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Mansueto A, Good DJ. Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis. J Mol Evol 2024; 92:266-277. [PMID: 38683367 PMCID: PMC11169010 DOI: 10.1007/s00239-024-10165-0] [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: 07/10/2023] [Accepted: 03/20/2024] [Indexed: 05/01/2024]
Abstract
Ascorbic acid functions as an antioxidant and facilitates other biochemical processes such as collagen triple helix formation, and iron uptake by cells. Animals which endogenously produce ascorbic acid have a functional gulonolactone oxidase gene (GULO); however, humans have a GULO pseudogene (GULOP) and depend on dietary ascorbic acid. In this study, the conservation of GULOP sequences in the primate haplorhini suborder were investigated and compared to the GULO sequences belonging to the primates strepsirrhini suborder. Phylogenetic analysis suggested that the conserved GULOP exons in the haplorhini primates experienced a high rate of mutations following the haplorhini/strepsirrhini divergence. This high mutation rate has decreased during the evolution of the haplorhini primates. Additionally, indels of the haplorhini GULOP sequences were conserved across the suborder. A separate analysis for GULO sequences and well-conserved GULOP sequences focusing on placental mammals identified an in-frame GULO sequence in the Brazilian guinea pig, and a potential GULOP sequence in the pika. Similar to haplorhini primates, the guinea pig and lagomorph species have experienced a high substitution rate when compared to the mammals used in this study. A shared synteny to examine the conservation of local genes near GULO/GULOP identified a conserved inversion around the GULO/GULOP locus between the haplorhini and strepsirrhini primates. Fischer's exact test did not support an association between GULOP and the chromosomal inversion. Mauve alignment showed that the inversion of the length of the syntenic block that the GULO/GULOP genes belonged to was variable. However, there were frequent rearrangements around ~ 2 million base pairs adjacent to GULOP involving the KIF13B and MSRA genes. These data may suggest that genes acquiring deleterious mutations in the coding sequence may respond to these deleterious mutations with rapid substitution rates.
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Affiliation(s)
- Alexander Mansueto
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
- Department of Biological Sciences, Vanderbilt University, Nashvile, TN, USA
| | - Deborah J Good
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA.
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, 1981 Kraft Drive (0913), ILSB Room 1020, Blacksburg, VA, 24060, USA.
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Niimura Y, Biswa BB, Kishida T, Toyoda A, Fujiwara K, Ito M, Touhara K, Inoue-Murayama M, Jenkins SH, Adenyo C, Kayang BB, Koide T. Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents. Mol Biol Evol 2024; 41:msae071. [PMID: 38649162 PMCID: PMC11035023 DOI: 10.1093/molbev/msae071] [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: 02/02/2023] [Revised: 02/02/2024] [Accepted: 03/03/2024] [Indexed: 04/25/2024] Open
Abstract
Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively.
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Affiliation(s)
- Yoshihito Niimura
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Bhim B Biswa
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Shizuoka, Japan
| | - Takushi Kishida
- Curatorial Division, Museum of Natural and Environmental History, Shizuoka, Japan
- Present address: College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Kazumichi Fujiwara
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
| | - Masato Ito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Scott H Jenkins
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Present address: Biosphere Informatics Laboratory, Department of Social Informatics, Graduate School of Informatics, Kyoto, Japan
| | - Christopher Adenyo
- Livestock and Poultry Research Centre, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Boniface B Kayang
- Department of Animal Science, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Tsuyoshi Koide
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Shizuoka, Japan
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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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Winn-Nuñez ET, Witt H, Bhaskar D, Huang RY, Reichner JS, Wong IY, Crawford L. Generative modeling of biological shapes and images using a probabilistic α-shape sampler. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574919. [PMID: 38260340 PMCID: PMC10802457 DOI: 10.1101/2024.01.09.574919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Understanding morphological variation is an important task in many areas of computational biology. Recent studies have focused on developing computational tools for the task of sub-image selection which aims at identifying structural features that best describe the variation between classes of shapes. A major part in assessing the utility of these approaches is to demonstrate their performance on both simulated and real datasets. However, when creating a model for shape statistics, real data can be difficult to access and the sample sizes for these data are often small due to them being expensive to collect. Meanwhile, the current landscape of generative models for shapes has been mostly limited to approaches that use black-box inference-making it difficult to systematically assess the power and calibration of sub-image models. In this paper, we introduce the α -shape sampler: a probabilistic framework for generating realistic 2D and 3D shapes based on probability distributions which can be learned from real data. We demonstrate our framework using proof-of-concept examples and in two real applications in biology where we generate (i) 2D images of healthy and septic neutrophils and (ii) 3D computed tomography (CT) scans of primate mandibular molars. The α -shape sampler R package is open-source and can be downloaded at https://github.com/lcrawlab/ashapesampler.
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Affiliation(s)
| | - Hadley Witt
- Graduate Program in Pathobiology, Brown University, Providence, RI, USA
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, Providence, RI, USA
| | | | - Ryan Y. Huang
- Department of Computer Science, Brown University, Providence, RI USA
| | - Jonathan S. Reichner
- Graduate Program in Pathobiology, Brown University, Providence, RI, USA
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, Providence, RI, USA
| | - Ian Y. Wong
- Graduate Program in Pathobiology, Brown University, Providence, RI, USA
- School of Engineering, Legoretta Cancer Center, Brown University, Providence, RI USA
| | - Lorin Crawford
- Microsoft Research, Cambridge, MA, USA
- Department of Biostatistics, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
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Horvath S, Haghani A, Zoller JA, Lu AT, Ernst J, Pellegrini M, Jasinska AJ, Mattison JA, Salmon AB, Raj K, Horvath M, Paul KC, Ritz BR, Robeck TR, Spriggs M, Ehmke EE, Jenkins S, Li C, Nathanielsz PW. Pan-primate studies of age and sex. GeroScience 2023; 45:3187-3209. [PMID: 37493860 PMCID: PMC10643767 DOI: 10.1007/s11357-023-00878-3] [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: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/27/2023] Open
Abstract
Age and sex have a profound effect on cytosine methylation levels in humans and many other species. Here we analyzed DNA methylation profiles of 2400 tissues derived from 37 primate species including 11 haplorhine species (baboons, marmosets, vervets, rhesus macaque, chimpanzees, gorillas, orangutan, humans) and 26 strepsirrhine species (suborders Lemuriformes and Lorisiformes). From these we present here, pan-primate epigenetic clocks which are highly accurate for all primates including humans (age correlation R = 0.98). We also carried out in-depth analysis of baboon DNA methylation profiles and generated five epigenetic clocks for baboons (Olive-yellow baboon hybrid), one of which, the pan-tissue epigenetic clock, was trained on seven tissue types (fetal cerebral cortex, adult cerebral cortex, cerebellum, adipose, heart, liver, and skeletal muscle) with ages ranging from late fetal life to 22.8 years of age. Using the primate data, we characterize the effect of age and sex on individual cytosines in highly conserved regions. We identify 11 sex-related CpGs on autosomes near genes (POU3F2, CDYL, MYCL, FBXL4, ZC3H10, ZXDC, RRAS, FAM217A, RBM39, GRIA2, UHRF2). Low overlap can be observed between age- and sex-related CpGs. Overall, this study advances our understanding of conserved age- and sex-related epigenetic changes in primates, and provides biomarkers of aging for all primates.
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Affiliation(s)
- Steve Horvath
- Altos Labs, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
| | | | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Jason Ernst
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and BiobehavioralSciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julie A Mattison
- Translational Gerontology Branch, National Institute On Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Adam B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies, and Department of Molecular Medicine, UT Health San Antonio, and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | | | - Kimberly C Paul
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Beate R Ritz
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Todd R Robeck
- Corporate Zoological Operations, SeaWorld Parks, Orlando, FL, USA
| | - Maria Spriggs
- Busch Gardens Tampa, SeaWorld Parks, Tampa, FL, 33612, USA
| | | | - Susan Jenkins
- Texas Pregnancy & Life-Course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources Department, Laramie, WY, USA
| | - Cun Li
- Texas Pregnancy & Life-Course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources Department, Laramie, WY, USA
| | - Peter W Nathanielsz
- Texas Pregnancy & Life-Course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources Department, Laramie, WY, USA
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Osozawa S. Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans. Ecol Evol 2023; 13:e10827. [PMID: 38116126 PMCID: PMC10728886 DOI: 10.1002/ece3.10827] [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: 05/11/2023] [Revised: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
A robust timetree for Mammalia was constructed using the time calibration function of BEAST v1.10.4 and MEGA 11. The analysis involved the application of times of the most recent common ancestors, including a total of 19 mammalian fossil calibration ages following Benton et al. (Palaeontologia Electronica, 2015, 1-106) for their minimum ages. Additionally, fossil calibration ages for Gorilla, Pan, and a geologic event calibration age for otters were incorporated. Using these calibration ages, I constructed a geologically calibrated tree that estimates the age of the Homo and Pan splitting to be 5.69 Ma. The tree carries several significant implications. First, after the initial rifting at 120 Ma, the Atlantic Ocean expanded by over 500 km around Chron 34 (84 Ma), and vicariant speciation between Afrotheria (Africa) and Xenarthra (South America) appears to have commenced around 70 Ma. Additionally, ordinal level differentiations began immediately following the K-Pg boundary (66.0 Ma), supporting previous hypothesis that mammalian radiation rapidly filled ecological niches left vacant by non-avian dinosaurs. I constructed a diagram depicting the relationship between base substitution rate and age using an additional function in BEAST v1.10.4. The diagram reveals an exponential increase in the base substitution rate approaching recent times. This increased base substitution rate during the Neogene period may have contributed to the expansion of biodiversity, including the extensive adaptive radiation that led to the evolution of Homo sapiens. One significant driving factor behind this radiation could be attributed to the emergence and proliferation of C4 grasses since 20 Ma. These grasses have played a role in increasing carbon fixation, reducing atmospheric CO2 concentration, inducing global cooling, and initiating Quaternary glacial-interglacial cycles, thereby causing significant climatic changes.
