1
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Slimak L, Vimala T, Seguin-Orlando A, Metz L, Zanolli C, Joannes-Boyau R, Frouin M, Arnold LJ, Demuro M, Devièse T, Comeskey D, Buckley M, Camus H, Muth X, Lewis JE, Bocherens H, Yvorra P, Tenailleau C, Duployer B, Coqueugniot H, Dutour O, Higham T, Sikora M. Long genetic and social isolation in Neanderthals before their extinction. CELL GENOMICS 2024; 4:100593. [PMID: 39265525 DOI: 10.1016/j.xgen.2024.100593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 11/23/2023] [Accepted: 06/05/2024] [Indexed: 09/14/2024]
Abstract
Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations' structure that mostly indicates that late European Neanderthals belonged to a single metapopulation with no significant evidence of population structure. Here, we report the discovery of a late Neanderthal individual, nicknamed "Thorin," from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of Neanderthal final technological traditions in this region ∼50-42 thousand years ago. Thorin's genome reveals a relatively early divergence of ∼105 ka with other late Neanderthals. Thorin belonged to a population with a small group size that showed no genetic introgression with other known late European Neanderthals, revealing some 50 ka of genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the disappearance of the Neanderthals.
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Affiliation(s)
- Ludovic Slimak
- Centre d'Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Faculté de Santé, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France.
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Faculté de Santé, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Laure Metz
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l'Homme, BP 647, 5 rue du Château de l'Horloge, 13094 Aix-en-Provence Cedex 2, France; University of Connecticut, College of Liberal Arts and Sciences, 215 Glenbrook Road, U-4098, Storrs, CT 06269-4098, USA
| | - Clément Zanolli
- Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600 Pessac, France
| | - Renaud Joannes-Boyau
- Geoarchaeology & Archaeometry Research Group (GARG), Southern Cross University, Military Rd., Lismore, NSW 2480, Australia
| | - Marine Frouin
- Department of Geosciences, Stony Brook University, 255 Earth and Space Sciences Building, Stony Brook, NY 11794-2100, USA; Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA
| | - Lee J Arnold
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Martina Demuro
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Thibaut Devièse
- CEREGE, Aix-Marseille University, CNRS, IRD, INRAE, Collège de France, Technopôle de l'Arbois, Aix-en-Provence, France
| | - Daniel Comeskey
- Syft Technologies Ltd., 3 Craft Place, Middleton, PO Box 28 149, Christchurch 8242, New Zealand
| | - Michael Buckley
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Hubert Camus
- PROTEE-EXPERT, 4 rue des Aspholdèles, 34750 Villeneuve-lès-Maguelone, France
| | - Xavier Muth
- Get in Situ, 1091 Bourg-en-Lavaux, Switzerland
| | - Jason E Lewis
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA; Chronicle Heritage, 319 E Palm Lane, Phoenix, AZ 85004, USA
| | - Hervé Bocherens
- Fachbereich Geowissenschaften Forschungsbereich Paläobiologie - Biogeologie Senckenberg, Centre for Human Evolution and Palaeoenvironment (SHEP), Universität Tübingen, Hölderlinstr. 12, 72074 Tübingen, Germany
| | - Pascale Yvorra
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l'Homme, BP 647, 5 rue du Château de l'Horloge, 13094 Aix-en-Provence Cedex 2, France
| | - Christophe Tenailleau
- Centre Inter-Universitaire de Recherche et d'Ingénierie des Matériaux, UMR 5085 CNRS-Université de Toulouse (Paul Sabatier), 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Benjamin Duployer
- Centre Inter-Universitaire de Recherche et d'Ingénierie des Matériaux, UMR 5085 CNRS-Université de Toulouse (Paul Sabatier), 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Hélène Coqueugniot
- École Pratique des Hautes Études - Paris Sciences et Lettres University, 4-14 rue Ferrus, 75014 Paris, France; University of Bordeaux-Montaigne, CNRS, EPHE, Archéosciences, UMR 6034, 33607 Pessac, France
| | - Olivier Dutour
- École Pratique des Hautes Études - Paris Sciences et Lettres University, 4-14 rue Ferrus, 75014 Paris, France; University of Bordeaux-Montaigne, CNRS, EPHE, Archéosciences, UMR 6034, 33607 Pessac, France
| | - Thomas Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna 1090, Austria
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark.
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2
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Zhang R, Drummond AJ, Mendes FK. Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters. Syst Biol 2024; 73:102-124. [PMID: 38085256 PMCID: PMC11129596 DOI: 10.1093/sysbio/syad067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/23/2023] [Accepted: 11/07/2023] [Indexed: 05/28/2024] Open
Abstract
Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remain challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous morphological characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.
