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Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rouselle 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, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Marques Bonet T, Farh KKH. Identification of constrained sequence elements across 239 primate genomes. Nature 2024; 625:735-742. [PMID: 38030727 PMCID: PMC10808062 DOI: 10.1038/s41586-023-06798-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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Affiliation(s)
- Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Jacob C Ulirsch
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Sabrina Rashid
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Mohamed Ameen
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Anthony J Cox
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Arvind Kumar
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Mareike C Janiak
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Martin Kuhlwilm
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Joseph D Orkin
- Département d'Anthropologie, Université de Montréal, Montréal, Quebec, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 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, Tefé, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Lidia Agueda
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Julie Blanc
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Rede de Pesquisa em Diversidade, Conservação e Uso da Fauna da Amazônia - RedeFauna, Manaus, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna, Iquitos, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
- Department of Biology, Trinity University, San Antonio, TX, 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, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | | | - Sree Kanthaswamy
- School of Interdisciplinary Forensics, Arizona State University, Phoenix, AZ, USA
- California National Primate Research Center, University of California, Davis, CA, 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, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Professorship for International Animal Health/One Health, Faculty of Veterinary Medicine, Justus Liebig University, Giessen, 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, 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, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- School of Geosciences, Edinburgh, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, Germany
| | - Ivo Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA.
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2
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Webb SE, Orkin JD, Williamson RE, Melin AD. Activity budget and gut microbiota stability and flexibility across reproductive states in wild capuchin monkeys in a seasonal tropical dry forest. Anim Microbiome 2023; 5:63. [PMID: 38102711 PMCID: PMC10724892 DOI: 10.1186/s42523-023-00280-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/05/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Energy demands associated with pregnancy and lactation are significant forces in mammalian evolution. To mitigate increased energy costs associated with reproduction, female mammals have evolved behavioural and physiological responses. Some species alter activity to conserve energy during pregnancy and lactation, while others experience changes in metabolism and fat deposition. Restructuring of gut microbiota with shifting reproductive states may also help females increase the energy gained from foods, especially during pregnancy. The goal of this study was to examine the relationships among behaviour, gut microbiota composition, and reproductive state in a wild, non-human primate to better understand reproductive ecology. We combined life history data with > 13,000 behavioural scans and 298 fecal samples collected longitudinally across multiple years from 33 white-faced capuchin monkey (Cebus imitator) females. We sequenced the V4 region of the 16S rRNA gene and used the DADA2 pipeline to analyze microbial diversity. We used PICRUSt2 to assess putative functions. RESULTS Reproductive state explained some variation in activity, but overall resting behaviours were relatively stable across pregnancy and lactation. Foraging was less frequent among females in the early stage of nursing compared to the cycling stage, though otherwise remained at comparable levels. Maximum temperature was a strong, significantly positive predictor of resting, while social dominance had a small but significantly negative effect on resting. Ecological variables such as available fruit biomass and rainfall had a small but significantly positive effects on measures of foraging time. Gut microbial community structure, including richness, alpha diversity, and beta diversity remained stable across the reproductive cycle. In pairwise comparisons, pregnant females exhibited increased relative abundances of multiple microbial ASVs, suggesting small changes in relation to reproductive state. Reproductive state was not linked to differential abundance of putative metabolic pathways. CONCLUSIONS Previous data suggest that activity budget and the gut microbiome shifts considerably during reproduction. The present study finds that both activity and gut microbial communities are less associated with reproduction compared to other predictors, including ecological contexts. This suggests that behavioural flexibility and gut microbial community plasticity is contrained by ecological factors in this population. These data contribute to a broader understanding of plasticity and stability in response to physiological shifts associated with mammalian reproduction.
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Affiliation(s)
- Shasta E Webb
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Joseph D Orkin
- Département d'anthropologie, Université de Montréal, 3150 Rue Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - Rachel E Williamson
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada.