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Affiliation(s)
- Soichi Osozawa
- Faculty of Science, Institute of Geology and PaleontologyTohoku UniversitySendaiJapan
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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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8
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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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Major T, Renk P, Reissig J, Paijmans JLA, Morris E, Hofreiter M, Barlow A, Broadley DG, Wüster W. Museum DNA reveals a new, potentially extinct species of rinkhals (Serpentes: Elapidae: Hemachatus) from the Eastern Highlands of Zimbabwe. PLoS One 2023; 18:e0291432. [PMID: 37756254 PMCID: PMC10529548 DOI: 10.1371/journal.pone.0291432] [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: 01/12/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Genetic information plays a pivotal role in species recognition and delimitation, but rare or extinct animals can be difficult to obtain genetic samples from. While natural history wet collections have proven invaluable in the description of novel species, the use of these historical samples in genetic studies has been greatly impeded by DNA degradation, especially because of formalin-fixation prior to preservation. Here, we use recently developed museum genomics approaches to determine the status of an isolated population of the elapid snake genus Hemachatus from Zimbabwe. We used multiple digestion phases followed by single strand sequencing library construction and hybridisation capture to obtain 12S and 16S rDNA sequences from a poorly preserved tissue sample of this population. Phylogenetic and morphological analyses in an integrated taxonomic framework demonstrate that the Zimbabwean rinkhals population represents an old and highly distinct lineage, which we describe as a new species, Hemachatus nyangensis sp. nov. Our phylogenetic dating analysis is compatible with venom spitting having evolved in response to the threat posed by early hominins, although more data are required for a robust test of this hypothesis. This description demonstrates the power of museum genomics in revealing rare or even extinct species: Hemachatus from Zimbabwe are only known from a small area of the Eastern Highlands known for high endemism. No living specimens have been seen since the 1980s, most likely due to dramatic land-use changes in the Eastern Highlands, suggesting that the species could be extinct. In view of its recognition as a highly distinct lineage, urgent action is required to determine whether any populations survive, and to safeguard remaining habitat.
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Affiliation(s)
- Tom Major
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Pia Renk
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jens Reissig
- Ultimate Creatures, Kelvin, Sandton, South Africa
| | | | - Ellie Morris
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | | | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
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10
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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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11
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Lo Y, Bruxaux J, Rodríguez de la Vega RC, O'Donnell S, Snirc A, Coton M, Le Piver M, Le Prieur S, Roueyre D, Dupont J, Houbraken J, Debuchy R, Ropars J, Giraud T, Branca A. Domestication in dry-cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision. Evol Appl 2023; 16:1637-1660. [PMID: 37752962 PMCID: PMC10519415 DOI: 10.1111/eva.13591] [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: 07/04/2022] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed HGTs, particularly between P. nalgiovense and P. salamii (representing almost 1.5 Mb of cumulative length). HGTs additionally involved P. biforme, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense and P. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.
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Affiliation(s)
- Ying‐Chu Lo
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Jade Bruxaux
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | | | - Samuel O'Donnell
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Alodie Snirc
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Stéphanie Le Prieur
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS‐MNHN, Muséum National d'Histoire NaturelleParis Cedex 05France
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity InstituteUtrechtThe Netherlands
| | - Robert Debuchy
- Université Paris‐Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Jeanne Ropars
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Tatiana Giraud
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Antoine Branca
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- IDEEV – Laboratoire Evolution, Génomes Comportement, EcologieCNRS Université Paris Saclay UMR 9191, IRD UMR 247Gif‐sur‐YvetteFrance
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12
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Kunze PE, Cortés-Hinojosa G, Williams CV, Archer LL, Ferrante JA, Wellehan JFX. Identification of 3 novel herpesviruses in prosimians with lymphoproliferative disease. J Vet Diagn Invest 2023; 35:514-520. [PMID: 37381927 PMCID: PMC10467458 DOI: 10.1177/10406387231183431] [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] [Indexed: 06/30/2023] Open
Abstract
Although many studies have characterized catarrhine and platyrrhine primate herpesviruses, little is known about herpesviruses in prosimians. We aimed to identify and characterize herpesviruses in prosimians with proliferative lymphocytic disease. DNA was extracted from tissues of 9 gray mouse lemurs (Microcebus murinus) and 3 pygmy slow lorises (Nycticebus pygmaeus) with lymphoproliferative lesions, and we performed nested PCR and sequencing for detection of herpesviruses and polyomaviruses. We identified 3 novel herpesviruses and performed phylogenetic analyses to characterize their relationship with other herpesviruses. A gray mouse lemur herpesvirus clustered with other primate herpesviruses within the subfamily Betaherpesvirinae, just basal to the genus Cytomegalovirus. The other gray mouse lemur herpesvirus and the pygmy slow loris herpesvirus clustered within the subfamily Gammaherpesvirinae, although the relationships within the subfamily were less resolved. Quantitative PCR assays were developed for the 2 new gray mouse lemur viruses, providing specific, faster, less expensive, and quantitative detection tools. Further studies are needed to elucidate the relationship between the presence of these viruses and the severity or presence of lymphoproliferative lesions in prosimians.
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Affiliation(s)
- Patricia E. Kunze
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Galaxia Cortés-Hinojosa
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Linda L. Archer
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Jason A. Ferrante
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - James F. X. Wellehan
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
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13
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Zhou B, He Y, Chen Y, Su B. Comparative Genomic Analysis Identifies Great-Ape-Specific Structural Variants and Their Evolutionary Relevance. Mol Biol Evol 2023; 40:msad184. [PMID: 37565562 PMCID: PMC10461412 DOI: 10.1093/molbev/msad184] [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: 03/16/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
During the origin of great apes about 14 million years ago, a series of phenotypic innovations emerged, such as the increased body size, the enlarged brain volume, the improved cognitive skill, and the diversified diet. Yet, the genomic basis of these evolutionary changes remains unclear. Utilizing the high-quality genome assemblies of great apes (including human), gibbon, and macaque, we conducted comparative genome analyses and identified 15,885 great ape-specific structural variants (GSSVs), including eight coding GSSVs resulting in the creation of novel proteins (e.g., ACAN and CMYA5). Functional annotations of the GSSV-related genes revealed the enrichment of genes involved in development and morphogenesis, especially neurogenesis and neural network formation, suggesting the potential role of GSSVs in shaping the great ape-shared traits. Further dissection of the brain-related GSSVs shows great ape-specific changes of enhancer activities and gene expression in the brain, involving a group of GSSV-regulated genes (such as NOL3) that potentially contribute to the altered brain development and function in great apes. The presented data highlight the evolutionary role of structural variants in the phenotypic innovations during the origin of the great ape lineage.
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Affiliation(s)
- Bin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 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, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 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, Yunnan, China
| | - Yongjie Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 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, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 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, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
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14
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Giacometti C, Amiez C, Hadj-Bouziane F. Multiple routes of communication within the amygdala-mPFC network: A comparative approach in humans and macaques. CURRENT RESEARCH IN NEUROBIOLOGY 2023; 5:100103. [PMID: 37601951 PMCID: PMC10432920 DOI: 10.1016/j.crneur.2023.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 06/14/2023] [Accepted: 07/15/2023] [Indexed: 08/22/2023] Open
Abstract
The network formed by the amygdala (AMG) and the medial Prefrontal Cortex (mPFC), at the interface between our internal and external environment, has been shown to support some important aspects of behavioral adaptation. Whether and how the anatomo-functional organization of this network evolved across primates remains unclear. Here, we compared AMG nuclei morphological characteristics and their functional connectivity with the mPFC in humans and macaques to identify potential homologies and differences between these species. Based on selected studies, we highlight two subsystems within the AMG-mPFC circuits, likely involved in distinct temporal dynamics of integration during behavioral adaptation. We also show that whereas the mPFC displays a large expansion but a preserved intrinsic anatomo-functional organization, the AMG displays a volume reduction and morphological changes related to specific nuclei. We discuss potential commonalities and differences in the dialogue between AMG nuclei and mPFC in humans and macaques based on available data.
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Affiliation(s)
- C. Giacometti
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500, Bron, France
| | - C. Amiez
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500, Bron, France
| | - F. Hadj-Bouziane
- Integrative Multisensory Perception Action & Cognition Team (ImpAct), INSERM U1028, CNRS UMR5292, Lyon Neuroscience Research Center (CRNL), University of Lyon 1, Lyon, France
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15
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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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16
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León J, Thiriau C, Crockford C, Zuberbühler K. Comprehension of own and other species' alarm calls in sooty mangabey vocal development. Behav Ecol Sociobiol 2023; 77:56. [PMID: 37234238 PMCID: PMC10205891 DOI: 10.1007/s00265-023-03318-6] [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: 09/07/2022] [Revised: 03/26/2023] [Accepted: 03/30/2023] [Indexed: 05/27/2023]
Abstract
Abstract Primates understand the meaning of their own and other species' alarm calls, but little is known about how they acquire such knowledge. Here, we combined direct behavioural observations with playback experiments to investigate two key processes underlying vocal development: comprehension and usage. Especifically, we studied the development of con- and heterospecific alarm call recognition in free-ranging sooty mangabeys, Cercocebus atys, across three age groups: young juveniles (1-2y), old juveniles (3-4y) and adults (> 5y). We observed that, during natural predator encounters, juveniles alarm called to a significantly wider range of species than adults, with evidence of refinement during the first four years of life. In the experiments, we exposed subjects to leopard, eagle and snake alarm calls given by other group members or sympatric Diana monkeys. We found that young juveniles' locomotor and vocal responses were least appropriate and that they engaged in more social referencing (look at adults when hearing an alarm call) than older individuals, suggesting that vocal competence is obtained via social learning. In conclusion, our results suggest that alarm call comprehension is socially learned during the juvenile stage, with comprehension preceding appropriate usage but no difference between learning their own or other species' alarm calls. Significance statement Under natural conditions, animals do not just interact with members of their own species, but usually operate in a network of associated species. However, ontogenetic research on primate communication frequently ignores this significant element. We studied the development of con- and heterospecific alarm call recognition in wild sooty mangabeys. We found that communicative competence was acquired during the juvenile stages, with alarm call comprehension learning preceding appropriate vocal usage and with no clear difference in learning of con- and heterospecific signals. We also found that, during early stages of life, social referencing, a proactive form of social learning, was key in the acquisition of competent alarm call behaviour. Our results show that primates equally learn to interpret alarm calls from their own and other species during their early stages of life and that this learning process is refined as the animals mature. Supplementary Information The online version contains supplementary material available at 10.1007/s00265-023-03318-6.
