations from resistant gorilla CD4 variants into the permissive human CD4 receptor, we demonstrate that acquired substitutions in gorilla CD4 did convey resistance to virus entry. We provide a population genetic analysis to support the theory that selection is acting in favor of more and more resistant CD4 alleles in ape species harboring SIV endemically (gorillas and chimpanzees), but not in other ape species that lack SIV infections (bonobos and orangutans). Taken together, our results show that SIV has placed intense selective pressure on ape CD4, acting to propagate SIV-resistant alleles in chimpanzee and gorilla populations.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Vanessa L. Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Alex C. Stabell
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Obaiah Dirasantha
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Qing Yang
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
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15
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Dafreville M, Guidetti M, Bourjade M. Attention-sensitive signalling by 7- to 20-month-old infants in a comparative perspective. Front Psychol 2024; 15:1257324. [PMID: 38562240 PMCID: PMC10982422 DOI: 10.3389/fpsyg.2024.1257324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Attention-sensitive signalling is the pragmatic skill of signallers who adjust the modality of their communicative signals to their recipient's attention state. This study provides the first comprehensive evidence for its onset and development in 7-to 20-month-olds human infants, and underlines its significance for language acquisition and evolutionary history. Mother-infant dyads (N = 30) were studied in naturalistic settings, sampled according to three developmental periods (in months); [7-10], [11-14], and [15-20]. Infant's signals were classified by dominant perceptible sensory modality and proportions compared according to their mother's visual attention, infant-directed speech and tactile contact. Maternal visual attention and infant-directed speech were influential on the onset and steepness of infants' communicative adjustments. The ability to inhibit silent-visual signals towards visually inattentive mothers (unimodal adjustment) predated the ability to deploy audible-or-contact signals in this case (cross-modal adjustment). Maternal scaffolding of infant's early pragmatic skills through her infant-directed speech operates on the facilitation of infant's unimodal adjustment, the preference for oral over gestural signals, and the audio-visual combinations of signals. Additionally, breakdowns in maternal visual attention are associated with increased use of the audible-oral modality/channel. The evolutionary role of the sharing of attentional resources between parents and infants into the emergence of modern language is discussed.
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Affiliation(s)
| | | | - Marie Bourjade
- CLLE, Université de Toulouse, CNRS, Toulouse, France
- Institut Universitaire de France, Paris, France
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16
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Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. Cell 2024; 187:1547-1562.e13. [PMID: 38428424 PMCID: PMC10947866 DOI: 10.1016/j.cell.2024.01.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/26/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.
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Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ricardo Del Rosario
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa L Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Will T Fattor
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA; Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Yuxiang Mao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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Zimmermann C, Watson GM, Bauersfeld L, Berry R, Ciblis B, Lan H, Gerke C, Oberhardt V, Fuchs J, Hofmann M, Freund C, Rossjohn J, Momburg F, Hengel H, Halenius A. Diverse cytomegalovirus US11 antagonism and MHC-A evasion strategies reveal a tit-for-tat coevolutionary arms race in hominids. Proc Natl Acad Sci U S A 2024; 121:e2315985121. [PMID: 38377192 PMCID: PMC10907249 DOI: 10.1073/pnas.2315985121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
Recurrent, ancient arms races between viruses and hosts have shaped both host immunological defense strategies as well as viral countermeasures. One such battle is waged by the glycoprotein US11 encoded by the persisting human cytomegalovirus. US11 mediates degradation of major histocompatibility class I (MHC-I) molecules to prevent CD8+ T-cell activation. Here, we studied the consequences of the arms race between US11 and primate MHC-A proteins, leading us to uncover a tit-for-tat coevolution and its impact on MHC-A diversification. We found that US11 spurred MHC-A adaptation to evade viral antagonism: In an ancestor of great apes, the MHC-A A2 lineage acquired a Pro184Ala mutation, which confers resistance against the ancestral US11 targeting strategy. In response, US11 deployed a unique low-complexity region (LCR), which exploits the MHC-I peptide loading complex to target the MHC-A2 peptide-binding groove. In addition, the global spread of the human HLA-A*02 allelic family prompted US11 to employ a superior LCR strategy with an optimally fitting peptide mimetic that specifically antagonizes HLA-A*02. Thus, despite cytomegaloviruses low pathogenic potential, the increasing commitment of US11 to MHC-A has significantly promoted diversification of MHC-A in hominids.
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Affiliation(s)
- Cosima Zimmermann
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Gabrielle M. Watson
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Liane Bauersfeld
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Barbara Ciblis
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Huan Lan
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195Berlin, Germany
| | - Carolin Gerke
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Valerie Oberhardt
- Department of Medicine II, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Jonas Fuchs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Maike Hofmann
- Department of Medicine II, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Christian Freund
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195Berlin, Germany
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, United Kingdom
| | - Frank Momburg
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, 69120Heidelberg, Germany
| | - Hartmut Hengel
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Anne Halenius
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
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18
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Cepeda AS, Mello B, Pacheco MA, Luo Z, Sullivan SA, Carlton JM, Escalante AA. The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites. Genome Biol Evol 2024; 16:evae027. [PMID: 38376987 PMCID: PMC10901558 DOI: 10.1093/gbe/evae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 02/03/2024] [Indexed: 02/22/2024] Open
Abstract
Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that are not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other characteristics with the human parasites Plasmodium ovale s.l. and Plasmodium malariae, also of African origin, and the human parasite Plasmodium vivax and species found in nonhuman primates from Southeast Asia. Using phylogenetically aware methods, newly identified syntenic blocks were found enriched with conserved metabolic genes. Regions outside those blocks harbored genes encoding proteins involved in the vertebrate host-Plasmodium relationship undergoing faster evolution. Such genome architecture may have facilitated colonizing vertebrate hosts. Phylogenomic analyses estimated the common ancestor between P. vivax and an African ape parasite P. vivax-like, within the Asian nonhuman primates parasites clade. Time estimates incorporating P. gonderi placed the P. vivax and P. vivax-like common ancestor in the late Pleistocene, a time of active migration of hominids between Africa and Asia. Thus, phylogenomic and time-tree analyses are consistent with an Asian origin for P. vivax and an introduction of P. vivax-like into Africa. Unlike other studies, time estimates for the clade with Plasmodium falciparum, the most lethal human malaria parasite, coincide with their host species radiation, African hominids. Overall, the newly assembled genome presented here has the quality to support comparative genomic investigations in Plasmodium.
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Affiliation(s)
- Axl S Cepeda
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
| | - Beatriz Mello
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
| | - Zunping Luo
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Steven A Sullivan
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Jane M Carlton
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
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19
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Rickelton K, Zintel TM, Pizzollo J, Miller E, Ely JJ, Raghanti MA, Hopkins WD, Hof PR, Sherwood CC, Bauernfeind AL, Babbitt CC. Tempo and mode of gene expression evolution in the brain across primates. eLife 2024; 13:e70276. [PMID: 38275218 PMCID: PMC10876213 DOI: 10.7554/elife.70276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/25/2024] [Indexed: 01/27/2024] Open
Abstract
Primate evolution has led to a remarkable diversity of behavioral specializations and pronounced brain size variation among species (Barton, 2012; DeCasien and Higham, 2019; Powell et al., 2017). Gene expression provides a promising opportunity for studying the molecular basis of brain evolution, but it has been explored in very few primate species to date (e.g. Khaitovich et al., 2005; Khrameeva et al., 2020; Ma et al., 2022; Somel et al., 2009). To understand the landscape of gene expression evolution across the primate lineage, we generated and analyzed RNA-seq data from four brain regions in an unprecedented eighteen species. Here, we show a remarkable level of variation in gene expression among hominid species, including humans and chimpanzees, despite their relatively recent divergence time from other primates. We found that individual genes display a wide range of expression dynamics across evolutionary time reflective of the diverse selection pressures acting on genes within primate brain tissue. Using our samples that represent a 190-fold difference in primate brain size, we identified genes with variation in expression most correlated with brain size. Our study extensively broadens the phylogenetic context of what is known about the molecular evolution of the brain across primates and identifies novel candidate genes for the study of genetic regulation of brain evolution.