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3
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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: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, 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, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, 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, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKH. The landscape of tolerated genetic variation in humans and primates. Science 2023; 380:eabn8153. [PMID: 37262156 DOI: 10.1126/science.abn8197] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | | | - Petko P Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Balick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Joseph D Orkin
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - 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
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, 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
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - 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
| | - Iracilda Sampaio
- Universidade Federal do Para, Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação "Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N F da Silva
- Instituto Nacional de Pesquisas da Amazonia, Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso, Boa Esperança, Cuiabá - MT, 78060-900, 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, 401, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University, New Haven, CT 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, PoB 16316, Addis Ababa 1000, 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 & 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 & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Center 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 - Insei 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 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
- 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
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore 168582, Republic of Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, 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 Science Campus 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
- Universitat Pompeu Fabra, Pg. Luís Companys 23, 08010 Barcelona, Spain
| | - Amanda Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, 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 EH8 9XP, 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
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
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5
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, 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, Batallion T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O’Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Kai-How Farh K. The landscape of tolerated genetic variation in humans and primates. bioRxiv 2023:2023.05.01.538953. [PMID: 37205491 PMCID: PMC10187174 DOI: 10.1101/2023.05.01.538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Joshua G. Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Anastasia Dietrich
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Petko Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Lukas Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Daniel Balick
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna; Djerassiplatz 1, 1030, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna; 1030, Vienna, Austria
| | - Joseph D. Orkin
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d’anthropologie, Université de Montréal; 3150 Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - 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
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University; Aarhus, 8000, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development; Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Faculty of Sciences, Department of Organismal Biology, Unit of Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB); Avenue Franklin D. Roosevelt 50, 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, United Kingdom
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
| | | | - Julie Horvath
- North Carolina Museum of Natural Sciences; Raleigh, North Carolina, 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University; Durham, North Carolina , 27707, USA
- Department of Biological Sciences, North Carolina State University; Raleigh, North Carolina , 27695, USA
- Department of Evolutionary Anthropology, Duke University; Durham, North Carolina , 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabricio 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, Utah, 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para; Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development; Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia – RedeFauna; Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica – ComFauna; Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação “Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N. F. da Silva
- Instituto Nacional de Pesquisas da Amazonia; Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso; Boa Esperança, Cuiabá - MT, 78060-900, 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, Texas, 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | | | - Joe H. Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University; New Haven, Connecticut, 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | | | - 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 & 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 & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen; Copenhagen, DK-2100, 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 - Isle of 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, 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart; 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Av. Doctor Aiguader, N88, Barcelona, 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation; C. Wellington 30, Barcelona, 08005, Spain
| | - Thomas Batallion
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune; Nho Quan District, Ninh Binh Province, 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature; 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre; Singapore 168582, Republic of Singapore
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland; Chambers Street, Edinburgh, EH1 1JF, UK
- School of Geosciences, University of Edinburgh; 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
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Amanda Melin
- Leibniz Science Campus Primate Cognition; 37077 Göttingen, Germany
- Department of Anthropology & Archaeology and Department of Medical Genetics
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
- Alberta Children’s Hospital Research Institute; University of Calgary; 2500 University Dr NW T2N 1N4, Calgary, Alberta, Canada
| | | | - Robin M. D. Beck
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - 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
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH8 9XP, UK
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Monkol Lek
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research; Kellnerweg 4, 37077 Göttingen, Germany
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Genetics, Yale School of Medicine; New Haven, Connecticut, 06520, USA
| | - Anne O’Donnell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Heidi Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Toyota Technological Institute at Chicago; Chicago, Illinois, 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 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; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
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6
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Palmada-Flores M, Orkin JD, Haase B, Mountcastle J, Bertelsen MF, Fedrigo O, Kuderna LFK, Jarvis ED, Marques-Bonet T. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). Gigascience 2022; 11:6562532. [PMID: 35365833 PMCID: PMC8975718 DOI: 10.1093/gigascience/giac026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/14/2022] [Accepted: 02/19/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in the popular media. Unfortunately, a recent population decline has resulted in the census population decreasing to <2,500 individuals in the wild, and the species's classification as an endangered species by the IUCN. As is the case for most strepsirrhine primates, only a limited amount of genomic research has been conducted on L. catta, in part owing to the lack of genomic resources. RESULTS We generated a new high-quality reference genome assembly for L. catta (mLemCat1) that conforms to the standards of the Vertebrate Genomes Project. This new long-read assembly is composed of Pacific Biosciences continuous long reads (CLR data), Optical Mapping Bionano reads, Arima HiC data, and 10X linked reads. The contiguity and completeness of the assembly are extremely high, with scaffold and contig N50 values of 90.982 and 10.570 Mb, respectively. Additionally, when compared to other high-quality primate assemblies, L. catta has the lowest reported number of Alu elements, which results predominantly from a lack of AluS and AluY elements. CONCLUSIONS mLemCat1 is an excellent genomic resource not only for the ring-tailed lemur community, but also for other members of the Lemuridae family, and is the first very long read assembly for a strepsirrhine.