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Affiliation(s)
- Julián León
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
- Taï Monkey Project, Centre Suisse de Recherches Scientifiques, 01 BP1303 Abidjan 01, Côte d’Ivoire
| | - Constance Thiriau
- Taï Monkey Project, Centre Suisse de Recherches Scientifiques, 01 BP1303 Abidjan 01, Côte d’Ivoire
| | - Catherine Crockford
- Tai Chimpanzee Project, Centre Suisse de Recherches Scientifiques, 01 BP1303 Abidjan 01, Côte d’Ivoire
- Institute of Cognitive Sciences Marc Jeannerod, CNRS, 69330 Lyon, France
| | - Klaus Zuberbühler
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
- Taï Monkey Project, Centre Suisse de Recherches Scientifiques, 01 BP1303 Abidjan 01, Côte d’Ivoire
- School of Psychology and Neuroscience, University of St. Andrews, Saint Andrews, KY16 9JP Scotland UK
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17
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Amiez C, Sallet J, Giacometti C, Verstraete C, Gandaux C, Morel-Latour V, Meguerditchian A, Hadj-Bouziane F, Ben Hamed S, Hopkins WD, Procyk E, Wilson CRE, Petrides M. A revised perspective on the evolution of the lateral frontal cortex in primates. SCIENCE ADVANCES 2023; 9:eadf9445. [PMID: 37205762 DOI: 10.1126/sciadv.adf9445] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
Detailed neuroscientific data from macaque monkeys have been essential in advancing understanding of human frontal cortex function, particularly for regions of frontal cortex without homologs in other model species. However, precise transfer of this knowledge for direct use in human applications requires an understanding of monkey to hominid homologies, particularly whether and how sulci and cytoarchitectonic regions in the frontal cortex of macaques relate to those in hominids. We combine sulcal pattern analysis with resting-state functional magnetic resonance imaging and cytoarchitectonic analysis to show that old-world monkey brains have the same principles of organization as hominid brains, with the notable exception of sulci in the frontopolar cortex. This essential comparative framework provides insights into primate brain evolution and a key tool to drive translation from invasive research in monkeys to human applications.
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Affiliation(s)
- Céline Amiez
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Jérôme Sallet
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
- Wellcome Integrative Neuroimaging Centre, Department of Experimental Psychology, University of Oxford, Oxford OX1 3SR, UK
| | - Camille Giacometti
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Charles Verstraete
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Clémence Gandaux
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Valentine Morel-Latour
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Adrien Meguerditchian
- Laboratoire de Psychologie Cognitive, UMR7290, Université Aix-Marseille, CNRS, 13331 Marseille, France
- Station de Primatologie CNRS, UPS846, 13790 Rousset, France
- Brain and Language Research Institute, Université Aix-Marseille, CNRS, 13604 Aix-en-Provence, France
| | - Fadila Hadj-Bouziane
- Integrative Multisensory Perception Action and Cognition Team (ImpAct), INSERM U1028, CNRS UMR5292, Lyon Neuroscience Research Center (CRNL), Lyon, France; University of Lyon 1, Lyon, France
| | - Suliann Ben Hamed
- Institut des Sciences Cognitives Marc Jeannerod, UMR5229, CNRS-Université Claude Bernard Lyon I, Bron, France
| | - William D Hopkins
- Department of Comparative Medicine, University of Texas MD Anderson Cancer Center, Bastrop, TX, 78602, USA
| | - Emmanuel Procyk
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Charles R E Wilson
- Univ Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Michael Petrides
- Department of Neurology and Neurosurgery and Department of Psychology, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
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18
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Leroux M, Schel AM, Wilke C, Chandia B, Zuberbühler K, Slocombe KE, Townsend SW. Call combinations and compositional processing in wild chimpanzees. Nat Commun 2023; 14:2225. [PMID: 37142584 PMCID: PMC10160036 DOI: 10.1038/s41467-023-37816-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Through syntax, i.e., the combination of words into larger phrases, language can express a limitless number of messages. Data in great apes, our closest-living relatives, are central to the reconstruction of syntax's phylogenetic origins, yet are currently lacking. Here, we provide evidence for syntactic-like structuring in chimpanzee communication. Chimpanzees produce "alarm-huus" when surprised and "waa-barks" when potentially recruiting conspecifics during aggression or hunting. Anecdotal data suggested chimpanzees combine these calls specifically when encountering snakes. Using snake presentations, we confirm call combinations are produced when individuals encounter snakes and find that more individuals join the caller after hearing the combination. To test the meaning-bearing nature of the call combination, we use playbacks of artificially-constructed call combinations and both independent calls. Chimpanzees react most strongly to call combinations, showing longer looking responses, compared with both independent calls. We propose the "alarm-huu + waa-bark" represents a compositional syntactic-like structure, where the meaning of the call combination is derived from the meaning of its parts. Our work suggests that compositional structures may not have evolved de novo in the human lineage, but that the cognitive building-blocks facilitating syntax may have been present in our last common ancestor with chimpanzees.
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Affiliation(s)
- Maël Leroux
- Department of Comparative Language Science, University of Zürich, Zürich, Switzerland.
- Budongo Conservation Field Station, Masindi, Uganda.
- Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zürich, Zürich, Switzerland.
| | - Anne M Schel
- Animal Behaviour and Cognition, Utrecht University, Utrecht, Netherlands
| | - Claudia Wilke
- Department of Comparative Language Science, University of Zürich, Zürich, Switzerland
- Budongo Conservation Field Station, Masindi, Uganda
- Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zürich, Zürich, Switzerland
| | | | - Klaus Zuberbühler
- Budongo Conservation Field Station, Masindi, Uganda
- Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zürich, Zürich, Switzerland
- Department of Comparative Cognition, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- School of Psychology and Neuroscience, University of St Andrews, St Andrews Scotland, UK
| | | | - Simon W Townsend
- Department of Comparative Language Science, University of Zürich, Zürich, Switzerland
- Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zürich, Zürich, Switzerland
- Department of Psychology, University of Warwick, Coventry, UK
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19
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Tello D, Gonzalez-Garcia LN, Gomez J, Zuluaga-Monares JC, Garcia R, Angel R, Mahecha D, Duarte E, Leon MDR, Reyes F, Escobar-Velásquez C, Linares-Vásquez M, Cardozo N, Duitama J. NGSEP 4: Efficient and accurate identification of orthogroups and whole-genome alignment. Mol Ecol Resour 2023; 23:712-724. [PMID: 36377253 DOI: 10.1111/1755-0998.13737] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/26/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.
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Affiliation(s)
- Daniel Tello
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | | | - Jorge Gomez
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | | | - Rogelio Garcia
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Ricardo Angel
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Daniel Mahecha
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Erick Duarte
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Maria Del Rosario Leon
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Fernando Reyes
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | | | - Mario Linares-Vásquez
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Nicolas Cardozo
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
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20
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Veith T, Bleicker T, Eschbach-Bludau M, Brünink S, Mühlemann B, Schneider J, Beheim-Schwarzbach J, Rakotondranary SJ, Ratovonamana YR, Tsagnangara C, Ernest R, Randriantafika F, Sommer S, Stetter N, Jones TC, Drosten C, Ganzhorn JU, Corman VM. Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host. Virus Evol 2023; 9:vead024. [PMID: 37091898 PMCID: PMC10121206 DOI: 10.1093/ve/vead024] [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: 05/11/2022] [Revised: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023] Open
Abstract
Adenoviruses (AdVs) are important human and animal pathogens and are frequently used as vectors for gene therapy and vaccine delivery. Surprisingly, there are only scant data regarding primate AdV origin and evolution, especially in the most basal primate hosts. We detect and sequence AdVs from faeces of two Madagascan lemur species. Complete genome sequence analyses define a new AdV species with a particularly large gene encoding a protein of unknown function in the early gene region 3. Unexpectedly, the new AdV species is not most similar to human or other simian AdVs but to bat adenovirus C. Genome characterisation shows signals of virus-host codivergence in non-structural genes, which show lower diversity than structural genes. Outside a lemur species mixing zone, recombination less frequently separates structural genes, as in human adenovirus C. The evolutionary history of lemur AdVs likely involves both a host switch and codivergence with the lemur hosts.