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Affiliation(s)
- Katherine Rickelton
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
| | - Trisha M Zintel
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
| | - Jason Pizzollo
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
| | - Emily Miller
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - John J Ely
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington UniversityWashingtonUnited States
- MAEBIOS Epidemiology UnitAlamogordoUnited States
| | - Mary Ann Raghanti
- Department of Anthropology, School of Biomedical Sciences, and Brain Health Research Institute, Kent State UniversityKentUnited States
| | - William D Hopkins
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine,The University of Texas M D Anderson Cancer CentreBastropUnited States
| | - Patrick R Hof
- New York Consortium in Evolutionary PrimatologyNew YorkUnited States
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington UniversityWashingtonUnited States
| | - Amy L Bauernfeind
- Department of Neuroscience, Washington University School of MedicineSt. LouisUnited States
- Department of Anthropology, Washington University in St. LouisSt. LouisUnited States
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
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20
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Nosková E, Sambucci KM, Petrželková KJ, Červená B, Modrý D, Pafčo B. Strongyloides in non-human primates: significance for public health control. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230006. [PMID: 38008123 PMCID: PMC10676817 DOI: 10.1098/rstb.2023.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/18/2023] [Indexed: 11/28/2023] Open
Abstract
Primates are an important source of infectious disease in humans. Strongyloidiasis affects an estimated 600 million people worldwide, with a global distribution and hotspots of infection in tropical and subtropical regions. Recently added to the list of neglected tropical diseases, global attention has been demanded in the drive for its control. Through a literature review of Strongyloides in humans and non-human primates (NHP), we analysed the most common identification methods and gaps in knowledge about this nematode genus. The rise of molecular-based methods for Strongyloides detection is evident in both humans and NHP and provides an opportunity to analyse all data available from primates. Dogs were also included as an important host species of Strongyloides and a potential bridge host between humans and NHP. This review highlights the lack of molecular data across all hosts-humans, NHP and dogs-with the latter highly underrepresented in the database. Despite the cosmopolitan nature of Strongyloides, there are still large gaps in our knowledge for certain species when considering transmission and pathogenicity. We suggest that a unified approach to Strongyloides detection be taken, with an optimized, repeatable molecular-based method to improve our understanding of this parasitic infection. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
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Affiliation(s)
- Eva Nosková
- Institute of Vertebrate Biology, Czech Academy of Sciences, 603 00 Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Kelly M. Sambucci
- Institute of Vertebrate Biology, Czech Academy of Sciences, 603 00 Brno, Czech Republic
- Department of Anthropology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Klára J. Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, 603 00 Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Barbora Červená
- Institute of Vertebrate Biology, Czech Academy of Sciences, 603 00 Brno, Czech Republic
| | - David Modrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, 603 00 Brno, Czech Republic
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21
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Kenyon-Flatt B, von Cramon-Taubadel N. Intrageneric taxonomic distinction based on morphological variation in the macaque (Macaca) skeleton. Anat Rec (Hoboken) 2024; 307:118-140. [PMID: 37439127 DOI: 10.1002/ar.25283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Taxonomic classification is important for understanding the natural world, yet current methods for species assessment often focus on craniodental morphology rather than the entire skeleton. Moreover, it is currently unknown how much variation could, or should, exist intragenerically. Here, we tested whether taxonomy can be accurately predicted based on patterns of morphological variation in macaques (H1 ) and whether postcranial bones reflect subgeneric macaque taxonomy similarly, or better, than the cranium (H2 ). Data included 3D scans of cranial and postcranial bones for eight macaque species (Macaca arctoides, Macaca fascicularis, Macaca fuscata, Macaca mulatta, Macaca nemestrina, Macaca nigra, Macaca radiata, and Macaca sylvanus). Fixed anatomical and semilandmarks were applied to scans of eight skeletal elements (crania = 45; mandible = 31; scapula = 66; humerus = 38; radius = 33; os coxa = 28; femur = 40; tibia = 40). For each skeletal element, regression analyses were performed to minimize the effects of sexual dimorphism. Between-groups principal components analysis was used to visualize the major patterns of among-species morphological variation, while the strength of correct taxon classification was measured with discriminant function analysis. Results suggested accepting the alternate hypothesis that different macaque species can be distinguished morphologically. Both cranial and many postcranial elements appeared to possess a taxonomic signal, and the limb bones-especially the upper limb-are reported to be more useful for taxonomic assessment than previously realized. Theoretically, certain behaviors and/or ecogeographical factors, as well as phylogeny, influenced skeletal morphology in macaques, likely contributing to taxonomic distinctions among different species.
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Affiliation(s)
- Brittany Kenyon-Flatt
- School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, New York, USA
| | - Noreen von Cramon-Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, New York, USA
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22
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Macionis V. Fetal head-down posture may explain the rapid brain evolution in humans and other primates: An interpretative review. Brain Res 2023; 1820:148558. [PMID: 37634686 DOI: 10.1016/j.brainres.2023.148558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Evolutionary cerebrovascular consequences of upside-down postural verticality of the anthropoid fetus have been largely overlooked in the literature. This working hypothesis-based report provides a literature interpretation from an aspect that the rapid evolution of the human brain has been promoted by fetal head-down position due to maternal upright and semi-upright posture. Habitual vertical torso posture is a feature not only of humans, but also of monkeys and non-human apes that spend considerable time in a sitting position. Consequently, the head-down position of the fetus may have caused physiological craniovascular hypertension that stimulated expansion of the intracranial vessels and acted as an epigenetic physiological stress, which enhanced neurogenesis and eventually, along with other selective pressures, led to the progressive growth of the anthropoid brain and its organization. This article collaterally opens a new insight into the conundrum of high cephalopelvic proportions (i.e., the tight fit between the pelvic birth canal and fetal head) in phylogenetically distant lineages of monkeys, lesser apes, and humans. Low cephalopelvic proportions in non-human great apes could be accounted for by their energetically efficient horizontal nest-sleeping and consequently by their larger body mass compared to monkeys and lesser apes that sleep upright. One can further hypothesize that brain size varies in anthropoids according to the degree of exposure of the fetus to postural verticality. The supporting evidence for this postulation includes a finding that in fossil hominins cerebral blood flow rate increased faster than brain volume. This testable hypothesis opens a perspective for research on fetal postural cerebral hemodynamics.
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23
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Magielse N, Heuer K, Toro R, Schutter DJLG, Valk SL. A Comparative Perspective on the Cerebello-Cerebral System and Its Link to Cognition. CEREBELLUM (LONDON, ENGLAND) 2023; 22:1293-1307. [PMID: 36417091 PMCID: PMC10657313 DOI: 10.1007/s12311-022-01495-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 11/24/2022]
Abstract
The longstanding idea that the cerebral cortex is the main neural correlate of human cognition can be elaborated by comparative analyses along the vertebrate phylogenetic tree that support the view that the cerebello-cerebral system is suited to support non-motor functions more generally. In humans, diverse accounts have illustrated cerebellar involvement in cognitive functions. Although the neocortex, and its transmodal association cortices such as the prefrontal cortex, have become disproportionately large over primate evolution specifically, human neocortical volume does not appear to be exceptional relative to the variability within primates. Rather, several lines of evidence indicate that the exceptional volumetric increase of the lateral cerebellum in conjunction with its connectivity with the cerebral cortical system may be linked to non-motor functions and mental operation in primates. This idea is supported by diverging cerebello-cerebral adaptations that potentially coevolve with cognitive abilities across other vertebrates such as dolphins, parrots, and elephants. Modular adaptations upon the vertebrate cerebello-cerebral system may thus help better understand the neuroevolutionary trajectory of the primate brain and its relation to cognition in humans. Lateral cerebellar lobules crura I-II and their reciprocal connections to the cerebral cortical association areas appear to have substantially expanded in great apes, and humans. This, along with the notable increase in the ventral portions of the dentate nucleus and a shift to increased relative prefrontal-cerebellar connectivity, suggests that modular cerebellar adaptations support cognitive functions in humans. In sum, we show how comparative neuroscience provides new avenues to broaden our understanding of cerebellar and cerebello-cerebral functions in the context of cognition.
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Affiliation(s)
- Neville Magielse
- Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour), Research Center Jülich, Jülich, Germany
- Otto Hahn Cognitive Neurogenetics Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Institute of Systems Neuroscience, Heinrich Heine University, Düsseldorf, Germany
| | - Katja Heuer
- Institute Pasteur, Unité de Neuroanatomie Appliquée et Théorique, Université Paris Cité, Paris, France
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Roberto Toro
- Institute Pasteur, Unité de Neuroanatomie Appliquée et Théorique, Université Paris Cité, Paris, France
| | - Dennis J L G Schutter
- Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
| | - Sofie L Valk
- Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour), Research Center Jülich, Jülich, Germany.
- Otto Hahn Cognitive Neurogenetics Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
- Institute of Systems Neuroscience, Heinrich Heine University, Düsseldorf, Germany.