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Affiliation(s)
- Marc Palmada-Flores
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain
| | - Joseph D Orkin
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain.,Département d'anthropologie, Université de Montréal, Montréal, QC H3T 1N8, Canada
| | - Bettina Haase
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065, USA
| | | | - Mads F Bertelsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksber 1870, Denmark
| | - Olivier Fedrigo
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065, USA
| | - Lukas F K Kuderna
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain
| | - Erich D Jarvis
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065, USA.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksber 1870, Denmark.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Laboratory of Neurogenetics of Language, The Rockefeller University, NY 10065, USA
| | - Tomas Marques-Bonet
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelon 08028a, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
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7
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Flachs A, Orkin JD. On pickles: biological and sociocultural links between fermented foods and the human gut microbiome. J Ethnobiol Ethnomed 2021; 17:39. [PMID: 34107988 PMCID: PMC8188661 DOI: 10.1186/s13002-021-00458-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa. METHODS In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods. RESULTS We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes. CONCLUSIONS By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.
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Affiliation(s)
- Andrew Flachs
- Department of Anthropology, Purdue University, West Lafayette, IN, USA.
| | - Joseph D Orkin
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain.
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8
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Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Alan Harris R, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Le MD, Manu S, Rabarivola CJ, Zaramody A, Andriaholinirina N, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KK, Rogers J, Marques‐Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. Am J Primatol 2021; 83:e23255. [PMID: 33792947 PMCID: PMC8250314 DOI: 10.1002/ajp.23255] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022]
Abstract
The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS-CoV-2 is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.
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Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
- Department of Medical GeneticsUniversity of CalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteUniversity of CalgaryAlbertaCanada
| | - Joseph D. Orkin
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Mareike C. Janiak
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Alejandro Valenzuela
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Lukas Kuderna
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Frank Marrone
- Department of ChemistryNew York UniversityNew YorkUSA
| | - Hasinala Ramangason
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
| | - Julie E. Horvath
- Genomics & Microbiology Research LaboratoryNorth Carolina Museum of Natural SciencesRaleighNorth CarolinaUSA
- Department of Biological and Biomedical SciencesNorth Carolina Central UniversityDurhamNorth CarolinaUSA
- Department of Evolutionary AnthropologyDuke UniversityDurhamNorth CarolinaUSA
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate CenterLeibniz Institute for Primate ResearchGöettingenGermany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland and School of GeosciencesUniversity of EdinburghEdinburghUK
| | - Chiea Chuen Khor
- Genome Institute of SingaporeAgency for Science, Technology and ResearchSingapore
- Singapore Eye Research InstituteSingapore National Eye CentreSingapore
| | - Weng Khong Lim
- SingHealth Duke‐NUS Institute of Precision MedicineSingapore Health ServicesSingapore
- SingHealth Duke‐NUS Genomic Medicine CentreSingapore Health ServicesSingapore
- Cancer and Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingapore
| | - Jessica G. H. Lee
- Department of Conservation, Research and Veterinary ServicesWildlife Reserves SingaporeSingapore
| | - Patrick Tan
- Genome Institute of SingaporeAgency for Science, Technology and ResearchSingapore
- SingHealth Duke‐NUS Institute of Precision MedicineSingapore Health ServicesSingapore
- Cancer and Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingapore
| | - Govindhaswamy Umapathy
- CSIR‐Laboratory for the Conservation of Endangered SpeciesCentre for Cellular and Molecular BiologyHyderabadIndia
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Ivo Gut
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Marta Gut
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Esther Lizano
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Tilo Nadler
- Cuc Phuong CommuneNho Quan DistrictNinh Binh ProvinceVietnam
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate CenterLeibniz Institute for Primate ResearchGoettingenGermany
- Leibniz Science Campus Primate CognitionGoettingenGermany
- Department of Primate CognitionGeorg‐August‐University, GoettingenGermany
| | - Minh D. Le
- Department of Environmental Ecology, University of Science and Central Institute for Natural Resources and Environmental StudiesVietnam National UniversityHanoiVietnam
| | - Sivakumara Manu
- CSIR‐Laboratory for the Conservation of Endangered SpeciesCentre for Cellular and Molecular BiologyHyderabadIndia
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Steig E. Johnson
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
| | - Erich D. Jarvis
- The Vertebrate Genomes LabThe Rockefeller UniversityNew YorkNew YorkUSA
- Laboratory of Neurogenetics of LanguageThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Olivier Fedrigo
- The Vertebrate Genomes LabThe Rockefeller UniversityNew YorkNew YorkUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Kunming Natural History Museum of Zoology, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- China National GenebankBGI‐ShenzhenShenzhenChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Tomas Marques‐Bonet
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Arcadi Navarro
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - David Juan
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | | | - James P. Higham
- Department of AnthropologyNew York UniversityNew YorkNew YorkUSA
- New York Consortium in Evolutionary PrimatologyNew YorkNew YorkUSA
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9
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Janiak MC, Montague MJ, Villamil CI, Stock MK, Trujillo AE, DePasquale AN, Orkin JD, Bauman Surratt SE, Gonzalez O, Platt ML, Martínez MI, Antón SC, Dominguez-Bello MG, Melin AD, Higham JP. Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques. Microbiome 2021; 9:68. [PMID: 33752735 PMCID: PMC7986251 DOI: 10.1186/s40168-021-01009-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/02/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND An individual's microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples. RESULTS Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes. CONCLUSIONS Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle. Video abstract.