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Affiliation(s)
- Rong Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School 169857, Singapore
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Fábio K Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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3
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Briand M, Boccarossa A, Rieux A, Jacques MA, Ganlanon L, Johnson C, Eveillard M, Marsollier L, Marion E. Emergence and spread of Mycobacterium ulcerans at different geographic scales. Microbiol Spectr 2024; 12:e0382723. [PMID: 38441471 PMCID: PMC10986537 DOI: 10.1128/spectrum.03827-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/10/2024] [Indexed: 04/06/2024] Open
Abstract
The classical lineage of Mycobacterium ulcerans is the most prevalent clonal group associated with Buruli ulcer in humans. Its reservoir is strongly associated with the environment. We analyzed together 1,045 isolates collected from 13 countries on two continents to define the evolutionary history and population dynamics of this lineage. We confirm that this lineage spread over 7,000 years from Australia to Africa with the emergence of outbreaks in distinct waves in the 18th and 19th centuries. In sharp contrast with its global spread over the last century, transmission chains are now mostly local, with little or no dissemination between endemic areas. This study provides new insights into the phylogeography and population dynamics of M. ulcerans, highlighting the importance of comparative genomic analyses to improve our understanding of pathogen transmission. IMPORTANCE Mycobacterium ulcerans is an environmental mycobacterial pathogen that can cause Buruli ulcer, a severe cutaneous infection, mostly spread in Africa and Australia. We conducted a large genomic study of M. ulcerans, combining genomic and evolutionary approaches to decipher its evolutionary history and pattern of spread at different geographic scales. At the scale of villages in an endemic area of Benin, the circulating genotypes have been introduced in recent decades and are not randomly distributed along the river. On a global scale, M. ulcerans has been spreading for much longer, resulting in distinct and compartmentalized endemic foci across Africa and Australia.
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Affiliation(s)
- Martial Briand
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint Pierre, La Réunion, France
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4
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Majander K, Pla-Díaz M, du Plessis L, Arora N, Filippini J, Pezo-Lanfranco L, Eggers S, González-Candelas F, Schuenemann VJ. Redefining the treponemal history through pre-Columbian genomes from Brazil. Nature 2024; 627:182-188. [PMID: 38267579 PMCID: PMC10917687 DOI: 10.1038/s41586-023-06965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions1,2. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico3-6. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.
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Affiliation(s)
- Kerttu Majander
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Marta Pla-Díaz
- Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain
- CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain
| | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Jose Filippini
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Luis Pezo-Lanfranco
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- Institute of Environmental Science and Technology (ICTA) and Prehistory Department, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sabine Eggers
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain.
- CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
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5
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Featherstone LA, McGaughran A. The effect of missing data on evolutionary analysis of sequence capture bycatch, with application to an agricultural pest. Mol Genet Genomics 2024; 299:11. [PMID: 38381254 PMCID: PMC10881687 DOI: 10.1007/s00438-024-02097-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/29/2023] [Indexed: 02/22/2024]
Abstract
Sequence capture is a genomic technique that selectively enriches target sequences before high throughput next-generation sequencing, to generate specific sequences of interest. Off-target or 'bycatch' data are often discarded from capture experiments, but can be leveraged to address evolutionary questions under some circumstances. Here, we investigated the effects of missing data on a variety of evolutionary analyses using bycatch from an exon capture experiment on the global pest moth, Helicoverpa armigera. We added > 200 new samples from across Australia in the form of mitogenomes obtained as bycatch from targeted sequence capture, and combined these into an additional larger dataset to total > 1000 mitochondrial cytochrome c oxidase subunit I (COI) sequences across the species' global distribution. Using discriminant analysis of principal components and Bayesian coalescent analyses, we showed that mitogenomes assembled from bycatch with up to 75% missing data were able to return evolutionary inferences consistent with higher coverage datasets and the broader literature surrounding H. armigera. For example, low-coverage sequences broadly supported the delineation of two H. armigera subspecies and also provided new insights into the potential for geographic turnover among these subspecies. However, we also identified key effects of dataset coverage and composition on our results. Thus, low-coverage bycatch data can offer valuable information for population genetic and phylodynamic analyses, but caution is required to ensure the reduced information does not introduce confounding factors, such as sampling biases, that drive inference. We encourage more researchers to consider maximizing the potential of the targeted sequence approach by examining evolutionary questions with their off-target bycatch where possible-especially in cases where no previous mitochondrial data exists-but recommend stratifying data at different genome coverage thresholds to separate sampling effects from genuine genomic signals, and to understand their implications for evolutionary research.
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Affiliation(s)
- Leo A Featherstone
- Research School of Biology, Division of Ecology and Evolution, Australian National University, Canberra, ACT, 2601, Australia
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Angela McGaughran
- Research School of Biology, Division of Ecology and Evolution, Australian National University, Canberra, ACT, 2601, Australia.
- Te Aka Mātuatua, School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand.
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6
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Fiddaman SR, Dimopoulos EA, Lebrasseur O, du Plessis L, Vrancken B, Charlton S, Haruda AF, Tabbada K, Flammer PG, Dascalu S, Marković N, Li H, Franklin G, Symmons R, Baron H, Daróczi-Szabó L, Shaymuratova DN, Askeyev IV, Putelat O, Sana M, Davoudi H, Fathi H, Mucheshi AS, Vahdati AA, Zhang L, Foster A, Sykes N, Baumberg GC, Bulatović J, Askeyev AO, Askeyev OV, Mashkour M, Pybus OG, Nair V, Larson G, Smith AL, Frantz LAF. Ancient chicken remains reveal the origins of virulence in Marek's disease virus. Science 2023; 382:1276-1281. [PMID: 38096384 DOI: 10.1126/science.adg2238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.