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Stoessel A, David R, Bornitz M, Ossmann S, Neudert M. Auditory thresholds compatible with optimal speech reception likely evolved before the human-chimpanzee split. Sci Rep 2023; 13:20732. [PMID: 38007561 PMCID: PMC10676368 DOI: 10.1038/s41598-023-47778-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023] Open
Abstract
The anatomy of the auditory region of fossil hominins may shed light on the emergence of human spoken language. Humans differ from other great apes in several features of the external, middle and inner ear (e.g., short external ear canal, small tympanic membrane, large oval window). However, the functional implications of these differences remain poorly understood as comparative audiometric data from great apes are scarce and conflicting. Here, we measure the sound transfer function of the external and middle ears of humans, chimpanzees and bonobos, using laser-Doppler vibrometry and finite element analysis. This sound transfer function affects auditory thresholds, which relate to speech reception thresholds in humans. Unexpectedly we find that external and middle ears of chimpanzees and bonobos transfer sound better than human ones in the frequency range of spoken language. Our results suggest that auditory thresholds of the last common ancestor of Homo and Pan were already compatible with speech reception as observed in humans. Therefore, it seems unlikely that the morphological evolution observed in the bony auditory region of fossil hominins was driven by the emergence of spoken language. Instead, the peculiar human configuration may be a by-product of morpho-functional constraints linked to brain expansion.
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Affiliation(s)
- Alexander Stoessel
- Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Erbertstr. 1, 07743, Jena, Germany.
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Romain David
- Centre for Human Evolution Research, The Natural History Museum, Cromwell Rd, South Kensington, London, SW7 5BD, UK.
| | - Matthias Bornitz
- Department of Otorhinolaryngology, Head and Neck Surgery, Carl Gustav Carus Faculty of Medicine, TU Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Steffen Ossmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Carl Gustav Carus Faculty of Medicine, TU Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Marcus Neudert
- Department of Otorhinolaryngology, Head and Neck Surgery, Carl Gustav Carus Faculty of Medicine, TU Dresden, Fetscherstr. 74, 01307, Dresden, Germany.
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Aghebatrafat AA, Lauber C, Merkel K, Fruth B, Langergraber K, Robbins MM, Wittig RM, Leendertz FH, Calvignac-Spencer S. Evolutionary Insight into the Association between New Jersey Polyomavirus and Humans. Viruses 2023; 15:2248. [PMID: 38005925 PMCID: PMC10675294 DOI: 10.3390/v15112248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Advances in viral discovery techniques have led to the identification of numerous novel viruses in human samples. However, the low prevalence of certain viruses in humans raises doubts about their association with our species. To ascertain the authenticity of a virus as a genuine human-infecting agent, it can be useful to investigate the diversification of its lineage within hominines, the group encompassing humans and African great apes. Building upon this rationale, we examined the case of the New Jersey polyomavirus (NJPyV; Alphapolyomavirus terdecihominis), which has only been detected in a single patient thus far. In this study, we obtained and analyzed sequences from closely related viruses infecting all African great ape species. We show that NJPyV nests within the diversity of these viruses and that its lineage placement is compatible with an ancient origin in humans, despite its apparent rarity in human populations.
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Affiliation(s)
- Aref-Abdolllah Aghebatrafat
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, 13353 Berlin, Germany; (A.-A.A.); (K.M.); (F.H.L.)
| | - Chris Lauber
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture between Medical School Hannover (MHH) and Helmholtz Centre for Infection Research (HZI), 30625 Hannover, Germany;
- Cluster of Excellence 2155 RESIST, 30625 Hannover, Germany
| | - Kevin Merkel
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, 13353 Berlin, Germany; (A.-A.A.); (K.M.); (F.H.L.)
| | - Barbara Fruth
- Max-Planck-Institute of Animal Behavior, 78467 Konstanz, Germany;
- Centre for Research and Conservation/KMDA, B-2018 Antwerp, Belgium
- Faculty of Science, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Kevin Langergraber
- School of Human Evolution and Social Change and Institute of Human Origins, Arizona State University, Tempe, AZ 85281, USA;
| | - Martha M. Robbins
- Departement of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany;
| | - Roman M. Wittig
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan 1303, Côte d’Ivoire;
- The Ape Social Mind Lab, Institut des Sciences Cognitives, CNRS UMR 5229, 69500 Bron, France
| | - Fabian H. Leendertz
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, 13353 Berlin, Germany; (A.-A.A.); (K.M.); (F.H.L.)
- Helmholtz Institute for One Health, Helmholtz-Centre for Infection Research (HZI), 17489 Greifswald, Germany
- Faculty of Mathematics and Natural Sciences, University of Greifswald, 17489 Greifswald, Germany
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, 13353 Berlin, Germany; (A.-A.A.); (K.M.); (F.H.L.)
- Helmholtz Institute for One Health, Helmholtz-Centre for Infection Research (HZI), 17489 Greifswald, Germany
- Faculty of Mathematics and Natural Sciences, University of Greifswald, 17489 Greifswald, Germany
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Tan X, Qi J, Liu Z, Fan P, Liu G, Zhang L, Shen Y, Li J, Roos C, Zhou X, Li M. Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation. Mol Biol Evol 2023; 40:msad229. [PMID: 37823401 PMCID: PMC10638670 DOI: 10.1093/molbev/msad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/06/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023] Open
Abstract
The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.
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Affiliation(s)
- Xinxin Tan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Jiwei Qi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing 100049, China
| | - Pengfei Fan
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Ying Shen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Ceravolo L, Debracque C, Pool E, Gruber T, Grandjean D. Frontal mechanisms underlying primate calls recognition by humans. Cereb Cortex Commun 2023; 4:tgad019. [PMID: 38025828 PMCID: PMC10661312 DOI: 10.1093/texcom/tgad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The ability to process verbal language seems unique to humans and relies not only on semantics but on other forms of communication such as affective vocalizations, that we share with other primate species-particularly great apes (Hominidae). Methods To better understand these processes at the behavioral and brain level, we asked human participants to categorize vocalizations of four primate species including human, great apes (chimpanzee and bonobo), and monkey (rhesus macaque) during MRI acquisition. Results Classification was above chance level for all species but bonobo vocalizations. Imaging analyses were computed using a participant-specific, trial-by-trial fitted probability categorization value in a model-based style of data analysis. Model-based analyses revealed the implication of the bilateral orbitofrontal cortex and inferior frontal gyrus pars triangularis (IFGtri) respectively correlating and anti-correlating with the fitted probability of accurate species classification. Further conjunction analyses revealed enhanced activity in a sub-area of the left IFGtri specifically for the accurate classification of chimpanzee calls compared to human voices. Discussion Our data-that are controlled for acoustic variability between species-therefore reveal distinct frontal mechanisms that shed light on how the human brain evolved to process vocal signals.
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Affiliation(s)
- Leonardo Ceravolo
- Neuroscience of Emotions and Affective Dynamics lab, Department of Psychology and Educational Sciences, University of Geneva, Unimail building, Boulevard Pont-d’Arve 40CH-1205, Geneva, Switzerland
- Swiss Center for Affective Sciences, University of Geneva, Campus Biotech building, Chemin des Mines 9CH-1202, Geneva, Switzerland
| | - Coralie Debracque
- Neuroscience of Emotions and Affective Dynamics lab, Department of Psychology and Educational Sciences, University of Geneva, Unimail building, Boulevard Pont-d’Arve 40CH-1205, Geneva, Switzerland
- Swiss Center for Affective Sciences, University of Geneva, Campus Biotech building, Chemin des Mines 9CH-1202, Geneva, Switzerland
| | - Eva Pool
- Swiss Center for Affective Sciences, University of Geneva, Campus Biotech building, Chemin des Mines 9CH-1202, Geneva, Switzerland
- E3 Lab, Department of Psychology and Educational Sciences, University of Geneva, Unimail building, Boulevard Pont-d’Arve 40CH-1205, Geneva, Switzerland
| | - Thibaud Gruber
- Neuroscience of Emotions and Affective Dynamics lab, Department of Psychology and Educational Sciences, University of Geneva, Unimail building, Boulevard Pont-d’Arve 40CH-1205, Geneva, Switzerland
- Swiss Center for Affective Sciences, University of Geneva, Campus Biotech building, Chemin des Mines 9CH-1202, Geneva, Switzerland
- eccePAN lab, Department of Psychology and Educational Sciences, University of Geneva, Campus Biotech building, Chemin des Mines 9CH-1202, Geneva, Switzerland
| | - Didier Grandjean
- Neuroscience of Emotions and Affective Dynamics lab, Department of Psychology and Educational Sciences, University of Geneva, Unimail building, Boulevard Pont-d’Arve 40CH-1205, Geneva, Switzerland
- Swiss Center for Affective Sciences, University of Geneva, Campus Biotech building, Chemin des Mines 9CH-1202, Geneva, Switzerland
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Miarisoa JE, Raveloson H, Randrianambinina B, Couette S. Deciphering the mandibular shape variation in a group of Malagasy primates using Fourier outline analysis. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:372-387. [PMID: 37676062 DOI: 10.1002/ajpa.24832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/12/2023] [Accepted: 07/26/2023] [Indexed: 09/08/2023]
Abstract
OBJECTIVES Among living Malagasy primates, the family Lemuridae has previously been recognized as presenting a higher mandibular morphological variation than other families. We conducted a quantitative analysis of mandibular size and shape within the five genera (Lemur, Eulemur, Hapalemur, Prolemur, and Varecia) associated with a set of covariables that could explain this variation. MATERIALS AND METHODS We used Fourier outline analysis on the left hemimandible of 182 specimens covering the Lemuridae family. The influence of the phylogeny but also seven covariables (genus, diet, sex, sexual behavior, mating system, ecoregion, and forest type) on mandibular variation was examined using multivariate statistics and model selection. RESULTS Our results indicate that the high level of morphological variation within the family, associated with a phylogenetic effect and differences in diet, is due to a strong distinction between the genera Prolemur and Hapalemur and the other genera of the family. A second analysis, correcting this strong effect, indicates that mandibular shape variation is influenced not only by the phylogeny and the diet but by a combination of all the covariables. DISCUSSION The analysis of morphological variation is a powerful tool with major applications, both for the estimation of biological diversity and for the understanding of the fundamental parameters of species' ecology. Our work indicates that, if mandibular shape variation is mainly driven by dietary adaptation, other variables describing ecology and habitat should be considered and taken into account for an integrative understanding of species resources and the establishment of conservation measures.