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Affiliation(s)
- Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada.
- Alberta Children's Hospital Research Institute, Alberta, Canada.
- Department of Anthropology, New York University, New York, USA.
- School of Science, Engineering and Environment, University of Salford, Salford, UK.
| | - Michael J Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Catalina I Villamil
- School of Chiropractic, Universidad Central del Caribe, Bayamón, Puerto Rico
| | - Michala K Stock
- Department of Sociology and Anthropology, Metropolitan State University of Denver, Denver, CO, USA
| | - Amber E Trujillo
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Allegra N DePasquale
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
| | - Joseph D Orkin
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | | | - Olga Gonzalez
- Disease Intervention and Prevention, Southwest National Primate Research Center, San Antonio, TX, USA
| | - Michael L Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Melween I Martínez
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Susan C Antón
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Alberta, Canada
| | - James P Higham
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
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10
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Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Harris RA, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KKH, Rogers J, Marques-Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. bioRxiv 2021:2021.02.03.429540. [PMID: 33564767 PMCID: PMC7872355 DOI: 10.1101/2021.02.03.429540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.
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Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and Archaeology, University of Calgary, Canada
- Department of Medical Genetics, University of Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Joseph D. Orkin
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford, United Kingdom
| | - Alejandro Valenzuela
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Lukas Kuderna
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Frank Marrone
- Department of Chemistry, New York University, United States
| | | | - Julie E. Horvath
- Genomics & Microbiology Research Laboratory, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göettingen, Germany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland and School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore Health Services, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jessica G. H. Lee
- Department of Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Govindhaswamy Umapathy
- CSIR-Laboratory for the Conservation of Endangered Species, Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Ivo Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Esther Lizano
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz Science Campus Primate Cognition, Goettingen, Germany
- Department of Primate Cognition, Georg-August-University, Goettingen, Germany
| | - Steig E. Johnson
- Department of Anthropology and Archaeology, University of Calgary, Canada
| | - Erich D. Jarvis
- The Vertebrate Genomes Lab, The Rockefeller University, New York, United States
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Olivier Fedrigo
- The Vertebrate Genomes Lab, The Rockefeller University, New York, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Tomas Marques-Bonet
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arcadi Navarro
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - David Juan
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | | | - James P. Higham
- Department of Anthropology, New York University, United States
- New York Consortium in Evolutionary Primatology, New York, United States
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11
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Abstract
Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.
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Affiliation(s)
- Joseph D Orkin
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , ,
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , ,
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , , .,Sequencing Unit, National Genomic Analysis Center, Centre for Genomic Regulation, Barcelona Institute of Science, 08036 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autónoma de Barcelona, 08193 Barcelona, Spain
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12
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Lee Q, Padula MP, Pinello N, Williams SH, O'Rourke MB, Fumagalli MJ, Orkin JD, Song R, Shaban B, Brenner O, Pimanda JE, Weninger W, de Souza WM, Melin AD, Wong JJL, Crim MJ, Monette S, Roediger B, Jolly CJ. Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys. PLoS Pathog 2020; 16:e1008262. [PMID: 31971979 PMCID: PMC6999912 DOI: 10.1371/journal.ppat.1008262] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/04/2020] [Accepted: 12/08/2019] [Indexed: 12/21/2022] Open
Abstract
Mouse kidney parvovirus (MKPV) is a member of the provisional genus Chapparvovirus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four major MKPV transcripts, created by alternative splicing, to a common initiator region, and use mass spectrometry to identify “p10” and “p15” as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and the splicing-dependent putative accessory protein NS2 are conserved in all near-complete amniote chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that many mammal chapparvoviruses are likely to be nephrotropic. Parvoviruses are small, genetically simple single-strand DNA viruses that remain viable outside their hosts for very long periods of time. They cause disease in several domesticated species and in humans. Mouse kidney parvovirus (MKPV) is a causative agent of kidney failure in immune-compromised mice and is the only member of the provisional Chapparvovirus genus for which the complete genome including telomeres is known. Here, we show that MKPV propagates almost exclusively in the kidneys of mice infected naturally, wherein it produces novel accessory proteins whose coding regions are conserved in amniote-associated chapparvovirus sequences. We assemble a closely related complete viral genome present in DNA extracted from the kidney of a wild Cebus imitator monkey, and show that another related chapparvovirus is preferentially found in kidneys of the vampire bat Desmodus rotundus. We conclude that many mammal-hosted chapparvovirus are adapted to the kidney niche and may therefore cause disease following kidney stress in multiple species.