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Affiliation(s)
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ophélie Lebrasseur
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS/Université Toulouse III Paul Sabatier, Toulouse, France
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Sophy Charlton
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Ashleigh F Haruda
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Kristina Tabbada
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | | | | | - Hannah Li
- Institute of Immunity and Transplantation, University College London, London, UK
| | | | | | | | | | - Dilyara N Shaymuratova
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | - Igor V Askeyev
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | | | - Maria Sana
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Hossein Davoudi
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | - Homa Fathi
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | - Amir Saed Mucheshi
- Department of Art and Architecture, Payame Noor University (PNU), Tehran, Iran
| | - Ali Akbar Vahdati
- Iranian Ministry of Cultural Heritage, Tourism, and Handicrafts, North Khorasan Office, Iran
| | - Liangren Zhang
- Department of Archaeology, School of History, Nanjing University, China
| | | | - Naomi Sykes
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Gabrielle Cass Baumberg
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Jelena Bulatović
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Arthur O Askeyev
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | - Oleg V Askeyev
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | - Marjan Mashkour
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
- CNRS, National Museum Natural History Paris, Paris, France
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Venugopal Nair
- Department of Biology, University of Oxford, Oxford, UK
- Viral Oncogenesis Group, Pirbright Institute, Woking, UK
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | - Laurent A F Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universitat, Munich, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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7
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Silcocks M, Dunstan SJ. Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history. Commun Biol 2023; 6:1037. [PMID: 37833496 PMCID: PMC10575886 DOI: 10.1038/s42003-023-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across Eurasia. A lack of ancient samples from tropical East Asia limits the resolution of this model. We consider insight afforded by patterns of variation within the human pathogen Mycobacterium tuberculosis (Mtb) by analysing its phylogeographic signatures jointly with the human Y-chromosome. We demonstrate the Y-chromosome lineages enriched in the traditionally hunter-gatherer groups associated with East Asia's first layer of peopling to display deep roots, low long-term effective population size, and diversity patterns consistent with a southern entry route. These characteristics mirror those of the evolutionarily ancient Mtb lineage 1. The remaining East Asian Y-chromosome lineage is almost entirely absent from traditionally hunter-gatherer groups and displays spatial and temporal characteristics which are incompatible with a southern entry route, and which link it to the development of agriculture in modern-day China. These characteristics mirror those of the evolutionarily modern Mtb lineage 2. This model paves the way for novel host-pathogen coevolutionary research hypotheses in East Asia.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| | - Sarah J Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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8
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Yao N, Zhang Z, Yu L, Hazarika R, Yu C, Jang H, Smith LM, Ton J, Liu L, Stachowicz JJ, Reusch TBH, Schmitz RJ, Johannes F. An evolutionary epigenetic clock in plants. Science 2023; 381:1440-1445. [PMID: 37769069 DOI: 10.1126/science.adh9443] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/08/2023] [Indexed: 09/30/2023]
Abstract
Molecular clocks are the basis for dating the divergence between lineages over macroevolutionary timescales (~105 to 108 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes display a clocklike behavior. This "epimutation clock" is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation clocks recapitulate known topologies and branching times of intraspecies phylogenetic trees in the self-fertilizing plant Arabidopsis thaliana and the clonal seagrass Zostera marina, which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.
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Affiliation(s)
- N Yao
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Z Zhang
- Plant Epigenomics, Technical University of Munich, Freising, Germany
| | - L Yu
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - R Hazarika
- Plant Epigenomics, Technical University of Munich, Freising, Germany
| | - C Yu
- Plant Epigenomics, Technical University of Munich, Freising, Germany
| | - H Jang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - L M Smith
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - J Ton
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - L Liu
- Department of Statistics, University of Georgia, Athens, GA, USA
| | - J J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - T B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - R J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - F Johannes
- Plant Epigenomics, Technical University of Munich, Freising, Germany
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9
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Guzmán-Solís AA, Navarro MA, Ávila-Arcos MC, Blanco-Melo D. A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History. Annu Rev Virol 2023; 10:49-75. [PMID: 37268008 DOI: 10.1146/annurev-virology-111821-123859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis of ancient nucleic acids from diverse human remains, the identification and characterization of ancient viruses became feasible. Recent studies have provided invaluable information about past epidemics and made it possible to examine assumptions and inferences on the origin and evolution of certain viral families. In parallel, the study of ancient viruses also uncovered their importance in the evolution of the human lineage and their key roles in shaping major events in human history. In this review, we describe the strategies used for the study of ancient viruses, along with their limitations, and provide a detailed account of what past viral infections have revealed about human history.
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Affiliation(s)
- Axel A Guzmán-Solís
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miguel Alejandro Navarro
- Licenciatura en Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, México;
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, México;
| | - Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA;
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10
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Ruiz-Puerta EJ, Keighley X, Desjardins SPA, Gotfredsen AB, Pan SE, Star B, Boessenkool S, Barrett JH, McCarthy ML, Andersen LW, Born EW, Howse LR, Szpak P, Pálsson S, Malmquist HJ, Rufolo S, Jordan PD, Olsen MT. Holocene deglaciation drove rapid genetic diversification of Atlantic walrus. Proc Biol Sci 2023; 290:20231349. [PMID: 37752842 PMCID: PMC10523089 DOI: 10.1098/rspb.2023.1349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/27/2023] [Indexed: 09/28/2023] Open
Abstract
Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.