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Affiliation(s)
- Jeanne Emma Miarisoa
- École Doctorale Ecosystèmes Naturels, (EDEN), University of Mahajanga, Mahajanga, BP, Madagascar
- UMR CNRS/uB/EPHE 6282 Biogéosciences, Dijon, France
- École Pratique des Hautes Etudes, PSL, Paris, France
| | - Herimalala Raveloson
- École Doctorale Ecosystèmes Naturels, (EDEN), University of Mahajanga, Mahajanga, BP, Madagascar
| | | | - Sébastien Couette
- UMR CNRS/uB/EPHE 6282 Biogéosciences, Dijon, France
- École Pratique des Hautes Etudes, PSL, Paris, France
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Li X, Li H, Yang Z, Wu Y, Zhang M. Exploring objective feature sets in constructing the evolution relationship of animal genome sequences. BMC Genomics 2023; 24:634. [PMID: 37872534 PMCID: PMC10594854 DOI: 10.1186/s12864-023-09747-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Exploring evolution regularities of genome sequences and constructing more objective species evolution relationships at the genomic level are high-profile topics. Based on the evolution mechanism of genome sequences proposed in our previous research, we found that only the 8-mers containing CG or TA dinucleotides correlate directly with the evolution of genome sequences, and the relative frequency rather than the actual frequency of these 8-mers is more suitable to characterize the evolution of genome sequences. RESULT Therefore, two types of feature sets were obtained, they are the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers. The evolution relationships of mammals and reptiles were constructed by the relative frequency set of CG1 + CG2 8-mers, and two types of evolution relationships of insects were constructed by the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers respectively. Through comparison and analysis, we found that evolution relationships are consistent with the known conclusions. According to the evolution mechanism, we considered that the evolution relationship constructed by CG1 + CG2 8-mers reflects the evolution state of genome sequences in current time, and the evolution relationship constructed by TA1 + TA2 8-mers reflects the evolution state in the early stage. CONCLUSION Our study provides objective feature sets in constructing evolution relationships at the genomic level.
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Affiliation(s)
- Xiaolong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Hong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Zhenhua Yang
- School of Economics and Management, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yuan Wu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Mengchuan Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
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Shimode S. Acquisition and Exaptation of Endogenous Retroviruses in Mammalian Placenta. Biomolecules 2023; 13:1482. [PMID: 37892164 PMCID: PMC10604696 DOI: 10.3390/biom13101482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Endogenous retroviruses (ERVs) are retrovirus-like sequences that were previously integrated into the host genome. Although most ERVs are inactivated by mutations, deletions, or epigenetic regulation, some remain transcriptionally active and impact host physiology. Several ERV-encoded proteins, such as Syncytins and Suppressyn, contribute to placenta acquisition, a crucial adaptation in mammals that protects the fetus from external threats and other risks while enabling the maternal supply of oxygen, nutrients, and antibodies. In primates, Syncytin-1 and Syncytin-2 facilitate cell-cell fusion for placental formation. Suppressyn is the first ERV-derived protein that inhibits cell fusion by binding to ASCT2, the receptor for Syncytin-1. Furthermore, Syncytin-2 likely inserted into the genome of the common ancestor of Anthropoidea, whereas Syncytin-1 and Suppressyn likely inserted into the ancestor of catarrhines; however, they were inactivated in some lineages, suggesting that multiple exaptation events had occurred. This review discusses the role of ERV-encoded proteins, particularly Syncytins and Suppressyn, in placental development and function, focusing on the integration of ERVs into the host genome and their contribution to the genetic mechanisms underlying placentogenesis. This review provides valuable insights into the molecular and genetic aspects of placentation, potentially shedding light on broader evolutionary and physiological processes in mammals.
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Affiliation(s)
- Sayumi Shimode
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan;
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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Feng P, Liang X, Yu H, Dong X, Liang Q, Dai C. The evolution of bitter taste receptor gene in primates: Gene duplication and selection. Ecol Evol 2023; 13:e10610. [PMID: 37841228 PMCID: PMC10571502 DOI: 10.1002/ece3.10610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 09/08/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
Bitter taste perception plays an important role in preventing animals from digesting poisonous and harmful substances. In primates, especially the Cercopithecidae species, most species feed on plants; thus, it is reasonable to speculate that most of the bitter taste receptor genes (T2Rs) of primates are under purifying selection to maintain the functional stability of bitter taste perception. Gene duplication has happened in T2Rs frequently, and what will be the fate of T2Rs copies is another question we are concerned about. To answer these questions, we selected the T2Rs of primates reported in another study and conducted corresponding selective pressure analyses to determine what kind of selective pressure was acting on them. Further, we carried out selective pressure analyses on gene copies and their corresponding ancestors by considering several possible situations. The results showed that among the 25 gene groups examined here, 15 groups are subject to purifying selection and others are under relaxed selection, with many positively selected sites detected. Gene copies existed in several groups, but only some groups (clade1_a1-b2, clade1_c-c2, clade1_d1-d3, clade1_f1-f2, T2R10, T2R13, and T2R42) have positively selected sites, inferring that they may have some relation to functional divergence. Taken together, T2Rs in primates are under diverse selective pressures, and most gene copies are subject to the same selective pressures. In such cases, the copies may be just to keep the function conservative, and more copies can increase the quantity of the bitter taste receptor, raise the efficiency of bitter substance recognition, and finally enhance the fitness of feeding during the evolutionary course of primates. This study can improve our understanding of T2Rs evolution in primates.
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Affiliation(s)
- Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Xinyue Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Hongling Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Xiaoyan Dong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Qiufang Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
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Dumesic DA, Abbott DH, Chazenbalk GD. An Evolutionary Model for the Ancient Origins of Polycystic Ovary Syndrome. J Clin Med 2023; 12:6120. [PMID: 37834765 PMCID: PMC10573644 DOI: 10.3390/jcm12196120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is a common endocrinopathy of reproductive-aged women, characterized by hyperandrogenism, oligo-anovulation and insulin resistance and closely linked with preferential abdominal fat accumulation. As an ancestral primate trait, PCOS was likely further selected in humans when scarcity of food in hunter-gatherers of the late Pleistocene additionally programmed for enhanced fat storage to meet the metabolic demands of reproduction in later life. As an evolutionary model for PCOS, healthy normal-weight women with hyperandrogenic PCOS have subcutaneous (SC) abdominal adipose stem cells that favor fat storage through exaggerated lipid accumulation during development to adipocytes in vitro. In turn, fat storage is counterbalanced by reduced insulin sensitivity and preferential accumulation of highly lipolytic intra-abdominal fat in vivo. This metabolic adaptation in PCOS balances energy storage with glucose availability and fatty acid oxidation for optimal energy use during reproduction; its accompanying oligo-anovulation allowed PCOS women from antiquity sufficient time and strength for childrearing of fewer offspring with a greater likelihood of childhood survival. Heritable PCOS characteristics are affected by today's contemporary environment through epigenetic events that predispose women to lipotoxicity, with excess weight gain and pregnancy complications, calling for an emphasis on preventive healthcare to optimize the long-term, endocrine-metabolic health of PCOS women in today's obesogenic environment.