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Affiliation(s)
- Talitha Veith
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Monika Eschbach-Bludau
- Institute of Virology, University Hospital, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Julia Schneider
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - S Jacques Rakotondranary
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Yedidya R Ratovonamana
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Cedric Tsagnangara
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | - Refaly Ernest
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | | | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, Ulm 89069, Germany
| | - Nadine Stetter
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, Hamburg 20359, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörg U Ganzhorn
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
- Labor Berlin, Charité—Vivantes GmbH, Sylter Straße 2, Berlin 13353, Germany
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21
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Luria V, Ma S, Shibata M, Pattabiraman K, Sestan N. Molecular and cellular mechanisms of human cortical connectivity. Curr Opin Neurobiol 2023; 80:102699. [PMID: 36921362 DOI: 10.1016/j.conb.2023.102699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/05/2023] [Indexed: 03/18/2023]
Abstract
Comparative studies of the cerebral cortex have identified various human and primate-specific changes in both local and long-range connectivity, which are thought to underlie our advanced cognitive capabilities. These changes are likely mediated by the divergence of spatiotemporal regulation of gene expression, which is particularly prominent in the prenatal and early postnatal human and non-human primate cerebral cortex. In this review, we describe recent advances in characterizing human and primate genetic and cellular innovations including identification of novel species-specific, especially human-specific, genes, gene expression patterns, and cell types. Finally, we highlight three recent studies linking these molecular changes to reorganization of cortical connectivity.
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Affiliation(s)
- Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Mikihito Shibata
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Kartik Pattabiraman
- Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06510, USA.
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA; Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06510, USA; Departments of Psychiatry, Genetics and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
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22
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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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Vallender EJ, Hotchkiss CE, Lewis AD, Rogers J, Stern JA, Peterson SM, Ferguson B, Sayers K. Nonhuman primate genetic models for the study of rare diseases. Orphanet J Rare Dis 2023; 18:20. [PMID: 36721163 PMCID: PMC9887761 DOI: 10.1186/s13023-023-02619-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Pre-clinical research and development relies heavily upon translationally valid models of disease. A major difficulty in understanding the biology of, and developing treatments for, rare disease is the lack of animal models. It is important that these models not only recapitulate the presentation of the disease in humans, but also that they share functionally equivalent underlying genetic causes. Nonhuman primates share physiological, anatomical, and behavioral similarities with humans resulting from close evolutionary relationships and high genetic homology. As the post-genomic era develops and next generation sequencing allows for the resequencing and screening of large populations of research animals, naturally occurring genetic variation in nonhuman primates with clinically relevant phenotypes is regularly emerging. Here we review nonhuman primate models of multiple rare genetic diseases with a focus on the similarities and differences in manifestation and etiologies across species. We discuss how these models are being developed and how they can offer new tools and opportunities for researchers interested in exploring novel therapeutics for these and other genetic diseases. Modeling human genetic diseases in translationally relevant nonhuman primates presents new prospects for development of therapeutics and a better understanding of rare diseases. The post-genomic era offers the opportunity for the discovery and further development of more models like those discussed here.
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Affiliation(s)
- Eric J. Vallender
- University of Mississippi Medical Center, Jackson, MS USA
- Tulane National Primate Research Center, Covington, LA USA
| | - Charlotte E. Hotchkiss
- University of Washington, Seattle, WA USA
- Washington National Primate Research Center, Seattle, WA USA
| | - Anne D. Lewis
- Oregon Health and Sciences University, Beaverton, OR USA
- Oregon National Primate Research Center, Beaverton, OR USA
| | - Jeffrey Rogers
- Baylor College of Medicine, Houston, TX USA
- Wisconsin National Primate Research Center, Madison, WI USA
| | - Joshua A. Stern
- University of California-Davis, Davis, CA USA
- California National Primate Research Center, Davis, CA USA
| | - Samuel M. Peterson
- Oregon Health and Sciences University, Beaverton, OR USA
- Oregon National Primate Research Center, Beaverton, OR USA
| | - Betsy Ferguson
- Oregon Health and Sciences University, Beaverton, OR USA
- Oregon National Primate Research Center, Beaverton, OR USA
| | - Ken Sayers
- Texas Biomedical Research Institute, San Antonio, TX USA
- Southwest National Primate Research Center, San Antonio, TX USA
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24
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Maskalenka K, Alagöz G, Krueger F, Wright J, Rostovskaya M, Nakhuda A, Bendall A, Krueger C, Walker S, Scally A, Rugg-Gunn PJ. NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells. Development 2023; 150:286291. [PMID: 36621005 PMCID: PMC10110494 DOI: 10.1242/dev.201155] [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: 07/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023]
Abstract
Gene duplication events can drive evolution by providing genetic material for new gene functions, and they create opportunities for diverse developmental strategies to emerge between species. To study the contribution of duplicated genes to human early development, we examined the evolution and function of NANOGP1, a tandem duplicate of the transcription factor NANOG. We found that NANOGP1 and NANOG have overlapping but distinct expression profiles, with high NANOGP1 expression restricted to early epiblast cells and naïve-state pluripotent stem cells. Sequence analysis and epitope-tagging revealed that NANOGP1 is protein coding with an intact homeobox domain. The duplication that created NANOGP1 occurred earlier in primate evolution than previously thought and has been retained only in great apes, whereas Old World monkeys have disabled the gene in different ways, including homeodomain point mutations. NANOGP1 is a strong inducer of naïve pluripotency; however, unlike NANOG, it is not required to maintain the undifferentiated status of human naïve pluripotent cells. By retaining expression, sequence and partial functional conservation with its ancestral copy, NANOGP1 exemplifies how gene duplication and subfunctionalisation can contribute to transcription factor activity in human pluripotency and development.
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Affiliation(s)
| | - Gökberk Alagöz
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Joshua Wright
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Asif Nakhuda
- Gene Targeting Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Bendall
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Christel Krueger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Walker
- Imaging Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
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25
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Anjum N, Nabil RL, Rafi RI, Bayzid MS, Rahman MS. CD-MAWS: An Alignment-Free Phylogeny Estimation Method Using Cosine Distance on Minimal Absent Word Sets. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:196-205. [PMID: 34928803 DOI: 10.1109/tcbb.2021.3136792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Multiple sequence alignment has been the traditional and well established approach of sequence analysis and comparison, though it is time and memory consuming. As the scale of sequencing data is increasing day by day, the importance of faster yet accurate alignment-free methods is on the rise. Several alignment-free sequence analysis methods have been established in the literature in recent years, which extract numerical features from genomic data to analyze sequences and also to estimate phylogenetic relationship among genes and species. Minimal Absent Word (MAW) is an effective concept for representing characteristics of a sequence in an alignment-free manner. In this study, we present CD-MAWS, a distance measure based on cosine of the angle between composition vectors constructed using minimal absent words, for sequence analysis in a computationally inexpensive manner. We have benchmarked CD-MAWS using several AFProject datasets, such as Fish mtDNA, E.coli, Plants, Shigella and Yersinia datasets, and found it to perform quite well. Applied on several other biological datasets such as mammal mtDNA, bacterial genomes and viral genomes, CD-MAWS resolved phylogenetic relationships similar to or better than state-of-the-art alignment-free methods such as Mash, Skmer, Co-phylog and kSNP3.
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26
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Calero-Layana M, López-Cruz C, Ocaña A, Tejera E, Armijos-Jaramillo V. Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes. PeerJ 2022; 10:e14431. [PMID: 36575684 PMCID: PMC9790151 DOI: 10.7717/peerj.14431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022] Open
Abstract
Background Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation. Results In this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily. Conclusions With the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.
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Affiliation(s)
- Melissa Calero-Layana
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador
| | - Carmen López-Cruz
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador
| | - Agustín Ocaña
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador
| | - Eduardo Tejera
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador,Grupo de Bio-Quimioinformática, Universidad de las Americas, Quito, Ecuador
| | - Vinicio Armijos-Jaramillo
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador,Grupo de Bio-Quimioinformática, Universidad de las Americas, Quito, Ecuador
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27
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Auerbach AA, Becker JT, Moraes SN, Moghadasi SA, Duda JM, Salamango DJ, Harris RS. Ancestral APOBEC3B Nuclear Localization Is Maintained in Humans and Apes and Altered in Most Other Old World Primate Species. mSphere 2022; 7:e0045122. [PMID: 36374108 PMCID: PMC9769932 DOI: 10.1128/msphere.00451-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
APOBEC3B is an innate immune effector enzyme capable of introducing mutations in viral genomes through DNA cytosine-to-uracil editing. Recent studies have shown that gamma-herpesviruses, such as Epstein-Barr virus (EBV), have evolved a potent APOBEC3B neutralization mechanism to protect lytic viral DNA replication intermediates in the nuclear compartment. APOBEC3B is additionally unique as the only human DNA deaminase family member that is constitutively nuclear. Nuclear localization has therefore been inferred to be essential for innate antiviral function. Here, we combine evolutionary, molecular, and cell biology approaches to address whether nuclear localization is a conserved feature of APOBEC3B in primates. Despite the relatively recent emergence of APOBEC3B approximately 30 to 40 million years ago (MYA) in Old World primates by genetic recombination (after the split from the New World monkey lineage 40 to 50 MYA), we find that the hallmark nuclear localization of APOBEC3B shows variability. For instance, although human and several nonhuman primate APOBEC3B enzymes are predominantly nuclear, rhesus macaque and other Old World primate APOBEC3B proteins are clearly cytoplasmic or cell wide. A series of human/rhesus macaque chimeras and mutants combined to map localization determinants to the N-terminal half of the protein with residues 15, 19, and 24 proving critical. Ancestral APOBEC3B reconstructed from present-day primate species also shows strong nuclear localization. Together, these results indicate that the ancestral nuclear localization of APOBEC3B is maintained in present-day human and ape proteins, but nuclear localization is not conserved in all Old World monkey species despite a need for antiviral functions in the nuclear compartment. IMPORTANCE APOBEC3 enzymes are single-stranded DNA cytosine-to-uracil deaminases with beneficial roles in antiviral immunity and detrimental roles in cancer mutagenesis. Regarding viral infection, all seven human APOBEC3 enzymes have overlapping roles in restricting virus types that require DNA for replication, including EBV, HIV, human papillomavirus (HPV), and human T-cell leukemia virus (HTLV). Regarding cancer, at least two APOBEC3 enzymes, APOBEC3B and APOBEC3A, are prominent sources of mutation capable of influencing clinical outcomes. Here, we combine evolutionary, molecular, and cell biology approaches to characterize primate APOBEC3B enzymes. We show that nuclear localization is an ancestral property of APOBEC3B that is maintained in present-day human and ape enzymes, but not conserved in other nonhuman primates. This partial mechanistic conservation indicates that APOBEC3B is important for limiting the replication of DNA-based viruses in the nuclear compartment. Understanding these pathogen-host interactions may contribute to the development of future antiviral and antitumor therapies.