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Affiliation(s)
- Emily J. Ruiz-Puerta
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
| | - Xénia Keighley
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- The Bureau of Meteorology, The Treasury Building, Parkes Place West, Parkes, Australian Capital Territory 2600, Australia
| | - Sean P. A. Desjardins
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Anne Birgitte Gotfredsen
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen Kobenhavn, Denmark
| | - Shyong En Pan
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - James H. Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, 7491 Trondheim, Norway
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Morgan L. McCarthy
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
| | - Liselotte W. Andersen
- Department of Ecoscience, Aarhus University, CF Møllers Allé 4-8, build. 1110, 8000 Aarhus C, Denmark
| | - Erik W. Born
- Greenland Institute of Natural Resources, PO Box 570, 3900 Nuuk, Greenland
| | - Lesley R. Howse
- Archaeology Centre, University of Toronto, 19 Ursula Franklin Street, Toronto, Ontario Canada M5S 2S2
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, Ontario, Canada K9L 0G2
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Askja, Sturlugata 7, 101 Reykjavik, Iceland
| | - Hilmar J. Malmquist
- Icelandic Museum of Natural History, Suðurlandsbraut 24, 108 Reykjavík, Iceland
| | - Scott Rufolo
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Peter D. Jordan
- Department of Archaeology and Ancient History, Lund University, Helgonavägen 3, 223 62 Lund, Sweden
- Global Station for Indigenous Studies and Cultural Diversity (GSI), GI-CoRE, HokkaidoUniversity, Japan
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Denmark
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11
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Torres Ortiz A, Kendall M, Storey N, Hatcher J, Dunn H, Roy S, Williams R, Williams C, Goldstein RA, Didelot X, Harris K, Breuer J, Grandjean L. Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. eLife 2023; 12:e84384. [PMID: 37732733 PMCID: PMC10602588 DOI: 10.7554/elife.84384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 09/20/2023] [Indexed: 09/22/2023] Open
Abstract
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low-frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is partially maintained among repeated serial samples from the same host, it can transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
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Affiliation(s)
- Arturo Torres Ortiz
- Department of Infectious Diseases, Imperial College LondonLondonUnited Kingdom
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | - Michelle Kendall
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Nathaniel Storey
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - James Hatcher
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - Helen Dunn
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | | | | | | | - Xavier Didelot
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Kathryn Harris
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
- Department of Virology, East & South East London Pathology Partnership, Royal London Hospital, Barts Health NHS TrustLondonUnited Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
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12
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Campos PE, Pruvost O, Boyer K, Chiroleu F, Cao TT, Gaudeul M, Baider C, Utteridge TMA, Becker N, Rieux A, Gagnevin L. Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history. Nat Commun 2023; 14:4306. [PMID: 37474518 PMCID: PMC10359311 DOI: 10.1038/s41467-023-39950-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).
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Affiliation(s)
- Paola E Campos
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | | | - Thuy Trang Cao
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
- Herbier national, Muséum national d'Histoire naturelle, CP39, 57 rue Cuvier, 75005, Paris, France
| | - Cláudia Baider
- The Mauritius Herbarium, Agricultural Services, Ministry of Agro-Industry and Food Security, R.E. Vaughan Building (MSIRI Compound), Reduit, 80835, Mauritius
| | | | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
- CIRAD, UMR PHIM, Montpellier, France.
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13
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Lu B, Curtius K, Graham TA, Yang Z, Barnes CP. CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples. Genome Biol 2023; 24:144. [PMID: 37340508 DOI: 10.1186/s13059-023-02983-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation.
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Affiliation(s)
- Bingxin Lu
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| | - Kit Curtius
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Trevor A Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
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14
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Latorre SM, Were VM, Foster AJ, Langner T, Malmgren A, Harant A, Asuke S, Reyes-Avila S, Gupta DR, Jensen C, Ma W, Mahmud NU, Mehebub MS, Mulenga RM, Muzahid ANM, Paul SK, Rabby SMF, Rahat AAM, Ryder L, Shrestha RK, Sichilima S, Soanes DM, Singh PK, Bentley AR, Saunders DGO, Tosa Y, Croll D, Lamour KH, Islam T, Tembo B, Win J, Talbot NJ, Burbano HA, Kamoun S. Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus. PLoS Biol 2023; 21:e3002052. [PMID: 37040332 PMCID: PMC10089362 DOI: 10.1371/journal.pbio.3002052] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/24/2023] [Indexed: 04/12/2023] Open
Abstract
Wheat, one of the most important food crops, is threatened by a blast disease pandemic. Here, we show that a clonal lineage of the wheat blast fungus recently spread to Asia and Africa following two independent introductions from South America. Through a combination of genome analyses and laboratory experiments, we show that the decade-old blast pandemic lineage can be controlled by the Rmg8 disease resistance gene and is sensitive to strobilurin fungicides. However, we also highlight the potential of the pandemic clone to evolve fungicide-insensitive variants and sexually recombine with African lineages. This underscores the urgent need for genomic surveillance to track and mitigate the spread of wheat blast outside of South America and to guide preemptive wheat breeding for blast resistance.