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Affiliation(s)
- Daniel A. Dumesic
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, Los Angeles, CA 90095, USA;
| | - David H. Abbott
- Department of Obstetrics and Gynecology, Wisconsin National Primate Research Center, University of Wisconsin, 1223 Capitol Court, Madison, WI 53715, USA;
| | - Gregorio D. Chazenbalk
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, Los Angeles, CA 90095, USA;
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Morrissey A, Shi J, James DQ, Mahony S. Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.556916. [PMID: 37745557 PMCID: PMC10515862 DOI: 10.1101/2023.09.12.556916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. Unfortunately, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory genomics analysis pipelines discard "multi-mapped" reads that align equally well to multiple genomic locations. Since multi-mapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions. To address this shortcoming, we developed Allo, a new approach to allocate multi-mapped reads in an efficient, accurate, and user-friendly manner. Allo combines probabilistic mapping of multi-mapped reads with a convolutional neural network that recognizes the read distribution features of potential peaks, offering enhanced accuracy in multi-mapping read assignment. Allo also provides read-level output in the form of a corrected alignment file, making it compatible with existing regulatory genomics analysis pipelines and downstream peak-finders. In a demonstration application on CTCF ChIP-seq data, we show that Allo results in the discovery of thousands of new CTCF peaks. Many of these peaks contain the expected cognate motif and/or serve as TAD boundaries. We additionally apply Allo to a diverse collection of ENCODE ChIP-seq datasets, resulting in multiple previously unidentified interactions between transcription factors and repetitive element families. Finally, we show that Allo may be particularly effective in identifying ChIP-seq peaks in younger TEs, which hold evolutionary significance due to their emergence during human evolution from primates.
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Affiliation(s)
- Alexis Morrissey
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Jeffrey Shi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Daniela Q. James
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
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Wagner B, Šlipogor V, Oh J, Varga M, Hoeschele M. A comparison between common marmosets (Callithrix jacchus) and human infants sheds light on traits proposed to be at the root of human octave equivalence. Dev Sci 2023; 26:e13395. [PMID: 37101383 DOI: 10.1111/desc.13395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 02/28/2023] [Accepted: 03/20/2023] [Indexed: 04/28/2023]
Abstract
Two notes separated by a doubling in frequency sound similar to humans. This "octave equivalence" is critical to perception and production of music and speech and occurs early in human development. Because it also occurs cross-culturally, a biological basis of octave equivalence has been hypothesized. Members of our team previousy suggested four human traits are at the root of this phenomenon: (1) vocal learning, (2) clear octave information in vocal harmonics, (3) differing vocal ranges, and (4) vocalizing together. Using cross-species studies, we can test how relevant these respective traits are, while controlling for enculturation effects and addressing questions of phylogeny. Common marmosets possess forms of three of the four traits, lacking differing vocal ranges. We tested 11 common marmosets by adapting an established head-turning paradigm, creating a parallel test to an important infant study. Unlike human infants, marmosets responded similarly to tones shifted by an octave or other intervals. Because previous studies with the same head-turning paradigm produced differential results to discernable acoustic stimuli in common marmosets, our results suggest that marmosets do not perceive octave equivalence. Our work suggests differing vocal ranges between adults and children and men and women and the way they are used in singing together may be critical to the development of octave equivalence. RESEARCH HIGHLIGHTS: A direct comparison of octave equivalence tests with common marmosets and human infants Marmosets show no octave equivalence Results emphasize the importance of differing vocal ranges between adults and infants.
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Affiliation(s)
- Bernhard Wagner
- Acoustics Research Institute, Austrian Academy of the Sciences, Vienna, Austria
| | - Vedrana Šlipogor
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Department of Behavioral and Cognitive Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Jinook Oh
- Cremer Group, Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Marion Varga
- Department of Behavioral and Cognitive Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Marisa Hoeschele
- Acoustics Research Institute, Austrian Academy of the Sciences, Vienna, Austria
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35
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Shin H, Leung A, Costello KR, Senapati P, Kato H, Moore RE, Lee M, Lin D, Tang X, Pirrotte P, Bouman Chen Z, Schones DE. Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome. eLife 2023; 12:e85595. [PMID: 37470704 PMCID: PMC10390045 DOI: 10.7554/elife.85595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/19/2023] [Indexed: 07/21/2023] Open
Abstract
The DNA methyltransferase activity of DNMT1 is vital for genomic maintenance of DNA methylation. We report here that DNMT1 function is regulated by O-GlcNAcylation, a protein modification that is sensitive to glucose levels, and that elevated O-GlcNAcylation of DNMT1 from high glucose environment leads to alterations to the epigenome. Using mass spectrometry and complementary alanine mutation experiments, we identified S878 as the major residue that is O-GlcNAcylated on human DNMT1. Functional studies in human and mouse cells further revealed that O-GlcNAcylation of DNMT1-S878 results in an inhibition of methyltransferase activity, resulting in a general loss of DNA methylation that preferentially occurs at partially methylated domains (PMDs). This loss of methylation corresponds with an increase in DNA damage and apoptosis. These results establish O-GlcNAcylation of DNMT1 as a mechanism through which the epigenome is regulated by glucose metabolism and implicates a role for glycosylation of DNMT1 in metabolic diseases characterized by hyperglycemia.
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Affiliation(s)
- Heon Shin
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Kevin R Costello
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Parijat Senapati
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Hiroyuki Kato
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Roger E Moore
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center DuarteDuarteUnited States
| | - Michael Lee
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Dimitri Lin
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Xiaofang Tang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
| | - Patrick Pirrotte
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center DuarteDuarteUnited States
- Cancer & Cell Biology Division, Translational Genomics Research InstitutePhoenixUnited States
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
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36
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Chiu KP, Stuart L, Ooi HS, Yu J, Smith DG, Pei KJC. Genome sequencing and application of Taiwanese macaque Macaca cyclopis. Sci Rep 2023; 13:11545. [PMID: 37460589 DOI: 10.1038/s41598-023-38402-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Formosan macaque (Macaca cyclopis) is the only non-human primate in Taiwan Island. We performed de novo hybrid assembly for M. cyclopis using Illumina paired-end short reads, mate-pair reads and Nanopore long reads and obtained 5065 contigs with a N50 of 2.66 megabases. M. cyclopis contigs > = 10 kb were assigned to chromosomes using Indian rhesus macaque (Macaca mulatta mulatta) genome assembly Mmul_10 as reference, resulting in a draft of M. cyclopis genome of 2,846,042,475 bases, distributed in 21 chromosomes. The draft genome contains 23,462 transcriptional origins (genes), capable of expressing 716,231 exons in 59,484 transcripts. Genome-based phylogenetic study using the assembled M. cyclopis genome together with genomes of four other macaque species, human, orangutan and chimpanzee showed similar result as previously reported. However, the M. cyclopis species was found to diverge from Chinese M. mulatta lasiota about 1.8 million years ago. Fossil gene analysis detected the presence of gap and pol endogenous viral elements of simian retrovirus in all macaques tested, including M. fascicularis, M. m. mulatta and M. cyclopis. However, M. cyclopis showed ~ 2 times less in number and more uniform in chromosomal locations. The constrain in foreign genome disturbance, presumably due to geographical isolation, should be able to simplify genomics-related investigations, making M. cyclopis an ideal primate species for medical research.
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Affiliation(s)
- Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
- Top Science Biotechnologies, Inc., 4F, 50-2 Dingping Rd., Sec. 1, Shiding District, New Taipei City, 223002, Taiwan.
| | - Lutimba Stuart
- Top Science Biotechnologies, Inc., 4F, 50-2 Dingping Rd., Sec. 1, Shiding District, New Taipei City, 223002, Taiwan
| | - Hong Sain Ooi
- Top Science Biotechnologies, Inc., 4F, 50-2 Dingping Rd., Sec. 1, Shiding District, New Taipei City, 223002, Taiwan
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, No.5, Fu-Shin St., Kuei Shang, Taoyuan, 333, Taiwan
| | - David Glenn Smith
- Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Kurtis Jai-Chyi Pei
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
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37
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Marivaux L, Negri FR, Antoine PO, Stutz NS, Condamine FL, Kerber L, Pujos F, Ventura Santos R, Alvim AMV, Hsiou AS, Bissaro MC, Adami-Rodrigues K, Ribeiro AM. An eosimiid primate of South Asian affinities in the Paleogene of Western Amazonia and the origin of New World monkeys. Proc Natl Acad Sci U S A 2023; 120:e2301338120. [PMID: 37399374 PMCID: PMC10334725 DOI: 10.1073/pnas.2301338120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/22/2023] [Indexed: 07/05/2023] Open
Abstract
Recent fossil discoveries in Western Amazonia revealed that two distinct anthropoid primate clades of African origin colonized South America near the Eocene/Oligocene transition (ca. 34 Ma). Here, we describe a diminutive fossil primate from Brazilian Amazonia and suggest that, surprisingly, a third clade of anthropoids was involved in the Paleogene colonization of South America by primates. This new taxon, Ashaninkacebus simpsoni gen. et sp. nov., has strong dental affinities with Asian African stem anthropoids: the Eosimiiformes. Morphology-based phylogenetic analyses of early Old World anthropoids and extinct and extant New World monkeys (platyrrhines) support relationships of both Ashaninkacebus and Amamria (late middle Eocene, North Africa) to the South Asian Eosimiidae. Afro-Arabia, then a mega island, played the role of a biogeographic stopover between South Asia and South America for anthropoid primates and hystricognathous rodents. The earliest primates from South America bear little adaptive resemblance to later Oligocene-early Miocene platyrrhine monkeys, and the scarcity of available paleontological data precludes elucidating firmly their affinities with or within Platyrrhini. Nonetheless, these data shed light on some of their life history traits, revealing a particularly small body size and a diet consisting primarily of insects and possibly fruit, which would have increased their chances of survival on a natural floating island during this extraordinary over-water trip to South America from Africa. Divergence-time estimates between Old and New World taxa indicate that the transatlantic dispersal(s) could source in the intense flooding events associated with the late middle Eocene climatic optimum (ca. 40.5 Ma) in Western Africa.