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Affiliation(s)
- Ashley A Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Jordan T Becker
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Sofia N Moraes
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Seyed Arad Moghadasi
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Jolene M Duda
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Daniel J Salamango
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
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28
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Penna A, Dillon R, Bearder SK, Karlsson J, Perkin A, Pozzi L. Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Assessing the true lineage diversity in elusive nocturnal organisms is particularly challenging due to their subtle phenotypic variation in diagnostic traits. The cryptic small-eared greater galago (Otolemur garnettii) offers a great opportunity to test if currently recognized subspecies, suggested by discontinuities in coat colour pattern and geographic barriers, represent distinct evolutionary lineages. To answer this question, we conducted the first population-level phylogeographic study of the species, sampling wild specimens from across almost its entire latitudinal range, including the Zanzibar Archipelago. We applied five species-delimitation algorithms to investigate the genetic diversity and distribution pattern of mitochondrial DNA across the geographic range of three out of four subspecies. Our results suggest that far-northern populations of O. g. lasiotis potentially represent an independently evolving lineage, but populations assigned to O. g. garnettii from Zanzibar Island and of O. g panganiensis from mainland Tanzania do not constitute two independent lineages. A dated phylogeny suggests that this northern clade diverged from all remaining samples approximately 4 Mya. Such old divergence age is in line with the split between many galagid species. This northern lineage could potentially represent an incipient species; however, there is not yet enough evidence to support a new taxonomic status for this unique mitochondrial group.
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Affiliation(s)
- Anna Penna
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Rosemarie Dillon
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
| | - Simon K Bearder
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Johan Karlsson
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Andrew Perkin
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Luca Pozzi
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
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29
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Ji X, Harrison T, Zhang Y, Wu Y, Zhang C, Hu J, Wu D, Hou Y, Li S, Wang G, Wang Z. The earliest hylobatid from the Late Miocene of China. J Hum Evol 2022; 171:103251. [PMID: 36113226 DOI: 10.1016/j.jhevol.2022.103251] [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: 06/06/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/15/2022]
Abstract
Yuanmoupithecus xiaoyuan, a small catarrhine from the Late Miocene of Yunnan in southern China, was initially suggested to be related to Miocene proconsuloids or dendropithecoids from East Africa, but subsequent reports indicated that it might be more closely related to hylobatids. Here, detailed comparisons of the material, including seven newly discovered teeth and a partial lower face of a juvenile individual, provide crucial evidence to help establish its phylogenetic relationships. Yuanmoupithecus exhibits a suite of synapomorphies that support a close phylogenetic relationship with extant hylobatids. Furthermore, based on the retention of several primitive features of the dentition, Yuanmoupithecus can be shown to be the sister taxon of crown hylobatids. The contention that Kapi ramnagarensis from the Middle Miocene of India might represent an earlier species of hylobatid is not supported here. Instead, Kapi is inferred to be a specialized pliopithecoid more closely related to Krishnapithecus krishnaii from the Late Miocene of India. Currently then, Yuanmoupithecus represents the earliest known definitively identified hylobatid and the only member of the clade predating the Pleistocene. It extends the fossil record of hylobatids back to 7-8 Ma and fills a critical gap in the evolutionary history of hominoids that has up until now remained elusive. Even so, molecular estimates of a divergence date of hylobatids from other hominoids at about 17-22 Ma signifies that there is still a substantial gap in the fossil record of more than 10 million years that needs to be filled in order to document the biogeographic origins and early evolution of hylobatids.
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Affiliation(s)
- Xueping Ji
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China; Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming, 650118, China
| | - Terry Harrison
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, NY, 10003, USA.
| | - Yingqi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
| | - Yun Wu
- Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming, 650118, China; School of History, Wuhan University, Wuhan, 430072, China
| | - Chunxia Zhang
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China; College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Jinming Hu
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650500, China
| | - Dongdong Wu
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yemao Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Song Li
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guofu Wang
- Chuxiong Prefectural Museum, Chuxiong, 657000, China
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30
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Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. Nat Ecol Evol 2022; 6:630-643. [PMID: 35332281 PMCID: PMC9090980 DOI: 10.1038/s41559-022-01703-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/15/2022] [Indexed: 01/31/2023]
Abstract
Primates have adapted to numerous environments and lifestyles, but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of hematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers between populations. Compared to baboons at low altitude, we found that high-altitude geladas exhibit significantly expanded chest circumferences, potentially allowing for greater lung surface area for increased oxygen diffusion. We identified gelada-specific amino acid substitutions in the alpha-chain subunit of adult hemoglobin but found that gelada hemoglobin does not exhibit markedly altered oxygenation properties compared to lowland primates. We also found that geladas at high altitude do not exhibit elevated blood hemoglobin concentrations, in contrast to the normal acclimatization response to hypoxia in lowland primates. The absence of altitude-related polycythemia suggests that geladas are able to sustain adequate tissue-oxygen delivery despite environmental hypoxia. Finally, we identified numerous genes and genomic regions exhibiting accelerated rates of evolution, as well as gene families exhibiting expansions in the gelada lineage, potentially reflecting altitude-related selection. Our findings lend insight into putative mechanisms of high-altitude adaptation while suggesting promising avenues for functional hypoxia research.
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31
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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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32
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Kappeler PM, Fichtel C, Radespiel U. The Island of Female Power? Intersexual Dominance Relationships in the Lemurs of Madagascar. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.858859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The extant primates of Madagascar (Lemuriformes) represent the endpoints of an adaptive radiation following a single colonization event more than 50 million years ago. They have since evolved a diversity of life history traits, ecological adaptations and social systems that rivals that of all other living primates combined. Their social systems are characterized by a unique combination of traits, including the ability of adult females to dominate adult males. In fact, there is no other group of mammals in which female dominance is so widespread. Yet, recent research has indicated that there is more interspecific variation in lemur intersexual relationships than previously acknowledged. Here, we therefore review and summarize the relevant literature, quantifying the extent of sex-bias in intersexual dominance relations documented in observational and experimental studies in captivity and the wild. Female dominance is often, but not always, implemented by spontaneous male submission in the absence of female aggression and linked to female sexual maturation. We connect the available evidence to the hypotheses that have been proposed to explain the evolution of female dominance among lemurs. The occurrence of female dominance in all lemur families and the interspecific variation in its extent indicate that it has evolved soon after lemurs colonized Madagascar – presumably in response to particular ecological challenges – and that it has since been reduced in magnitude independently in some taxa. Our study contributes important comparative information on sex roles from an independent primate radiation and provides general insights into the conditions, opportunities and obstacles in the evolution of female-biased power.
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Pan Y, Fan Y, Lu Y, Peng S, Lin H, Deng Q. Molecular characterization of matrix metalloproteinase gene family across primates. Aging (Albany NY) 2022; 14:3425-3445. [PMID: 35444067 PMCID: PMC9085222 DOI: 10.18632/aging.204021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/12/2022] [Indexed: 11/25/2022]
Abstract
Deregulation of matrix metalloproteinases (MMPs) contributes considerably to cancers, psychiatric disorders, macular degeneration and bone diseases. The use of humans in the development of MMPs as prognostic biomarkers and therapeutic targets is complicated by many factors, while primate models can be useful alternatives for this purpose. Here, we performed genome-enabled identification of putative MMPs across primate species, and comprehensively investigated the genes. Phylogenetic topology of the MMP family showed each type formulates a distinct clade, and was further clustered to classes, largely agreeing with classification based on biochemical properties and domain organization. Across primates, the excess of candidate sites of positive selection was detected for MMP-19, in addition to 1-3 sites in MMP-8, MMP-10 and MMP-26. MMP-26 showed Ka/Ks value above 1 between human and chimpanzee copies. We observed two copies of MMP-19 in the old-world monkey genomes, suggesting gene duplication at the early stage of or prior to the emergence of the lineage. Furin-activatable MMPs demonstrate the most variable properties regarding Domain organization and gene structure. During human aging, MMP-11 showed gradually decreased expression in testis, so as MMP-2, MMP-14, MMP15 and MMP-28 in ovary, while MMP-7 and MMP-21 showed elevated expression, implying their distinct roles in different reproductive organs. Co-expression clusters were formed among human MMPs both within and across classes, and expression correlation was observed in MMP genes across primates. Our results illuminate the utilization of MMPs for the discovery of prognostic biomarkers and therapeutic targets for aging-related diseases and carry new messages on MMP classification.