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Affiliation(s)
- Quintin Lee
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, University of Technology Sydney, Sydney, NSW, Australia
| | - Natalia Pinello
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Simon H. Williams
- Center for Infection & Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States of America
| | - Matthew B. O'Rourke
- Kolling Institute of Medical Research, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcilio Jorge Fumagalli
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Joseph D. Orkin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
| | - Renhua Song
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Babak Shaban
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - John E. Pimanda
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Wolfgang Weninger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - William Marciel de Souza
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Amanda D. Melin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Justin J.-L. Wong
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcus J. Crim
- Microbiology and Aquatic Diagnostics, IDEXX BioAnalytics, Discovery Drive, Columbia, MO, United States of America
| | - Sébastien Monette
- Laboratory of Comparative Pathology, Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY, United States of America
| | - Ben Roediger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Autoimmunity, Transplantation, Inflammation (ATI) Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail: (BR); (CJJ)
| | - Christopher J. Jolly
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
- * E-mail: (BR); (CJJ)
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13
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Janiak MC, Burrell AS, Orkin JD, Disotell TR. Duplication and parallel evolution of the pancreatic ribonuclease gene (RNASE1) in folivorous non-colobine primates, the howler monkeys (Alouatta spp.). Sci Rep 2019; 9:20366. [PMID: 31889139 PMCID: PMC6937293 DOI: 10.1038/s41598-019-56941-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 12/27/2022] Open
Abstract
In foregut-fermenting mammals (e.g., colobine monkeys, artiodactyl ruminants) the enzymes pancreatic ribonuclease (RNASE1) and lysozyme C (LYZ), originally involved in immune defense, have evolved new digestive functions. Howler monkeys are folivorous non-colobine primates that lack the multi-chambered stomachs of colobines and instead digest leaves using fermentation in the caeco-colic region. We present data on the RNASE1 and LYZ genes of four species of howler monkey (Alouatta spp.). We find that howler monkey LYZ is conserved and does not share the substitutions found in colobine and cow sequences, whereas RNASE1 was duplicated in the common ancestor of A. palliata, A. seniculus, A. sara, and A. pigra. While the parent gene (RNASE1) is conserved, the daughter gene (RNASE1B) has multiple amino acid substitutions that are parallel to those found in RNASE1B genes of colobines. The duplicated RNase in Alouatta has biochemical changes similar to those in colobines, suggesting a novel, possibly digestive function. These findings suggest that pancreatic ribonuclease has, in parallel, evolved a new role for digesting the products of microbial fermentation in both foregut- and hindgut-fermenting folivorous primates. This may be a vital digestive enzyme adaptation allowing howler monkeys to survive on leaves during periods of low fruit availability.
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Affiliation(s)
- Mareike C Janiak
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA. .,Center for Human Evolutionary Studies, Rutgers University, New Brunswick, NJ, USA. .,Department of Anthropology & Archaeology, University of Calgary, Calgary, AB, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| | - Andrew S Burrell
- Department of Anthropology, New York University, New York, NY, USA
| | - Joseph D Orkin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Todd R Disotell
- Department of Anthropology, New York University, New York, NY, USA.,Department of Anthropology, University of Massachusetts, Amherst, MA, USA
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14
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Abstract
Fermentation preserves and transforms foods through autochthonous or introduced microorganisms. Fermentation is of special interest to ethnobiologists because it relies on place- and practice-based knowledge, local flora and microbial taxa, is sensitive to cultural and ecological conditions, and illuminates the interactions through which communities shape and are shaped by the world around them. In this short topical review, we discuss recent anthropological and ethnobiological research into fermentation, arguing that this topic deserves further attention during the current moment of microbial interest across social and natural sciences. We present a typology of scholarship on human-microbial relationships that delineates three intellectual camps in this literature: neo-cultural ecology, microbiopolitics, and the environmental humanities. In light of biomedical and scientific attention to microbes—not only as threats but also as complex and beneficial actors in our lives—it is crucial to understand how socioecological practices including growing, preparing, and consuming fermented foods sustain microbial communities, heritage foodways, and human wellbeing.