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Affiliation(s)
- Sergio M. Latorre
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Vincent M. Were
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J. Foster
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Angus Malmgren
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Soichiro Asuke
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Sarai Reyes-Avila
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Cassandra Jensen
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Weibin Ma
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Md. Shabab Mehebub
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Rabson M. Mulenga
- Zambia Agricultural Research Institute, Mt. Makulu Central Research Station, Lusaka, Zambia
| | - Abu Naim Md. Muzahid
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Sanjoy Kumar Paul
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - S. M. Fajle Rabby
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Abdullah Al Mahbub Rahat
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Lauren Ryder
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Suwilanji Sichilima
- Zambia Agricultural Research Institute, Mt. Makulu Central Research Station, Lusaka, Zambia
| | - Darren M. Soanes
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Pawan Kumar Singh
- International Maize and Wheat Improvement Center, (CIMMYT), Texcoco, Mexico
| | - Alison R. Bentley
- International Maize and Wheat Improvement Center, (CIMMYT), Texcoco, Mexico
| | | | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Kurt H. Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Batiseba Tembo
- Zambia Agricultural Research Institute, Mt. Makulu Central Research Station, Lusaka, Zambia
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Hernán A. Burbano
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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15
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Latorre SM, Were VM, Foster AJ, Langner T, Malmgren A, Harant A, Asuke S, Reyes-Avila S, Gupta DR, Jensen C, Ma W, Mahmud NU, Mehebub MS, Mulenga RM, Muzahid ANM, Paul SK, Rabby SMF, Rahat AAM, Ryder L, Shrestha RK, Sichilima S, Soanes DM, Singh PK, Bentley AR, Saunders DGO, Tosa Y, Croll D, Lamour KH, Islam T, Tembo B, Win J, Talbot NJ, Burbano HA, Kamoun S. Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus. PLoS Biol 2023; 21:e3002052. [PMID: 37040332 DOI: 10.1101/2022.06.06.494979] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/24/2023] [Indexed: 05/21/2023] Open
Abstract
Wheat, one of the most important food crops, is threatened by a blast disease pandemic. Here, we show that a clonal lineage of the wheat blast fungus recently spread to Asia and Africa following two independent introductions from South America. Through a combination of genome analyses and laboratory experiments, we show that the decade-old blast pandemic lineage can be controlled by the Rmg8 disease resistance gene and is sensitive to strobilurin fungicides. However, we also highlight the potential of the pandemic clone to evolve fungicide-insensitive variants and sexually recombine with African lineages. This underscores the urgent need for genomic surveillance to track and mitigate the spread of wheat blast outside of South America and to guide preemptive wheat breeding for blast resistance.
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Affiliation(s)
- Sergio M Latorre
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Vincent M Were
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J Foster
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Angus Malmgren
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Soichiro Asuke
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Sarai Reyes-Avila
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Cassandra Jensen
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Weibin Ma
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Md Shåbab Mehebub
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Rabson M Mulenga
- Zambia Agricultural Research Institute, Mt. Makulu Central Research Station, Lusaka, Zambia
| | - Abu Naim Md Muzahid
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Sanjoy Kumar Paul
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - S M Fajle Rabby
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Abdullah Al Mahbub Rahat
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Lauren Ryder
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Suwilanji Sichilima
- Zambia Agricultural Research Institute, Mt. Makulu Central Research Station, Lusaka, Zambia
| | - Darren M Soanes
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Pawan Kumar Singh
- International Maize and Wheat Improvement Center, (CIMMYT), Texcoco, Mexico
| | - Alison R Bentley
- International Maize and Wheat Improvement Center, (CIMMYT), Texcoco, Mexico
| | | | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Kurt H Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Batiseba Tembo
- Zambia Agricultural Research Institute, Mt. Makulu Central Research Station, Lusaka, Zambia
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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16
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Doizy A, Prin A, Cornu G, Chiroleu F, Rieux A. Phylostems: a new graphical tool to investigate temporal signal of heterochronous sequences datasets. BIOINFORMATICS ADVANCES 2023; 3:vbad026. [PMID: 36936370 PMCID: PMC10017117 DOI: 10.1093/bioadv/vbad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/16/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
Motivation Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. Importantly, such inferences should only be performed on datasets displaying sufficient temporal signal, a feature important to test prior to any tip-dating inference. For this purpose, the most popular method considered to-date has been the 'root-to-tip regression' which consist in fitting a linear regression of the number of substitutions accumulated from the root to the tips of a phylogenetic tree as a function of sampling times. The main limitation of the regression method, in its current implementation, relies in the fact that the temporal signal can only be tested at the whole-tree scale (i.e. its root). Results To overcome this limitation we introduce Phylostems, a new graphical user-friendly tool developed to investigate temporal signal within every clade of a phylogenetic tree. We provide a 'how to' guide by running Phylostems on an empirical dataset and supply guidance for results interpretation. Availability and implementation Phylostems is freely available at https://pvbmt-apps.cirad.fr/apps/phylostems.
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Affiliation(s)
- Anna Doizy
- CIRAD, UMR PVBMT, La Réunion, St Pierre 97410, France
- DoAna—Statistiques Réunion, Reunion Island, Saint-Joseph F-97480, France
| | - Amaury Prin
- CIRAD, UMR PVBMT, La Réunion, St Pierre 97410, France
| | - Guillaume Cornu
- CIRAD, Univ Montpellier, UR Forests and Societies, 34398 Montpellier Cedex 5, France
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17
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Gao Y, Fan G, Cheng S, Zhang W, Bai Y. Evolutionary history and global spatiotemporal pattern of alfalfa mosaic virus. Front Microbiol 2022; 13:1051834. [PMID: 36620025 PMCID: PMC9812523 DOI: 10.3389/fmicb.2022.1051834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/27/2022] [Indexed: 12/24/2022] Open
Abstract
Alfalfa mosaic virus (AMV) is an important plant virus causing considerable economic loss to alfalfa production. Knowledge of the evolutionary and demographic history of the pathogen is limited but essential to the development of effective and sustainable pathogen management schemes. In this study, we performed worldwide phylodynamic analyses of AMV based on 154 nucleotide sequences of the coat protein gene, sampled from 1985 to 2020, to understand the epidemiology of this pathogen. Bayesian phylogenetic reconstruction estimates that the crown group of AMV dates back to 1840 (95% credibility interval, 1687-1955). We revealed that AMV continuously evolves at a rate of 4.14 × 10-4 substitutions/site/year (95% credibility interval, 1.04 × 10-4 - 6.68 × 10-4). Our phylogeographic analyses identified multiple migration links between Europe and other regions, implying that Europe played a key role in spreading the virus worldwide. Further analyses showed that the clustering pattern of AMV isolates is significantly correlated to geographic regions, indicating that geography-driven adaptation may be a factor that affects the evolution of AMV. Our findings may be potentially used in the development of effective control strategies for AMV.