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Affiliation(s)
- Laurent Marivaux
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
| | - Francisco R. Negri
- Laboratório de Paleontologia, Universidade Federal do Acre, 69980-000Cruzeiro do Sul, Brazil
| | - Pierre-Olivier Antoine
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
| | - Narla S. Stutz
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
- Programa de Pós-Graduação em Geociências, Universidade Federal do Rio Grande do Sul, 91501-970Porto Alegre, Brazil
| | - Fabien L. Condamine
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
| | - Leonardo Kerber
- Centro de Apoio à Pesquisa Paleontológica da Quarta Colônia, Universidade Federal de Santa Maria, 97230-000São João do Polêsine, Brazil
| | - François Pujos
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales, CONICET–Universidad Nacional de Cuyo-Mendoza, 5500Mendoza, Argentina
| | - Roberto Ventura Santos
- Laboratório de Geocronologia, Instituto de Geociências, Universidade de Brasília, 70910-000Brasília, Brazil
| | - André M. V. Alvim
- Laboratório de Geocronologia, Instituto de Geociências, Universidade de Brasília, 70910-000Brasília, Brazil
| | - Annie S. Hsiou
- Laboratório de Paleontologia, Universidade de São Paulo, 14040-901Ribeirão Preto, Brazil
| | - Marcos C. Bissaro
- Laboratório de Paleontologia, Universidade de São Paulo, 14040-901Ribeirão Preto, Brazil
| | - Karen Adami-Rodrigues
- Núcleo de Estudos em Paleontologia e Estratigrafia, Centro das Engenharias, Universidade Federal de Pelotas, 96010-020Pelotas, Brazil
| | - Ana Maria Ribeiro
- Programa de Pós-Graduação em Geociências, Universidade Federal do Rio Grande do Sul, 91501-970Porto Alegre, Brazil
- Seção de Paleontologia, Museu de Ciências Naturais, Secretaria do Meio Ambiente e Infraestrutura, 90690-000Porto Alegre, Brazil
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Carneiro J, Sampaio I, Silva-Júnior JDSE, Martins-Junior A, Farias I, Hrbek T, Boubli J, Schneider H. Molecular Evidence Supports Five Lineages within Chiropotes (Pitheciidae, Platyrrhini). Genes (Basel) 2023; 14:1309. [PMID: 37510215 PMCID: PMC10379672 DOI: 10.3390/genes14071309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 07/30/2023] Open
Abstract
Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all endemic to the Amazon region. Because of the uncertainties about interspecific relationships, we reviewed the systematics and taxonomy of the genus Chiropotes. The phylogenetic analyses were performed based on Maximum Likelihood and Bayesian Inference, while species delimitation analyses were carried out using multispecies coalescent methods. In addition, we estimated genetic distances, divergence time and the probable ancestral distribution of this genus. Our results support five species of Chiropotes that emerged during the Plio-Pleistocene. Biogeographic estimates suggest that the ancestor of the current Chiropotes species occupied the endemism areas from Rondônia and Tapajós. Later, subsequent radiation and founder effects associated with the formation of the Amazonian basins probably determined the speciation events within Chiropotes.
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Affiliation(s)
- Jeferson Carneiro
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
| | - Iracilda Sampaio
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
| | | | - Antonio Martins-Junior
- Federal Institute of Education, Science and Technology of Pará, Campus Tucuruí, Tucuruí 68455-210, Pará, Brazil
| | - Izeni Farias
- Laboratório de Evolução e Genética Animal, Federal University of Amazonas, Manaus 69067-005, Amazonas, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Federal University of Amazonas, Manaus 69067-005, Amazonas, Brazil
| | - Jean Boubli
- School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK
| | - Horacio Schneider
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
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Rivas-González I, Rousselle M, Li F, Zhou L, Dutheil JY, Munch K, Shao Y, Wu D, Schierup MH, Zhang G. Pervasive incomplete lineage sorting illuminates speciation and selection in primates. Science 2023; 380:eabn4409. [PMID: 37262154 DOI: 10.1126/science.abn4409] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/19/2023] [Indexed: 06/03/2023]
Abstract
Incomplete lineage sorting (ILS) causes the phylogeny of some parts of the genome to differ from the species tree. In this work, we investigate the frequencies and determinants of ILS in 29 major ancestral nodes across the entire primate phylogeny. We find up to 64% of the genome affected by ILS at individual nodes. We exploit ILS to reconstruct speciation times and ancestral population sizes. Estimated speciation times are much more recent than genomic divergence times and are in good agreement with the fossil record. We show extensive variation of ILS along the genome, mainly driven by recombination but also by the distance to genes, highlighting a major impact of selection on variation along the genome. In many nodes, ILS is reduced more on the X chromosome compared with autosomes than expected under neutrality, which suggests higher impacts of natural selection on the X chromosome. Finally, we show an excess of ILS in genes with immune functions and a deficit of ILS in housekeeping genes. The extensive ILS in primates discovered in this study provides insights into the speciation times, ancestral population sizes, and patterns of natural selection that shape primate evolution.
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Affiliation(s)
- Iker Rivas-González
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Fang Li
- BGI-Research, BGI-Wuhan, Wuhan 430074, China
- Institute of Animal Sex and Development, ZhejiangWanli University, Ningbo 315104, China
- BGI-Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Long Zhou
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou 310058, China
- Women's Hospital, School of Medicine, Zhejiang University, Shangcheng District, Hangzhou 310006, China
| | - Julien Y Dutheil
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou 310058, China
- Women's Hospital, School of Medicine, Zhejiang University, Shangcheng District, Hangzhou 310006, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
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40
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Qi XG, Wu J, Zhao L, Wang L, Guang X, Garber PA, Opie C, Yuan Y, Diao R, Li G, Wang K, Pan R, Ji W, Sun H, Huang ZP, Xu C, Witarto AB, Jia R, Zhang C, Deng C, Qiu Q, Zhang G, Grueter CC, Wu D, Li B. Adaptations to a cold climate promoted social evolution in Asian colobine primates. Science 2023; 380:eabl8621. [PMID: 37262163 DOI: 10.1126/science.abl8621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 07/06/2022] [Indexed: 06/03/2023]
Abstract
The biological mechanisms that underpin primate social evolution remain poorly understood. Asian colobines display a range of social organizations, which makes them good models for investigating social evolution. By integrating ecological, geological, fossil, behavioral, and genomic analyses, we found that colobine primates that inhabit colder environments tend to live in larger, more complex groups. Specifically, glacial periods during the past 6 million years promoted the selection of genes involved in cold-related energy metabolism and neurohormonal regulation. More-efficient dopamine and oxytocin pathways developed in odd-nosed monkeys, which may have favored the prolongation of maternal care and lactation, increasing infant survival in cold environments. These adaptive changes appear to have strengthened interindividual affiliation, increased male-male tolerance, and facilitated the stepwise aggregation from independent one-male groups to large multilevel societies.
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Affiliation(s)
- Xiao-Guang Qi
- College of Life Sciences, Northwest University, Xi'an, China
| | - Jinwei Wu
- College of Life Sciences, Northwest University, Xi'an, China
| | - Lan Zhao
- College of Life Sciences, Northwest University, Xi'an, China
| | - Lu Wang
- College of Life Sciences, Northwest University, Xi'an, China
| | | | - Paul A Garber
- Department of Anthropology, University of Illinois, Urbana, IL, USA
| | - Christopher Opie
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
| | - Yuan Yuan
- College of Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Runjie Diao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Kun Wang
- College of Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Ruliang Pan
- College of Life Sciences, Northwest University, Xi'an, China
| | - Weihong Ji
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | | | - Zhi-Pang Huang
- College of Life Sciences, Northwest University, Xi'an, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Shanghai, China
| | - Arief B Witarto
- Faculty of Medicine, Universitas Pertahanan, Jabodetabek, Indonesia
| | - Rui Jia
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | | | - Cheng Deng
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiang Qiu
- College of Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Guojie Zhang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Dongdong Wu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Baoguo Li
- College of Life Sciences, Northwest University, Xi'an, China
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41
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Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
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42
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Shao Y, Zhou L, Li F, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KKH, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD. Phylogenomic analyses provide insights into primate evolution. Science 2023; 380:913-924. [PMID: 37262173 DOI: 10.1126/science.abn6919] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2023] [Indexed: 06/03/2023]
Abstract
Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.