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Affiliation(s)
- Yinglian Pan
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, People's Republic of China
| | - Yadan Fan
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan, People's Republic of China
| | - Yanda Lu
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, People's Republic of China
| | - Siyuan Peng
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan, People's Republic of China
| | - Haixue Lin
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan, People's Republic of China
| | - Qingchun Deng
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan, People's Republic of China
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34
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Rheinemann L, Downhour DM, Davenport KA, McKeown AN, Sundquist WI, Elde NC. Recurrent evolution of an inhibitor of ESCRT-dependent virus budding and LINE-1 retrotransposition in primates. Curr Biol 2022; 32:1511-1522.e6. [PMID: 35245459 PMCID: PMC9007875 DOI: 10.1016/j.cub.2022.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 12/20/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022]
Abstract
Most antiviral proteins recognize specific features of viruses. In contrast, the recently described antiviral factor retroCHMP3 interferes with the "host endosomal complexes required for transport" (ESCRT) pathway to inhibit the budding of enveloped viruses. RetroCHMP3 arose independently on multiple occasions via duplication and truncation of the gene encoding the ESCRT-III factor CHMP3. However, since the ESCRT pathway is essential for cellular membrane fission reactions, ESCRT inhibition is potentially cytotoxic. This raises fundamental questions about how hosts can repurpose core cellular functions into antiviral functions without incurring a fitness cost due to excess cellular toxicity. We reveal the evolutionary process of detoxification for retroCHMP3 in New World monkeys using a combination of ancestral reconstructions, cytotoxicity, and virus release assays. A duplicated, full-length copy of retroCHMP3 in the ancestors of New World monkeys provides modest inhibition of virus budding while exhibiting subtle cytotoxicity. Ancient retroCHMP3 then accumulated mutations that reduced cytotoxicity but preserved virus inhibition before a truncating stop codon arose in the more recent ancestors of squirrel monkeys, resulting in potent inhibition. In species where full-length copies of retroCHMP3 still exist, their artificial truncation generated potent virus-budding inhibitors with little cytotoxicity, revealing the potential for future antiviral defenses in modern species. In addition, we discovered that retroCHMP3 restricts LINE-1 retrotransposition, revealing how different challenges to genome integrity might explain multiple independent origins of retroCHMP3 in different species to converge on new immune functions.
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Affiliation(s)
- Lara Rheinemann
- Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East, Salt Lake City, UT 84112, USA
| | - Diane Miller Downhour
- Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA
| | - Kristen A Davenport
- Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA
| | - Alesia N McKeown
- Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East, Salt Lake City, UT 84112, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, 15 N 2030 E, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA.
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35
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Pugh KD. Phylogenetic analysis of Middle-Late Miocene apes. J Hum Evol 2022; 165:103140. [DOI: 10.1016/j.jhevol.2021.103140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 01/18/2023]
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36
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Bjornson-Hooper ZB, Fragiadakis GK, Spitzer MH, Chen H, Madhireddy D, Hu K, Lundsten K, McIlwain DR, Nolan GP. A Comprehensive Atlas of Immunological Differences Between Humans, Mice, and Non-Human Primates. Front Immunol 2022; 13:867015. [PMID: 35359965 PMCID: PMC8962947 DOI: 10.3389/fimmu.2022.867015] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 01/01/2023] Open
Abstract
Animal models are an integral part of the drug development and evaluation process. However, they are unsurprisingly imperfect reflections of humans, and the extent and nature of many immunological differences are unknown. With the rise of targeted and biological therapeutics, it is increasingly important that we understand the molecular differences in the immunological behavior of humans and model organisms. However, very few antibodies are raised against non-human primate antigens, and databases of cross-reactivity between species are incomplete. Thus, we screened 332 antibodies in five immune cell populations in blood from humans and four non-human primate species generating a comprehensive cross-reactivity catalog that includes cell type-specificity. We used this catalog to create large mass cytometry universal cross-species phenotyping and signaling panels for humans, along with three of the model organisms most similar to humans: rhesus and cynomolgus macaques and African green monkeys; and one of the mammalian models most widely used in drug development: C57BL/6 mice. As a proof-of-principle, we measured immune cell signaling responses across all five species to an array of 15 stimuli using mass cytometry. We found numerous instances of different cellular phenotypes and immune signaling events occurring within and between species, and detailed three examples (double-positive T cell frequency and signaling; granulocyte response to Bacillus anthracis antigen; and B cell subsets). We also explore the correlation of herpes simian B virus serostatus on the immune profile. Antibody panels and the full dataset generated are available online as a resource to enable future studies comparing immune responses across species during the evaluation of therapeutics.
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Affiliation(s)
| | - Gabriela K. Fragiadakis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
- Department of Medicine, Division of Rheumatology, University of California San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- University of California, San Francisco (UCSF) Data Science CoLab and University of California, San Francisco (UCSF) Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Matthew H. Spitzer
- Immunology Program, Stanford University, Stanford, CA, United States
- Departments of Otolaryngology – Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Han Chen
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Deepthi Madhireddy
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Kevin Hu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Kelly Lundsten
- BioLegend Inc, Advanced Cytometry, San Diego, CA, United States
| | - David R. McIlwain
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Garry P. Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
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37
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Identification of multiple TAR DNA binding protein retropseudogene lineages during the evolution of primates. Sci Rep 2022; 12:3823. [PMID: 35264686 PMCID: PMC8907276 DOI: 10.1038/s41598-022-07908-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 02/22/2022] [Indexed: 11/08/2022] Open
Abstract
The TAR DNA Binding Protein (TARDBP) gene has become relevant after the discovery of its several pathogenic mutations. The lack of evolutionary history is in contrast to the amount of studies found in the literature. This study investigated the evolutionary dynamics associated with the retrotransposition of the TARDBP gene in primates. We identified novel retropseudogenes that likely originated in the ancestors of anthropoids, catarrhines, and lemuriformes, i.e. the strepsirrhine clade that inhabit Madagascar. We also found species-specific retropseudogenes in the Philippine tarsier, Bolivian squirrel monkey, capuchin monkey and vervet. The identification of a retropseudocopy of the TARDBP gene overlapping a lncRNA that is potentially expressed opens a new avenue to investigate TARDBP gene regulation, especially in the context of TARDBP associated pathologies.
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38
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Iwasaki SI, Yoshimura K, Asami T, Erdoğan S. Comparative morphology and physiology of the vocal production apparatus and the brain in the extant primates. Ann Anat 2022; 240:151887. [PMID: 35032565 DOI: 10.1016/j.aanat.2022.151887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 01/04/2023]
Abstract
Objective data mainly from the comparative anatomy of various organs related to human speech and language is considered to unearth clues about the mechanisms behind language development. The two organs of the larynx and hyoid bone are considered to have evolved towards suitable positions and forms in preparation for the occurrence of the large repertoire of vocalization necessary for human speech. However, some researchers have asserted that there is no significant difference of these organs between humans and non-human primates. Speech production is dependent on the voluntary control of the respiratory, laryngeal, and vocal tract musculature. Such control is fully present in humans but only partially so in non-human primates, which appear to be able to voluntarily control only supralaryngeal articulators. Both humans and non-human primates have direct cortical innervation of motor neurons controlling the supralaryngeal vocal tract but only human appear to have direct cortical innervation of motor neurons controlling the larynx. In this review, we investigate the comparative morphology and function of the wide range of components involved in vocal production, including the larynx, the hyoid bone, the tongue, and the vocal brain. We would like to emphasize the importance of the tongue in the primary development of human speech and language. It is now time to reconsider the possibility of the tongue playing a definitive role in the emergence of human speech.
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Affiliation(s)
- Shin-Ichi Iwasaki
- Faculty of Health Science, Gunma PAZ University, Takasaki, Japan; The Nippon Dental University, Tokyo and Niigata, Japan
| | - Ken Yoshimura
- Department of Anatomy, The Nippon Dental University School of Life Dentistry at Niigata, Niigata, Japan
| | - Tomoichiro Asami
- Faculty of Rehabilitation, Gunma Paz University, Takasaki, Japan
| | - Serkan Erdoğan
- Department of Anatomy, Faculty of Veterinary Medicine, Tekirdağ Namık Kemal University, Tekirdağ, Turkey.
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39
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Harris RJ, Nekaris KAI, Fry BG. Monkeying around with venom: an increased resistance to α-neurotoxins supports an evolutionary arms race between Afro-Asian primates and sympatric cobras. BMC Biol 2021; 19:253. [PMID: 34823526 PMCID: PMC8613972 DOI: 10.1186/s12915-021-01195-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 11/12/2021] [Indexed: 12/17/2022] Open
Abstract
Background Snakes and primates have a multi-layered coevolutionary history as predators, prey, and competitors with each other. Previous work has explored the Snake Detection Theory (SDT), which focuses on the role of snakes as predators of primates and argues that snakes have exerted a selection pressure for the origin of primates’ visual systems, a trait that sets primates apart from other mammals. However, primates also attack and kill snakes and so snakes must simultaneously avoid primates. This factor has been recently highlighted in regard to the movement of hominins into new geographic ranges potentially exerting a selection pressure leading to the evolution of spitting in cobras on three independent occasions. Results Here, we provide further evidence of coevolution between primates and snakes, whereby through frequent encounters and reciprocal antagonism with large, diurnally active neurotoxic elapid snakes, Afro-Asian primates have evolved an increased resistance to α-neurotoxins, which are toxins that target the nicotinic acetylcholine receptors. In contrast, such resistance is not found in Lemuriformes in Madagascar, where venomous snakes are absent, or in Platyrrhini in the Americas, where encounters with neurotoxic elapids are unlikely since they are relatively small, fossorial, and nocturnal. Within the Afro-Asian primates, the increased resistance toward the neurotoxins was significantly amplified in the last common ancestor of chimpanzees, gorillas, and humans (clade Homininae). Comparative testing of venoms from Afro-Asian and American elapid snakes revealed an increase in α-neurotoxin resistance across Afro-Asian primates, which was likely selected against cobra venoms. Through structure-activity studies using native and mutant mimotopes of the α-1 nAChR receptor orthosteric site (loop C), we identified the specific amino acids responsible for conferring this increased level of resistance in hominine primates to the α-neurotoxins in cobra venom. Conclusion We have discovered a pattern of primate susceptibility toward α-neurotoxins that supports the theory of a reciprocal coevolutionary arms-race between venomous snakes and primates. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01195-x.