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Affiliation(s)
- Yanling Gao
- Industrial Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guoquan Fan
- Industrial Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Shengqun Cheng
- College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Wei Zhang
- Industrial Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yanju Bai
- Industrial Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China,*Correspondence: Yanju Bai,
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18
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Agwati EO, Oduor CI, Ayieko C, Ong’echa JM, Moormann AM, Bailey JA. Profiling genome-wide recombination in Epstein Barr virus reveals type-specific patterns and associations with endemic-Burkitt lymphoma. Virol J 2022; 19:208. [PMID: 36482473 PMCID: PMC9733152 DOI: 10.1186/s12985-022-01942-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Endemic Burkitt lymphoma (eBL) is potentiated through the interplay of Epstein Barr virus (EBV) and holoendemic Plasmodium falciparum malaria. To better understand EBV's biology and role in eBL, we characterized genome-wide recombination sites and patterns as a source of genetic diversity in EBV genomes in our well-defined population of eBL cases and controls from Western Kenya. METHODS EBV genomes representing 54 eBL cases and 32 healthy children from the same geographic region in Western Kenya that we previously sequenced were analyzed. Whole-genome multiple sequence alignment, recombination analyses, and phylogenetic inference were made using multiple alignment with fast Fourier transform, recombination detection program 4, and molecular evolutionary genetics analysis. RESULTS We identified 28 different recombination events and 71 (82.6%) of the 86 EBV genomes analyzed contained evidence of one or more recombinant segments. Associated recombination breakpoints were found to occur in a total of 42 different genes, with only 7 (16.67%) being latent genes. Recombination events were major drivers of clustering within genome-wide phylogenetic trees. The occurrence of recombination segments was comparable between genomes from male and female participants and across age groups. More recombinant segments were found in EBV type 1 genomes (p = 6.4e - 06) and the genomes from the eBLs (p = 0.037). Two recombination events were enriched in the eBLs; event 47 (OR = 4.07, p = 0.038) and event 50 (OR = 14.24, p = 0.012). CONCLUSIONS EBV genomes have extensive evidence of recombination likely acquired progressively and cumulatively over time. Recombination patterns display a heterogeneous occurrence rate across the genome with enrichment in lytic genes. Overall, recombination appears to be a major evolutionary force impacting EBV diversity and genome structure with evidence of the association of specific recombinants with eBL.
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Affiliation(s)
- Eddy O. Agwati
- grid.442486.80000 0001 0744 8172Department of Zoology, Maseno University, Maseno, Kenya ,grid.33058.3d0000 0001 0155 5938Center for Global Health Research (CGHR), Kenya Medical Research Institute, Kisumu, Kenya
| | - Cliff I. Oduor
- grid.40263.330000 0004 1936 9094Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903 USA
| | - Cyrus Ayieko
- grid.442486.80000 0001 0744 8172Department of Zoology, Maseno University, Maseno, Kenya
| | - John Michael Ong’echa
- grid.33058.3d0000 0001 0155 5938Center for Global Health Research (CGHR), Kenya Medical Research Institute, Kisumu, Kenya
| | - Ann M. Moormann
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine and the Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Jeffrey A. Bailey
- grid.40263.330000 0004 1936 9094Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903 USA
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19
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Wirth W, Mutch S, Turnbull R, Duchene S. Phytest: quality control for phylogenetic analyses. Bioinformatics 2022; 38:5124-5125. [PMID: 36205601 PMCID: PMC9676013 DOI: 10.1093/bioinformatics/btac664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION The ability to automatically conduct quality control checks on phylogenetic analyses is becoming more important with the increase in genetic sequencing and the use of real-time pipelines e.g. in the SARS-CoV-2 era. Implementations of real-time phylogenetic analyses require automated testing to make sure that problems in the data are caught automatically within analysis pipelines and in a timely manner. Here, we present Phytest (version 1.1) a tool for automating quality control checks on sequences, trees and metadata during phylogenetic analyses. RESULTS Phytest is a phylogenetic analysis testing program that easily integrates into existing phylogenetic pipelines. We demonstrate the utility of Phytest with real-world examples. AVAILABILITY AND IMPLEMENTATION Phytest source code is available on GitHub (https://github.com/phytest-devs/phytest) and can be installed via PyPI with the command 'pip install phytest'. Extensive documentation can be found at https://phytest-devs.github.io/phytest/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Simon Mutch