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Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Long Zhou
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fang Li
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Institute of Animal Sex and Development, ZhejiangWanli University, Ningbo 315100, China
| | - Lan Zhao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
| | | | - Chun-Yan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xupeng Bi
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiao-Lin Zhuang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
| | | | - Jiang Hu
- Grandomics Biosciences, Beijing 102206, China
| | - Zongyi Sun
- Grandomics Biosciences, Beijing 102206, China
| | - Xin Li
- Grandomics Biosciences, Beijing 102206, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102206, China
| | | | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hui-Meng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - George P Tiley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Yong-Gang Yao
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650204, China
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43
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Valdivieso-Cortadella S, Bernardi-Gómez C, Aureli F, Llorente M, Amici F. Yawning and scratching contagion in wild spider monkeys (Ateles geoffroyi). Sci Rep 2023; 13:8367. [PMID: 37225745 DOI: 10.1038/s41598-023-35693-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/22/2023] [Indexed: 05/26/2023] Open
Abstract
Behavioural contagion is a widespread phenomenon in animal species, which is thought to promote coordination and group cohesion. Among non-human primates, however, there is no evidence of behavioural contagion in Platyrrhines (i.e. primates from South and Central America) yet. Here, we investigated whether behavioural contagion is also present in this taxon, by assessing yawning and scratching contagion in a wild group (N = 49) of Geoffroy's spider monkeys (Ateles geoffroyi). We conducted focal samples to examine whether individuals observing the triggering event (i.e. a naturally occurring yawning or scratching event in the group) would be more likely to yawn or scratch in the following 3 min, as compared to individuals who did not observe the triggering event. We ran generalized linear mixed models using a Bayesian approach, and found that the probability of yawning and scratching was higher for individuals observing others yawning and scratching, respectively, as compared to individuals who did not observe such an event. Behavioural contagion did not vary depending on the observer's sex, kinship or relationship quality with the individual performing the triggering event. These findings provide the first evidence for yawning and scratching contagion in a wild group of spider monkeys, and importantly contribute to the debate about the evolutionary origins of behavioural contagion in primates.
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Affiliation(s)
| | | | - Filippo Aureli
- Instituto de Neuroetologia, Universidad Veracruzana, 91190, Xalapa-Enríquez, Mexico
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, L1 2SF, UK
| | - Miquel Llorente
- Universitat de Girona, Fundació UdG: Innovació i Formació, 17003, Girona, Spain
- Departament de Psicologia, Universitat de Girona, 17004, Girona, Spain
| | - Federica Amici
- Institute of Biology, Human Biology and Primate Cognition Group, University of Leipzig, 04109, Leipzig, Germany.
- Department of Comparative Cultural Psychology, Max-Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
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44
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Martins AB, Valença-Montenegro MM, Lima MGM, Lynch JW, Svoboda WK, Silva-Júnior JDSE, Röhe F, Boubli JP, Fiore AD. A New Assessment of Robust Capuchin Monkey ( Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation. Genes (Basel) 2023; 14:genes14050970. [PMID: 37239330 DOI: 10.3390/genes14050970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Robust capuchin monkeys, Sapajus genus, are among the most phenotypically diverse and widespread groups of primates in South America, with one of the most confusing and often shifting taxonomies. We used a ddRADseq approach to generate genome-wide SNP markers for 171 individuals from all putative extant species of Sapajus to access their evolutionary history. Using maximum likelihood, multispecies coalescent phylogenetic inference, and a Bayes Factor method to test for alternative hypotheses of species delimitation, we inferred the phylogenetic history of the Sapajus radiation, evaluating the number of discrete species supported. Our results support the recognition of three species from the Atlantic Forest south of the São Francisco River, with these species being the first splits in the robust capuchin radiation. Our results were congruent in recovering the Pantanal and Amazonian Sapajus as structured into three monophyletic clades, though new morphological assessments are necessary, as the Amazonian clades do not agree with previous morphology-based taxonomic distributions. Phylogenetic reconstructions for Sapajus occurring in the Cerrado, Caatinga, and northeastern Atlantic Forest were less congruent with morphology-based phylogenetic reconstructions, as the bearded capuchin was recovered as a paraphyletic clade, with samples from the Caatinga biome being either a monophyletic clade or nested with the blond capuchin monkey.
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Affiliation(s)
- Amely Branquinho Martins
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mônica Mafra Valença-Montenegro
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
| | - Marcela Guimarães Moreira Lima
- Laboratório de Biogeografia da Conservação e Macroecologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66077-530, PA, Brazil
| | - Jessica W Lynch
- Institute for Society and Genetics, Department of Anthropology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Walfrido Kühl Svoboda
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Centro Interdisciplinar de Ciências da Vida, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu 85870-650, PR, Brazil
| | - José de Sousa E Silva-Júnior
- Museu Paraense Emílio Goeldi, Ministério da Ciência, Tecnologia, Inovações e Comunicações, Coordenação de Zoologia, Campus de Pesquisa, Setor de Mastozoologia, Belém 66077-830, PA, Brazil
| | - Fábio Röhe
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus 69067-005, AM, Brazil
| | - Jean Philippe Boubli
- School of Science, Engineering and the Environment, University of Salford, Salford M5 4WT, UK
| | - Anthony Di Fiore
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
- Tiputini Biodiversity Station, Universidad San Francisco de Quito, Quito 170901, Ecuador
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45
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Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Gordon DS, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Lu Q, Paten B, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531415. [PMID: 36945442 PMCID: PMC10028934 DOI: 10.1101/2023.03.07.531415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
To better understand the pattern of primate genome structural variation, we sequenced and assembled using multiple long-read sequencing technologies the genomes of eight nonhuman primate species, including New World monkeys (owl monkey and marmoset), Old World monkey (macaque), Asian apes (orangutan and gibbon), and African ape lineages (gorilla, bonobo, and chimpanzee). Compared to the human genome, we identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. Across 50 million years of primate evolution, we estimate that 819.47 Mbp or ~27% of the genome has been affected by SVs based on analysis of these primate lineages. We identify 1,607 structurally divergent regions (SDRs) wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (CARDs, ABCD7, OLAH) and new lineage-specific genes are generated (e.g., CKAP2, NEK5) and have become targets of rapid chromosomal diversification and positive selection (e.g., RGPDs). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species for the first time.
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Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ricardo Del Rosario
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa L Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Will T Fattor
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA
- Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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46
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Blair ME, Cao GTH, López-Nandam EH, Veronese-Paniagua DA, Birchette MG, Kenyon M, Md-Zain BM, Munds RA, Nekaris KAI, Nijman V, Roos C, Thach HM, Sterling EJ, Le MD. Molecular Phylogenetic Relationships and Unveiling Novel Genetic Diversity among Slow and Pygmy Lorises, including Resurrection of Xanthonycticebus intermedius. Genes (Basel) 2023; 14:643. [PMID: 36980915 PMCID: PMC10048081 DOI: 10.3390/genes14030643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Genetic analysis of historical museum collections presents an opportunity to clarify the evolutionary history of understudied primate groups, improve taxonomic inferences, and inform conservation efforts. Among the most understudied primate groups, slow and pygmy lorises (genera Nycticebus and Xanthonycticebus) are nocturnal strepsirrhines found in South and Southeast Asia. Previous molecular studies have supported five species, but studies using morphological data suggest the existence of at least nine species. We sequenced four mitochondrial loci, CO1, cytb, d-loop, and ND4, for a total of 3324 aligned characters per sample from 41 historical museum specimens for the most comprehensive geographic coverage to date for these genera. We then combined these sequences with a larger dataset composed of samples collected in Vietnam as well as previously published sequences (total sample size N = 62). We inferred phylogenetic relationships using Bayesian inference and maximum likelihood methods based on data from each locus and on concatenated sequences. We also inferred divergence dates for the most recent common ancestors of major lineages using a BEAST analysis. Consistent with previous studies, we found support for Xanthonycticebus pygmaeus as a basal taxon to the others in the group. We also confirmed the separation between lineages of X. pygmaeus from northern Vietnam/Laos/China and southern Vietnam/Cambodia and included a taxonomic revision recognizing a second taxon of pygmy loris, X. intermedius. Our results found support for multiple reciprocally monophyletic taxa within Borneo and possibly Java. The study will help inform conservation management of these trade-targeted animals as part of a genetic reference database for determining the taxonomic unit and provenance of slow and pygmy lorises confiscated from illegal wildlife trade activities.