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Affiliation(s)
- Richard J Harris
- Venom Evolution Lab, University of Queensland, Biological Sciences, St. Lucia, Brisbane, 4072, Australia
| | - K Anne-Isola Nekaris
- Nocturnal Primate Research Group, Department of Social Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Bryan G Fry
- Venom Evolution Lab, University of Queensland, Biological Sciences, St. Lucia, Brisbane, 4072, Australia.
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40
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Bouchet F, Urciuoli A, Beaudet A, Pina M, Moyà-Solà S, Alba DM. Comparative anatomy of the carotid canal in the Miocene small-bodied catarrhine Pliobates cataloniae. J Hum Evol 2021; 161:103073. [PMID: 34628300 DOI: 10.1016/j.jhevol.2021.103073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 01/12/2023]
Abstract
The small-bodied Miocene catarrhine Pliobates cataloniae (11.6 Ma, Spain) displays a mosaic of catarrhine symplesiomorphies and hominoid synapomorphies that hinders deciphering its phylogenetic relationships. Based on cladistic analyses, it has been interpreted as a stem hominoid or as a pliopithecoid. Intriguingly, the carotid canal orientation of Pliobates was originally described as hylobatid-like. The variation in carotid canal morphology among anthropoid clades shown in previous studies suggests that this structure might be phylogenetically informative. However, its potential for phylogenetic reconstruction among extinct catarrhines remains largely unexplored. Here we quantify the orientation, proportions, and course of the carotid canal in Pliobates, extant anthropoids and other Miocene catarrhines (Epipliopithecus, Victoriapithecus, and Ekembo) using three-dimensional morphometric techniques. We also compute phylogenetic signal and reconstruct the ancestral carotid canal course for main anthropoid clades. Our results reveal that carotid canal morphology embeds strong phylogenetic signal but mostly discriminates between platyrrhines and catarrhines, with an extensive overlap among extant catarrhine families. The analyzed extinct taxa display a quite similar carotid canal morphology more closely resembling that of extant catarrhines. Nevertheless, our results for Pliobates highlight some differences compared with the pliopithecid Epipliopithecus, which displays a somewhat more platyrrhine-like morphology. In contrast, Pliobates appears as derived toward the modern catarrhine condition as the stem cercopithecid Victoriapithecus and the stem hominoid Ekembo, which more closely resemble one another. Moreover, Pliobates appears somewhat derived toward the reconstructed ancestral hominoid morphotype, being more similar than other Miocene catarrhines to the condition of great apes and the hylobatid Symphalangus. Overall, our results rule out previously noted similarities in carotid canal morphology between Pliobates and hylobatids, but do not show particular similarities with pliopithecoids either-as opposed to extant and other extinct catarrhines. Additional analyses will be required to clarify the phylogenetic relationships of Pliobates, particularly given its dental similarities with dendropithecids.
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Affiliation(s)
- Florian Bouchet
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Campus de la UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain.
| | - Alessandro Urciuoli
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Campus de la UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Amélie Beaudet
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Campus de la UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain; Department of Archaeology, University of Cambridge, The Old Schools, Trinity Lane, Cambridge CB2 1TN, UK; School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, 1 Jan Smuts Avenue, Braamfontein 2000, Johannesburg, South Africa; Department of Anatomy, University of Pretoria, Lynnwood Road, Hatfield 0002, Pretoria, South Africa
| | - Marta Pina
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Campus de la UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain; Department of Earth and Environmental Sciences, University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
| | - Salvador Moyà-Solà
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Campus de la UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain; Unitat d'Antropologia (Dept. BABVE), Universitat Autònoma de Barcelona, Edifici C, Facultat de Biociències, Campus de la UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - David M Alba
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Campus de la UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain.
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Kocher A, Papac L, Barquera R, Key FM, Spyrou MA, Hübler R, Rohrlach AB, Aron F, Stahl R, Wissgott A, van Bömmel F, Pfefferkorn M, Mittnik A, Villalba-Mouco V, Neumann GU, Rivollat M, van de Loosdrecht MS, Majander K, Tukhbatova RI, Musralina L, Ghalichi A, Penske S, Sabin S, Michel M, Gretzinger J, Nelson EA, Ferraz T, Nägele K, Parker C, Keller M, Guevara EK, Feldman M, Eisenmann S, Skourtanioti E, Giffin K, Gnecchi-Ruscone GA, Friederich S, Schimmenti V, Khartanovich V, Karapetian MK, Chaplygin MS, Kufterin VV, Khokhlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Tejedor-Rodríguez C, de Lagrán ÍGM, Arcusa-Magallón H, Garrido-Pena R, Royo-Guillén JI, Nováček J, Rottier S, Kacki S, Saintot S, Kaverzneva E, Belinskiy AB, Velemínský P, Limburský P, Kostka M, Loe L, Popescu E, Clarke R, Lyons A, Mortimer R, Sajantila A, de Armas YC, Hernandez Godoy ST, Hernández-Zaragoza DI, Pearson J, Binder D, Lefranc P, Kantorovich AR, Maslov VE, Lai L, Zoledziewska M, Beckett JF, Langová M, Danielisová A, Ingman T, Atiénzar GG, de Miguel Ibáñez MP, Romero A, Sperduti A, Beckett S, Salter SJ, Zilivinskaya ED, Vasil'ev DV, von Heyking K, Burger RL, Salazar LC, Amkreutz L, Navruzbekov M, Rosenstock E, Alonso-Fernández C, Slavchev V, Kalmykov AA, Atabiev BC, Batieva E, Calmet MA, Llamas B, Schultz M, Krauß R, Jiménez-Echevarría J, Francken M, Shnaider S, de Knijff P, Altena E, Van de Vijver K, Fehren-Schmitz L, Tung TA, Lösch S, Dobrovolskaya M, Makarov N, Read C, Van Twest M, Sagona C, Ramsl PC, Akar M, Yener KA, Ballestero EC, Cucca F, Mazzarello V, Utrilla P, Rademaker K, Fernández-Domínguez E, Baird D, Semal P, Márquez-Morfín L, Roksandic M, Steiner H, Salazar-García DC, Shishlina N, Erdal YS, Hallgren F, Boyadzhiev Y, Boyadzhiev K, Küßner M, Sayer D, Onkamo P, Skeates R, Rojo-Guerra M, Buzhilova A, Khussainova E, Djansugurova LB, Beisenov AZ, Samashev Z, Massy K, Mannino M, Moiseyev V, Mannermaa K, Balanovsky O, Deguilloux MF, Reinhold S, Hansen S, Kitov EP, Dobeš M, Ernée M, Meller H, Alt KW, Prüfer K, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 2021; 374:182-188. [PMID: 34618559 DOI: 10.1126/science.abi5658] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Florian van Bömmel
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Maria Pfefferkorn
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France
| | | | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland
| | - Rezeda I Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia
| | - Lyazzat Musralina
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cody Parker
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA
| | - Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | | | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Marina K Karapetian
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir V Kufterin
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey A Chizhevsky
- Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia
| | - Dmitry A Stashenkov
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Anna F Kochkina
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Cristina Tejedor-Rodríguez
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | | | | | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain
| | | | - Jan Nováček
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.,University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany
| | | | - Sacha Kacki
- Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.,Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Sylvie Saintot
- INRAP, ARAR UMR 5138, Maison de l'Orient et de la Méditerranée, Lyon, France
| | | | | | - Petr Velemínský
- Department of Anthropology, The National Museum, Prague, Czech Republic
| | - Petr Limburský
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK
| | | | - Rachel Clarke
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.,Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland
| | | | - Silvia Teresita Hernandez Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | - Diana I Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Didier Binder
- Université Côte d'Azur, CNRS, CEPAM UMR 7264, Nice, France
| | - Philippe Lefranc
- Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA.,Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michaela Langová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Danielisová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tara Ingman
- Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Maria Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.,Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome, Italy.,Dipartimento Asia Africa e Mediterraneo, Università di Napoli L'Orientale, Napoli, Italy
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.,Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK
| | - Susannah J Salter
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Emma D Zilivinskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany
| | - Richard L Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lucy C Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Luc Amkreutz
- National Museum of Antiquities, 2301 EC Leiden, Netherlands
| | | | - Eva Rosenstock
- Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany
| | | | | | | | - Biaslan Ch Atabiev
- Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.,Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.,National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Schultz
- University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.,Institute of Biology, University of Hildeshein, Germany
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Michael Francken
- State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany
| | - Svetlana Shnaider
- ArchaeoZoology in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Center for Archaeological Sciences, University of Leuven, Belgium.,Dienst Archeologie-Stad Mechelen, Belgium
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Chris Read
- Applied Archaeology School of Science, Institute of Technology Sligo, Ireland
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK
| | - Claudia Sagona
- School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia
| | - Peter C Ramsl
- Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria
| | - Murat Akar
- Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Eduardo Carmona Ballestero
- Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.,Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica-CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Pilar Utrilla
- Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lourdes Márquez-Morfín
- Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.,Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools," University of Tübingen, Tübingen, Germany
| | - Hubert Steiner
- South Tyrol Provincial Heritage Service, South Tyrol, Italy
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Natalia Shishlina
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.,State Historical Museum, Moscow, Russia
| | - Yilmaz Selim Erdal
- Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany
| | - Duncan Sayer
- School of Natural Sciences, University of Central Lancashire, Preston, UK
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20500 Turku, Finland
| | - Robin Skeates
- Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Manuel Rojo-Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Arman Z Beisenov
- Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Zainolla Samashev
- Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.,State Historical and Cultural Museum-Reserve "Berel," Katon-Karagay district, East Kazakhstan region, Kazakhstan
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Marcello Mannino
- Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Egor P Kitov
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.,Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Ernée
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Kurt W Alt
- Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.,Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.,Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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Feliciello I, Pezer Ž, Kordiš D, Bruvo Mađarić B, Ugarković Đ. Evolutionary History of Alpha Satellite DNA Repeats Dispersed within Human Genome Euchromatin. Genome Biol Evol 2021; 12:2125-2138. [PMID: 33078196 PMCID: PMC7719264 DOI: 10.1093/gbe/evaa224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 01/03/2023] Open
Abstract
Major human alpha satellite DNA repeats are preferentially assembled within (peri)centromeric regions but are also dispersed within euchromatin in the form of clustered or short single repeat arrays. To study the evolutionary history of single euchromatic human alpha satellite repeats (ARs), we analyzed their orthologous loci across the primate genomes. The continuous insertion of euchromatic ARs throughout the evolutionary history of primates starting with the ancestors of Simiformes (45-60 Ma) and continuing up to the ancestors of Homo is revealed. Once inserted, the euchromatic ARs were stably transmitted to the descendant species, some exhibiting copy number variation, whereas their sequence divergence followed the species phylogeny. Many euchromatic ARs have sequence characteristics of (peri)centromeric alpha repeats suggesting heterochromatin as a source of dispersed euchromatic ARs. The majority of euchromatic ARs are inserted in the vicinity of other repetitive elements such as L1, Alu, and ERV or are embedded within them. Irrespective of the insertion context, each AR insertion seems to be unique and once inserted, ARs do not seem to be subsequently spread to new genomic locations. In spite of association with (retro)transposable elements, there is no indication that such elements play a role in ARs proliferation. The presence of short duplications at most of ARs insertion sites suggests site-directed recombination between homologous motifs in ARs and in the target genomic sequence, probably mediated by extrachromosomal circular DNA, as a mechanism of spreading within euchromatin.