- Melbourne Data Analytics Platform, University of Melbourne, Melbourne 3010, Australia
| | - Robert Turnbull
- Melbourne Data Analytics Platform, University of Melbourne, Melbourne 3010, Australia
| | - Sebastian Duchene
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3010, Australia
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20
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Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
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Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
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21
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Randriambololona M, Rakotonirina TJ, Rieux A, Grisoni M. First report of Odontoglossum ringspot virus in Vanilla (Orchidaceae) in Madagascar. PLANT DISEASE 2022; 107:1250. [PMID: 36018553 DOI: 10.1094/pdis-06-22-1399-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Vanilla (Vanilla planifolia, Orchidaceae) is Madagascar's leading agricultural export resource which provides 80% of world's consumption. During a phytosanitary survey conducted from November 2019 to March 2021 in the main vanilla production regions of Madagascar, 250 plots were indexed for cymbidium mosaic virus (CymMV, Potexvirus genus) and odontoglossum ringspot virus (ORSV, Tobamovirus genus) the two most prevalent viruses of cultivated orchids worldwide (Zettler et al., 1990). For each plot, bulk samples (ten leaves taken at random) were assayed using Immunostrips (AGDIA, ISK 13301). A quarter of the plots (63/250) tested positive for CymMV. The highest prevalence of CymMV was observed in the SAVA region (57 out of 153 plots = 37,2%) where the virus has been reported since 1997 (Grisoni et al., 2010). Six plots located in the district of Mahanoro (Atsinanana) tested positive for ORSV. A few plants in these plots showed chlorotic often annular spots on their leaves. They were individually tested positive for ORSV, and negative for CymMV and potyviruses (Immunostrips AGDIA ISK 27200), the other two viruses reported so far in vanilla in Madagascar. To confirm the diagnosis of ORSV, leaf samples from five of the six infected plots were analysed by Tube Capture-RT-PCR (Grisoni et al., 2017) using two pairs of primers flanking the ORSV coat protein (CP) gene: OrCP1 (GGTCGGTAATGGTGTTAG) / OrCP2 (TGCATTATCGTATGCTCC), and CPOR-F(ATGTCTTACACTATTACAGACC) / CPOR-R(TTAGGAAGAGGTCCAAGTAAG). The five samples gave amplicons of the expected size (820 nt and 476 nt, respectively) and were sequenced with Sanger technology (Macrogen, The Netherlands). The ORSV-CP sequences of the Mahanoro isolates showed very close similarity to 198 ORSV-CP sequences from GenBank (95.8% to 99.6% nucleotide and 94.5 to 100% amino-acid identities), and less than 75.4% nucleotide (80.1% amino-acid) identities with Bell pepper mosaic virus (DQ355023), the tobamovirus closest to ORSV. The five ORSV-CP sequences from vanilla were deposited in GenBank under accessions numbers OM847399 to OM847403. These data confirmed that ORSV infects vanilla vines in Madagascar. To our knowledge, this is the first report of this virus in Madagascar and of its ability to infect symptomatically V. planifolia. The five ORSV isolates from vanilla had more than 98.7 % nucleotide identities of CP gene and clustered into a monophyletic group in maximum likelihood phylogenetic tree, suggesting a single origin of these isolates. To further investigate the origin of ORSV in Madagascar, we made use of RNA sequences isolated at different points in time to infer the timing of evolutionary events (Rieux et al., 2016). We estimated the CP gene substitution rate to 4.8E-4 subst/site/year [95%HPD 2.1E-4 - 8.7E-4] which is close to the estimate of He et al. (2019) based on a slightly different sequences set (1.25E-3 subst/site/year). We dated the initial contamination of vanilla plts by ORSV between 2004 and 2013. Both ORSV and CymMV have deleterious effects on many ornamental orchids, and the pathogenicity of CymMV is exacerbated when co-infecting with ORSV (Lee et al., 2021). Therefore, ORSV represents a new threat to the Malagasy vanilla crop, especially in regions where CymMV is already rife. Given the economic importance of vanilla cultivation in the country, the implementation of prophylactic measures aimed at preventing the spread of ORSV, in particular through the sanitary control of cuttings, should be a priority for the vanilla industry.
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Affiliation(s)
- Mendrikaja Randriambololona
- Université d'Antananarivo, Department of Plant Biology and Ecology, Antananarivo, Madagascar
- Centre Technique Horticole de Tamatave, Toamasina, Madagascar;
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22
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Översti S, Palo JU. Variation in the substitution rates among the human mitochondrial haplogroup U sublineages. Genome Biol Evol 2022; 14:6613373. [PMID: 35731946 PMCID: PMC9250076 DOI: 10.1093/gbe/evac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.