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Affiliation(s)
- Mary E. Blair
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - Giang T. H. Cao
- Department of Genetics, Vietnam National University, Hanoi 10000, Vietnam
| | - Elora H. López-Nandam
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- Institute for Biodiversity and Sustainability Science, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Daniel A. Veronese-Paniagua
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- The Division of Biology & Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mark G. Birchette
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- Department of Biology, Long Island University Brooklyn, Brooklyn, NY 11201, USA
| | - Marina Kenyon
- Dao Tien Endangered Primate Species Centre, Dong Nai 76000, Vietnam
| | - Badrul M. Md-Zain
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi Selangor 43600, Malaysia
| | - Rachel A. Munds
- Department of Anthropology & Archeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - K. Anne-Isola Nekaris
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
- School of Social Sciences and Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Vincent Nijman
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
- School of Social Sciences and Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Hoàng M. Thach
- Department of Anthropology, Vietnam National University, Hanoi 10000, Vietnam
- Department of Geography & Human Ecology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Eleanor J. Sterling
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - Minh D. Le
- Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 10000, Vietnam
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47
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Ducournau C, Cantin P, Alerte V, Quintard B, Popelin-Wedlarski F, Wedlarski R, Ollivet-Courtois F, Ferri-Pisani Maltot J, Herkt C, Fasquelle F, Sannier M, Berthet M, Fretay V, Aubert D, Villena I, Betbeder D, Moiré N, Dimier-Poisson I. Vaccination of squirrel monkeys (Saimiri spp.) with nanoparticle based-Toxoplasma gondii antigens: new hope for captive susceptible species. Int J Parasitol 2023; 53:333-346. [PMID: 36997082 DOI: 10.1016/j.ijpara.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 03/31/2023]
Abstract
Squirrel monkeys (Saimiri spp.), new world primates from South America, are very susceptible to toxoplasmosis. Numerous outbreaks of fatal toxoplasmosis in zoos have been identified around the world, resulting in acute respiratory distress and sudden death. To date, preventive hygiene measures or available treatments are not able to significantly reduce this mortality in zoos. Therefore, vaccination seems to be the best long-term solution to control acute toxoplasmosis. Recently, we developed a nasal vaccine composed of total extract of soluble proteins of Toxoplasma gondii associated with muco-adhesive maltodextrin-nanoparticles. The vaccine, which generated specific cellular immune responses, demonstrated efficacy against toxoplasmosis in murine and ovine experimental models. In collaboration with six French zoos, our vaccine was used as a last resort in 48 squirrel monkeys to prevent toxoplasmosis. The full protocol of vaccination includes two intranasal sprays followed by combined intranasal and s.c. administration. No local or systemic side-effects were observed irrespective of the route of administration. Blood samples were collected to study systemic humoral and cellular immune responses up to 1 year after the last vaccination. Vaccination induced a strong and lasting systemic cellular immune response mediated by specific IFN-γ secretion by peripheral blood mononuclear cells. Since the introduction of vaccination, no deaths of squirrel monkeys due to T. gondii has been observed for more than 4 years suggesting the promising usage of our vaccine. Moreover, to explain the high susceptibility of naive squirrel monkeys to toxoplasmosis, their innate immune sensors were investigated. It was observed that Toll-like and Nod-like receptors appear to be functional following T. gondii recognition suggesting that the extreme susceptibility to toxoplasmosis may not be linked to innate detection of the parasite.
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48
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Podgorski II, Harrach B, Benkő M, Papp T. Characterization of monkey adenoviruses with three fiber genes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 108:105403. [PMID: 36610683 DOI: 10.1016/j.meegid.2023.105403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Although the occurrence of three fiber genes in monkey adenoviruses had already been described, the relatedness of the "extra" fibers have not yet been discussed. Here we report the genome analysis of two simian adenovirus (SAdV) serotypes from Old World monkeys and the phylogenetic analysis of the multiple fiber genes found in these and related AdVs. One of the newly sequenced serotypes (SAdV-2), isolated from a rhesus macaque (Macaca mulatta), was classified into species Human mastadenovirus G (HAdV-G), while the other serotype (SAdV-17), originating from a grivet (Chlorocebus aethiops), classified to Simian mastadenovirus F (SAdV-F). We identified unique features in the gene content of these SAdVs compared to those typical for other members of the genus Mastadenovirus. Namely, in the E1B region of SAdV-2, the 19K gene was replaced by an ITR repetition and a copy of the E4 ORF1 gene. Among the 37 genes in both SAdVs, three genes of different lengths, predicted to code for the cellular attachment proteins (the fibers), were found. These proteins exhibit high diversity. Yet, phylogenetic calculations of their conserved parts could reveal the probable evolutionary steps leading to the multiple-fibered contemporary HAdV and SAdV species. Seemingly, there existed (a) common ancestor(s) with two fiber genes for the lineages of the AdVs in species SAdV-B, -E, -F and HAdV-F, alongside a double-fibered ancestor for today's SAdV-C and HAdV-G, which later diverged into descendants forming today's species. Additionally, some HAdV-G members picked up a third fiber gene either to the left-hand or to the in-between position from the existing two. A SAdV-F progenitor also obtained a third copy to the middle, as observed in SAdV-17. The existence of three fiber genes in these contemporary AdVs brings novel possibilities for the design of optimised AdV-based vectors with potential multiple target binding abilities.
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Affiliation(s)
- Iva I Podgorski
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary.
| | - Balázs Harrach
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary.
| | - Mária Benkő
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary.
| | - Tibor Papp
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary.
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49
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King SB, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol 2023; 19:e1010966. [PMID: 36952575 PMCID: PMC10035887 DOI: 10.1371/journal.pcbi.1010966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
Despite the vast phenotypic differences observed across primates, their protein products are largely similar to each other at the sequence level. We hypothesized that, since proteins accomplish all their functions via interactions with other molecules, alterations in the sites that participate in these interactions may be of critical importance. To uncover the extent to which these sites evolve across primates, we built a structurally-derived dataset of ~4,200 one-to-one orthologous sequence groups across 18 primate species, consisting of ~68,000 ligand-binding sites that interact with DNA, RNA, small molecules, ions, or peptides. Using this dataset, we identify functionally important patterns of conservation and variation within the amino acid residues that facilitate protein-ligand interactions across the primate phylogeny. We uncover that interaction sites are significantly more conserved than other sites, and that sites binding DNA and RNA further exhibit the lowest levels of variation. We also show that the subset of ligand-binding sites that do vary are enriched in components of gene regulatory pathways and uncover several instances of human-specific ligand-binding site changes within transcription factors. Altogether, our results suggest that ligand-binding sites have experienced selective pressure in primates and propose that variation in these sites may have an outsized effect on phenotypic variation in primates through pleiotropic effects on gene regulation.
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Affiliation(s)
- Sean B. King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
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50
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Ramírez-Pedraza I, Martínez LM, Aouraghe H, Rivals F, Tornero C, Haddoumi H, Estebaranz-Sánchez F, Rodríguez-Hidalgo A, van der Made J, Oujaa A, Ibáñez JJ, Mhamdi H, Souhir M, Aissa AM, Chacón MG, Sala-Ramos R. Multiproxy approach to reconstruct fossil primate feeding behavior: Case study for macaque from the Plio-Pleistocene site Guefaït-4.2 (eastern Morocco). Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1011208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
The genus Macaca belongs to Cercopithecidae (Old World monkeys), Cercopithecinae, Papionini. The presence of Macaca in North Africa is well known from the Late Miocene to the Late Pleistocene. However, the diet of fossil Macaca has been poorly described in the literature. In this study, we investigated the feeding habits of Macaca cf. sylvanus (n = 4) from the Plio-Pleistocene site Guefaït-4.2 in eastern Morocco through multiproxy analysis combining analyses of stable carbon and oxygen isotopes from tooth enamel, buccal microtexture, and low-magnification occlusal dental microwear. For both microwear analyses, we compared the macaques with a new reference collection of extant members of Cercopithecoidea. Our occlusal microwear results show for the fossil macaque a pattern similar to the extant Cercocebus atys and Lophocebus albigena, African forest-dwelling species that are characterized by a durophagous diet based mainly on hard fruit and seed intake. Buccal microtexture results also suggest the consumption of some grasses and the exploitation of more open habitats, similar to that observed in Theropithecus gelada. The δ13C of M. cf. sylvanus indicates a C3 based-diet without the presence of C4 plants typical of the savanna grassland in eastern Africa during this period. The high δ18O values of M. cf. sylvanus, compared with the contemporary ungulates recovered from Guefaït-4.2, could be associated with the consumption of a different resource by the primate such as leaves or fresh fruits from the upper part of trees. The complementarity of these methods allows for a dietary reconstruction covering a large part of the individual’s life.
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