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15
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Storer JM, Mierl JR, Brantley SA, Threeton B, Sukharutski Y, Rewerts LC, St Romain CP, Foreman MM, Baker JN, Walker JA, Orkin JD, Melin AD, Phillips KA, Konkel MK, Batzer MA. Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage. Genome Biol Evol 2019; 11:1105-1116. [PMID: 30888417 PMCID: PMC6464705 DOI: 10.1093/gbe/evz062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2019] [Indexed: 12/11/2022] Open
Abstract
Platy-1 elements are Platyrrhine-specific, short interspersed elements originally discovered in the Callithrix jacchus (common marmoset) genome. To date, only the marmoset genome has been analyzed for Platy-1 repeat content. Here, we report full-length Platy-1 insertions in other New World monkey (NWM) genomes (Saimiri boliviensis, squirrel monkey; Cebus imitator, capuchin monkey; and Aotus nancymaae, owl monkey) and analyze the amplification dynamics of lineage-specific Platy-1 insertions. A relatively small number of full-length and lineage-specific Platy-1 elements were found in the squirrel, capuchin, and owl monkey genomes compared with the marmoset genome. In addition, only a few older Platy-1 subfamilies were recovered in this study, with no Platy-1 subfamilies younger than Platy-1-6. By contrast, 62 Platy-1 subfamilies were discovered in the marmoset genome. All of the lineage-specific insertions found in the squirrel and capuchin monkeys were fixed present. However, ∼15% of the lineage-specific Platy-1 loci in Aotus were polymorphic for insertion presence/absence. In addition, two new Platy-1 subfamilies were identified in the owl monkey genome with low nucleotide divergences compared with their respective consensus sequences, suggesting minimal ongoing retrotransposition in the Aotus genus and no current activity in the Saimiri, Cebus, and Sapajus genera. These comparative analyses highlight the finding that the high number of Platy-1 elements discovered in the marmoset genome is an exception among NWM analyzed thus far, rather than the rule. Future studies are needed to expand upon our knowledge of Platy-1 amplification in other NWM genomes.
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Affiliation(s)
| | - Jackson R Mierl
- Department of Biological Sciences, Louisiana State University
| | | | | | | | - Lydia C Rewerts
- Department of Biological Sciences, Louisiana State University
| | | | | | - Jasmine N Baker
- Department of Biological Sciences, Louisiana State University
| | | | - Joseph D Orkin
- Department of Anthropology and Archaeology & Department of Medical Genetics, University of Calgary, Alberta, Canada
| | - Amanda D Melin
- Department of Anthropology and Archaeology & Department of Medical Genetics, University of Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, N.W. Calgary, Alberta, Canada
| | - Kimberley A Phillips
- Department of Psychology, Trinity University.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Miriam K Konkel
- Department of Biological Sciences, Louisiana State University.,Department of Genetics & Biochemistry, Clemson University
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University
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Kries K, Barros MAS, Duytschaever G, Orkin JD, Janiak MC, Pessoa DMA, Melin AD. Colour vision variation in leaf-nosed bats (Phyllostomidae): Links to cave roosting and dietary specialization. Mol Ecol 2018; 27:3627-3640. [PMID: 30059176 DOI: 10.1111/mec.14818] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 11/30/2022]
Abstract
Bats are a diverse radiation of mammals of enduring interest for understanding the evolution of sensory specialization. Colour vision variation among species has previously been linked to roosting preferences and echolocation form in the suborder Yinpterochiroptera, yet questions remain about the roles of diet and habitat in shaping bat visual ecology. We sequenced OPN1SW and OPN1LW opsin genes for 20 species of leaf-nosed bats (family Phyllostomidae; suborder Yangochiroptera) with diverse roosting and dietary ecologies, along with one vespertilionid species (Myotis lavali). OPN1LW genes appear intact for all species, and predicted spectral tuning of long-wavelength opsins varied among lineages. OPN1SW genes appear intact and under purifying selection for Myotis lavali and most phyllostomid bats, with two exceptions: (a) We found evidence of ancient OPN1SW pseudogenization in the vampire bat lineage, and loss-of-function mutations in all three species of extant vampire bats; (b) we additionally found a recent, independently derived OPN1SW pseudogene in Lonchophylla mordax, a cave-roosting species. These mutations in leaf-nosed bats are independent of the OPN1SW pseudogenization events previously reported in Yinpterochiropterans. Therefore, the evolution of monochromacy (complete colour blindness) has occurred in both suborders of bats and under various evolutionary drivers; we find independent support for the hypothesis that obligate cave roosting drives colour vision loss. We additionally suggest that haematophagous dietary specialization and corresponding selection on nonvisual senses led to loss of colour vision through evolutionary sensory trade-off. Our results underscore the evolutionary plasticity of opsins among nocturnal mammals.