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Affiliation(s)
- Isidoro Feliciello
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.,Dipartimento di Medicina Clinica e Chirurgia, Universita' degli Studi di Napoli Federico II, Italy
| | - Željka Pezer
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Dušan Kordiš
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | | | - Đurđica Ugarković
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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43
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Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing. Heredity (Edinb) 2021; 127:312-322. [PMID: 34188193 PMCID: PMC8405704 DOI: 10.1038/s41437-021-00452-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.
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44
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Clive J, Wisden W, Savolainen V. The De-Scent of Sexuality: Should We Smell a Rat? ARCHIVES OF SEXUAL BEHAVIOR 2021; 50:2283-2288. [PMID: 31808032 PMCID: PMC8416816 DOI: 10.1007/s10508-019-01591-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 05/17/2023]
Affiliation(s)
- Jackson Clive
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, UK
| | - William Wisden
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, UK
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, UK.
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45
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Nicolas V, Mikula O, Lavrenchenko LA, Šumbera R, Bartáková V, Bryjová A, Meheretu Y, Verheyen E, Missoup AD, Lemmon AR, Moriarty Lemmon E, Bryja J. Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera. Mol Phylogenet Evol 2021; 163:107263. [PMID: 34273505 DOI: 10.1016/j.ympev.2021.107263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022]
Abstract
The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.
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Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Veronika Bartáková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Yonas Meheretu
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic.
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Reid MJC, Switzer WM, Alonso SK, Lowenberger CA, Schillaci MA. Evolutionary history of orangutan plasmodia revealed by phylogenetic analysis of complete mtDNA genomes and new biogeographical divergence dating calibration models. Am J Primatol 2021; 84:e23298. [PMID: 34227139 DOI: 10.1002/ajp.23298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/30/2021] [Accepted: 06/16/2021] [Indexed: 11/06/2022]
Abstract
During the past 15 years, researchers have shown a renewed interest in the study of the Plasmodium parasites that infect orangutans. Most recently, studies examined the phylogenetic relationships and divergence dates of these parasites in orangutans using complete mitochondrial DNA genomes. Questions regarding the dating of these parasites, however, remain. In the present study, we provide a new calibration model for dating the origins of Plasmodium parasites in orangutans using a modified date range for the origin of macaques in Asia. Our Bayesian phylogenetic analyses of complete Plasmodium sp. mitochondrial DNA genomes inferred two clades of plasmodia in orangutans (Pongo 1 and Pongo 2), and that these clades likely represent the previously identified species Plasmodium pitheci and Plasmodium silvaticum. However, we cannot identify which Pongo clade is representative of the morphologically described species. The most recent common ancestor of both Pongo sp. plasmodia, Plasmodium. hylobati, and Plasmodium. inui dates to 3-3.16 million years ago (mya) (95% highest posterior density [HPD]: 2.09-4.08 mya). The Pongo 1 parasite diversified 0.33-0.36 mya (95% HPD: 0.12-0.63), while the Pongo 2 parasite diversified 1.15-1.22 mya (95% HPD: 0.63-1.82 mya). It now seems likely that the monkey Plasmodium (P. inui) is the result of a host switch event from the Pongo 2 parasite to sympatric monkeys, or P. hylobati. Our new estimates for the divergence of orangutan malaria parasites, and subsequent diversification, are all several hundred thousand years later than previous Bayesian estimates.
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Affiliation(s)
- Michael J C Reid
- School of Interdisciplinary Studies, Durham College, Oshawa, Ontario, Canada.,Canadian Cameroon Ape Network, Toronto, Ontario, Canada
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Carl A Lowenberger
- Centre for Cell Biology, Development and Disease, Department of Biological Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael A Schillaci
- Department of Anthropology, University of Toronto Scarborough, Toronto, Ontario, Canada
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Zanoli A, Gamba M, Lemasson A, Palagi E, Norscia I. Looking into each other's eyes makes it better: eye-to-eye contact enhances sexual interactions in wild geladas. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2021.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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48
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Bergeron LA, Besenbacher S, Bakker J, Zheng J, Li P, Pacheco G, Sinding MHS, Kamilari M, Gilbert MTP, Schierup MH, Zhang G. The germline mutational process in rhesus macaque and its implications for phylogenetic dating. Gigascience 2021; 10:giab029. [PMID: 33954793 PMCID: PMC8099771 DOI: 10.1093/gigascience/giab029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/05/2021] [Accepted: 03/29/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. RESULTS Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ∼76× per individual and estimated a mean rate of 0.77 × 10-8de novo mutations per site per generation (95% CI: 0.69 × 10-8 to 0.85 × 10-8). By phasing 50% of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed a mean of 81% of the de novo mutations, with a trend of an increasing male contribution for older fathers. Approximately 3.5% of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated on the basis of the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecoidea/Hominoidea molecular divergence dated at 58 Mya using our new estimate of the yearly mutation rate. CONCLUSIONS When compared to the traditional molecular clock methods, new estimated rates from pedigree samples can provide insights into the evolution of well-studied groups such as primates.
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Affiliation(s)
- Lucie A Bergeron
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Brendstrupgårdsvej 21A, 8200 Aarhus N, Denmark
| | - Jaco Bakker
- Animal Science Department, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, Netherlands
| | - Jiao Zheng
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China
| | - Panyi Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Mikkel-Holger S Sinding
- Department of genetics, Trinity College Dublin, 2 college green, D02 VF25, Dublin, Ireland
- Greenland Institute of Natural Resources, Kivioq 2, 3900 Nuuk, Greenland
| | - Maria Kamilari
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen K, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, C.F.Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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Ogata FT, Branco V, Vale FF, Coppo L. Glutaredoxin: Discovery, redox defense and much more. Redox Biol 2021; 43:101975. [PMID: 33932870 PMCID: PMC8102999 DOI: 10.1016/j.redox.2021.101975] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 01/15/2023] Open
Abstract
Glutaredoxin, Grx, is a small protein containing an active site cysteine pair and was discovered in 1976 by Arne Holmgren. The Grx system, comprised of Grx, glutathione, glutathione reductase, and NADPH, was first described as an electron donor for Ribonucleotide Reductase but, from the first discovery in E.coli, the Grx family has impressively grown, particularly in the last two decades. Several isoforms have been described in different organisms (from bacteria to humans) and with different functions. The unique characteristic of Grxs is their ability to catalyse glutathione-dependent redox regulation via glutathionylation, the conjugation of glutathione to a substrate, and its reverse reaction, deglutathionylation. Grxs have also recently been enrolled in iron sulphur cluster formation. These functions have been implied in various physiological and pathological conditions, from immune defense to neurodegeneration and cancer development thus making Grx a possible drug target. This review aims to give an overview on Grxs, starting by a phylogenetic analysis of vertebrate Grxs, followed by an analysis of the mechanisms of action, the specific characteristics of the different human isoforms and a discussion on aspects related to human physiology and diseases.
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Affiliation(s)
- Fernando T Ogata
- Department of Biochemistry/Molecular Biology, CTCMol, Universidade Federal de São Paulo, Rua Mirassol, 207. 04044-010, São Paulo - SP, Brazil
| | - Vasco Branco
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Lucia Coppo
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, SE-17165, Stockholm, Sweden.
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Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution. Nat Ecol Evol 2021; 5:808-819. [PMID: 33795855 DOI: 10.1038/s41559-021-01431-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 02/25/2021] [Indexed: 12/18/2022]
Abstract
Quantifying speciation times during human evolution is fundamental as it provides a timescale to test for the correlation between key evolutionary transitions and extrinsic factors such as climatic or environmental change. Here, we applied a total evidence dating approach to a hominin phylogeny to estimate divergence times under different topological hypotheses. The time-scaled phylogenies were subsequently used to perform ancestral state reconstructions of body mass and phylogenetic encephalization quotient (PEQ). Our divergence-time estimates are consistent with other recent studies that analysed extant species. We show that the origin of the genus Homo probably occurred between 4.30 and 2.56 million years ago. The ancestral state reconstructions show a general trend towards a smaller body mass before the emergence of Homo, followed by a trend towards a greater body mass. PEQ estimations display a general trend of gradual but accelerating encephalization evolution. The obtained results provide a rigorous temporal framework for human evolution.
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