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Affiliation(s)
- Kelly Kries
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri
| | - Marília A S Barros
- Department of Physiology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Gwen Duytschaever
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Joseph D Orkin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Mareike C Janiak
- Department of Anthropology, Rutgers University, New Brunswick, New Jersey
| | - Daniel M A Pessoa
- Department of Physiology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada.,Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Orkin JD, Campos FA, Myers MS, Cheves Hernandez SE, Guadamuz A, Melin AD. Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest. ISME J 2018; 13:183-196. [PMID: 30135468 DOI: 10.1038/s41396-018-0256-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/24/2018] [Accepted: 07/19/2018] [Indexed: 02/08/2023]
Abstract
Research on the gut microbiota of free-ranging mammals is offering new insights into dietary ecology. However, for free-ranging primates, little information is available for how microbiomes are influenced by ecological variation through time. Primates inhabiting seasonal tropical dry forests undergo seasonally specific decreases in food abundance and water availability, which have been linked to adverse health effects. Throughout the course of a seasonal transition in 2014, we collected fecal samples from three social groups of free-ranging white-faced capuchin monkeys (Cebus capucinus imitator) in Sector Santa Rosa, Área de Conservación Guanacaste, Costa Rica. 16S rRNA sequencing data reveal that unlike other primates, the white-faced capuchin monkey gut is dominated by Bifidobacterium and Streptococcus. Linear mixed effects models indicate that abundances of these genera are associated with fluctuating availability and consumption of fruit and arthropods, whereas beta diversity clusters by rainfall season. Whole shotgun metagenomics revealed that the capuchin gut is dominated by carbohydrate-binding modules associated with digestion of plant polysaccharides and chitin, matching seasonal dietary patterns. We conclude that rainfall and diet are associated with the diversity, composition, and function of the capuchin gut microbiome. Additionally, microbial fluctuations are likely contributing to nutrient uptake and the health of wild primate populations.
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Affiliation(s)
- Joseph D Orkin
- Department of Anthropology & Archaeology, University of Calgary, Calgary, AB, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada. .,Department of Anthropology, Washington University in St. Louis, St. Louis, MO, USA.
| | - Fernando A Campos
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.,Department of Biology, Duke University, Durham, NC, USA
| | - Monica S Myers
- Department of Anthropology & Archaeology, University of Calgary, Calgary, AB, Canada.,Área de Conservación Guanacaste, Guanacaste, Costa Rica
| | - Saul E Cheves Hernandez
- Department of Anthropology & Archaeology, University of Calgary, Calgary, AB, Canada.,Área de Conservación Guanacaste, Guanacaste, Costa Rica
| | | | - Amanda D Melin
- Department of Anthropology & Archaeology, University of Calgary, Calgary, AB, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada. .,Department of Anthropology, Washington University in St. Louis, St. Louis, MO, USA.
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18
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Orkin JD, Yang Y, Yang C, Yu DW, Jiang X. Cost-effective scat-detection dogs: unleashing a powerful new tool for international mammalian conservation biology. Sci Rep 2016; 6:34758. [PMID: 27721442 PMCID: PMC5056371 DOI: 10.1038/srep34758] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/19/2016] [Indexed: 11/30/2022] Open
Abstract
Recently, detection dogs have been utilized to collect fecal samples from cryptic and rare mammals. Despite the great promise of this technique for conservation biology, its broader application has been limited by the high cost (tens to hundreds of thousands of dollars) and logistical challenges of employing a scat-detection dog team while conducting international, collaborative research. Through an international collaboration of primatologists and the Chinese Ministry of Public Security, we trained and used a detection dog to find scat from three species of unhabituated, free-ranging primates, for less than $3,000. We collected 137 non-human primate fecal samples that we confirmed by sequencing taxonomically informative genetic markers. Our detection dog team had a 92% accuracy rate, significantly outperforming our human-only team. Our results demonstrate that detection dogs can locate fecal samples from unhabituated primates with variable diets, locomotion, and grouping patterns, despite challenging field conditions. We provide a model for in-country training, while also building local capacity for conservation and genetic monitoring. Unlike previous efforts, our approach will allow for the wide adoption of scat-detection dogs in international conservation biology.
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Affiliation(s)
- Joseph D. Orkin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
- Department of Anthropology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada
| | - Yuming Yang
- Kunming Police Dog Training Base, Chinese Ministry of Security, 579 Baiyunlu Kunming, Yunnan, 650204, China
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
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Melin AD, Wells K, Moritz GL, Kistler L, Orkin JD, Timm RM, Bernard H, Lakim MB, Perry GH, Kawamura S, Dominy NJ. Euarchontan Opsin Variation Brings New Focus to Primate Origins. Mol Biol Evol 2016; 33:1029-41. [PMID: 26739880 PMCID: PMC4776711 DOI: 10.1093/molbev/msv346] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, that is, the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Here, we report on the genes (OPN1SW and OPN1LW) that encode SWS1 and M/LWS opsins in seven species of treeshrew, including the sole nocturnal scandentian Ptilocercus lowii. In addition, we examined the opsin genes of the Central American woolly opossum (Caluromys derbianus), an enduring ecological analogue in the debate on primate origins. Our results indicate: 1) retention of ultraviolet (UV) visual sensitivity in C. derbianus and a shift from UV to blue spectral sensitivities at the base of Euarchonta; 2) ancient pseudogenization of OPN1SW in the ancestors of P. lowii, but a signature of purifying selection in those of C. derbianus; and, 3) the absence of OPN1LW polymorphism among diurnal treeshrews. These findings suggest functional variation in the color vision of nocturnal mammals and a distinctive visual ecology of early primates, perhaps one that demanded greater spatial resolution under light levels that could support cone-mediated color discrimination.
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Affiliation(s)
- Amanda D Melin
- Department of Anthropology, Dartmouth College, Hanover, NH Department of Anthropology and Archaeology, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB
| | - Konstans Wells
- Environmental Futures Research Institute, Griffith University, Brisbane, QLD, Australia
| | - Gillian L Moritz
- Department of Biological Sciences, Class of 1978 Life Sciences Center, Dartmouth College, Hanover, NH Department of Evolutionary Anthropology, Duke University
| | - Logan Kistler
- Departments of Anthropology and Biology, Pennsylvania State University School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Joseph D Orkin
- Department of Anthropology and Archaeology, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB Department of Anthropology, Washington University in St. Louis
| | - Robert M Timm
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence
| | - Henry Bernard
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Maklarin B Lakim
- Sabah Parks, Lot 45 & 46 KK Times Square Coastal Highway, Kota Kinabalu, Sabah, Malaysia
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, Hanover, NH Department of Biological Sciences, Class of 1978 Life Sciences Center, Dartmouth College, Hanover, NH
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Ma C, Luo Z, Liu C, Orkin JD, Xiao W, Fan P. Population and Conservation Status of Indochinese Gray Langurs (Trachypithecus crepusculus) in the Wuliang Mountains, Jingdong, Yunnan, China. INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9852-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Orkin JD, Pontzer H. The Narrow Niche hypothesis: Gray squirrels shed new light on primate origins. Am J Phys Anthropol 2011; 144:617-24. [DOI: 10.1002/ajpa.21450] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 10/05/2010] [Indexed: 11/10/2022]
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Welker KL, Orkin JD, Ryan TM. Analysis of intraindividual and intraspecific variation in semicircular canal dimensions using high-resolution x-ray computed tomography. J Anat 2009; 215:444-51. [PMID: 19619167 DOI: 10.1111/j.1469-7580.2009.01124.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The semicircular canal system tracks head rotation and provides sensory input for the reflexive stabilization of gaze and posture. The purpose of this study was to investigate the intraspecific and intraindividual variation in the size of the three semicircular canals. The right and left temporal bones were extracted from 31 individuals of the short-tailed shrew (Blarina brevicauda) and scanned on a high-resolution x-ray computed tomography system. The radius of curvature was calculated for each of the three semicircular canals for each side. Paired t-tests and independent sample t-tests indicated no significant differences in canal size between the right and left canals of the same individuals or between those of males and females of the same species. Pearson product moment correlation analyses demonstrated that there was no significant correlation between canal size and body mass in this sample.
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Affiliation(s)
- Kelli L Welker
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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