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Affiliation(s)
- Sanni Översti
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany Kahlaische Straße 10, 07745, Jena, Germany.,Organismal and Evolutionary Biology Research Programme, Faculty of Biological Sciences, University of Helsinki, Helsinki, Finland P.O. Box 56, FI-00014, Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, Faculty of Medicine, University of Helsinki, Helsinki, Finland P.O. Box 40, FI-00014, Helsinki, Finland.,Forensic Chemistry Unit, Forensic Genetics Team, Finnish Institute for Health and Welfare, Helsinki, Finland P.O. Box 30, FI-00271, Helsinki, Finland
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23
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Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
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24
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Ortiz AT, Kendall M, Storey N, Hatcher J, Dunn H, Roy S, Williams R, Williams C, Goldstein RA, Didelot X, Harris K, Breuer J, Grandjean L. Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.07.495142. [PMID: 35702156 PMCID: PMC9196117 DOI: 10.1101/2022.06.07.495142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches to reconstruct outbreaks exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is stable among repeated serial samples from the same host, is transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
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Affiliation(s)
| | - Michelle Kendall
- Department of Statistics, University of Warwick, Coventry, CV4 7AL
| | - Nathaniel Storey
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - James Hatcher
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - Helen Dunn
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
| | - Rachel Williams
- UCL Genomics, Institute of Child Health, UCL, London WC1N 1EH
| | | | | | - Xavier Didelot
- Department of Statistics, University of Warwick, Coventry, CV4 7AL
| | - Kathryn Harris
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
- Department of Virology, East South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London E12ES
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
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25
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Forni D, Cagliani R, Pozzoli U, Mozzi A, Arrigoni F, De Gioia L, Clerici M, Sironi M. Dating the Emergence of Human Endemic Coronaviruses. Viruses 2022; 14:v14051095. [PMID: 35632836 PMCID: PMC9148137 DOI: 10.3390/v14051095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 01/09/2023] Open
Abstract
Four endemic coronaviruses infect humans and cause mild symptoms. Because previous analyses were based on a limited number of sequences and did not control for effects that affect molecular dating, we re-assessed the timing of endemic coronavirus emergence. After controlling for recombination, selective pressure, and molecular clock model, we obtained similar tMRCA (time to the most recent common ancestor) estimates for the four coronaviruses, ranging from 72 (HCoV-229E) to 54 (HCoV-NL63) years ago. The split times of HCoV-229E and HCoV-OC43 from camel alphacoronavirus and bovine coronavirus were dated ~268 and ~99 years ago. The split times of HCoV-HKU1 and HCoV-NL63 could not be calculated, as their zoonoticic sources are unknown. To compare the timing of coronavirus emergence to that of another respiratory virus, we recorded the occurrence of influenza pandemics since 1500. Although there is no clear relationship between pandemic occurrence and human population size, the frequency of influenza pandemics seems to intensify starting around 1700, which corresponds with the initial phase of exponential increase of human population and to the emergence of HCoV-229E. The frequency of flu pandemics in the 19th century also suggests that the concurrence of HCoV-OC43 emergence and the Russian flu pandemic may be due to chance.
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Affiliation(s)
- Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
- Correspondence:
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
| | - Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy; (F.A.); (L.D.G.)
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy; (F.A.); (L.D.G.)
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20122 Milan, Italy;
- Don Carlo Gnocchi Foundation ONLUS, IRCCS, 20148 Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
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26
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Acman M, Wang R, van Dorp L, Shaw LP, Wang Q, Luhmann N, Yin Y, Sun S, Chen H, Wang H, Balloux F. Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene bla NDM. Nat Commun 2022; 13:1131. [PMID: 35241674 PMCID: PMC8894482 DOI: 10.1038/s41467-022-28819-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
The mobile resistance gene blaNDM encodes the NDM enzyme which hydrolyses carbapenems, a class of antibiotics used to treat some of the most severe bacterial infections. The blaNDM gene is globally distributed across a variety of Gram-negative bacteria on multiple plasmids, typically located within highly recombining and transposon-rich genomic regions, which leads to the dynamics underlying the global dissemination of blaNDM to remain poorly resolved. Here, we compile a dataset of over 6000 bacterial genomes harbouring the blaNDM gene, including 104 newly generated PacBio hybrid assemblies from clinical and livestock-associated isolates across China. We develop a computational approach to track structural variants surrounding blaNDM, which allows us to identify prevalent genomic contexts, mobile genetic elements, and likely events in the gene's global spread. We estimate that blaNDM emerged on a Tn125 transposon before 1985, but only reached global prevalence around a decade after its first recorded observation in 2005. The Tn125 transposon seems to have played an important role in early plasmid-mediated jumps of blaNDM, but was overtaken in recent years by other elements including IS26-flanked pseudo-composite transposons and Tn3000. We found a strong association between blaNDM-carrying plasmid backbones and the sampling location of isolates. This observation suggests that the global dissemination of the blaNDM gene was primarily driven by successive between-plasmid transposon jumps, with far more restricted subsequent plasmid exchange, possibly due to adaptation of plasmids to their specific bacterial hosts.
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Affiliation(s)
- Mislav Acman
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| | - Liam P Shaw
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Nina Luhmann
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
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27
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Torres Ortiz A, Coronel J, Vidal JR, Bonilla C, Moore DAJ, Gilman RH, Balloux F, Kon OM, Didelot X, Grandjean L. Genomic signatures of pre-resistance in Mycobacterium tuberculosis. Nat Commun 2021; 12:7312. [PMID: 34911948 PMCID: PMC8674244 DOI: 10.1038/s41467-021-27616-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022] Open
Abstract
Recent advances in bacterial whole-genome sequencing have resulted in a comprehensive catalog of antibiotic resistance genomic signatures in Mycobacterium tuberculosis. With a view to pre-empt the emergence of resistance, we hypothesized that pre-existing polymorphisms in susceptible genotypes (pre-resistance mutations) could increase the risk of becoming resistant in the future. We sequenced whole genomes from 3135 isolates sampled over a 17-year period. After reconstructing ancestral genomes on time-calibrated phylogenetic trees, we developed and applied a genome-wide survival analysis to determine the hazard of resistance acquisition. We demonstrate that M. tuberculosis lineage 2 has a higher risk of acquiring resistance than lineage 4, and estimate a higher hazard of rifampicin resistance evolution following isoniazid mono-resistance. Furthermore, we describe loci and genomic polymorphisms associated with a higher risk of resistance acquisition. Identifying markers of future antibiotic resistance could enable targeted therapy to prevent resistance emergence in M. tuberculosis and other pathogens.
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Affiliation(s)
- Arturo Torres Ortiz
- grid.7445.20000 0001 2113 8111Imperial College London, Department of Infectious Diseases, London, UK
| | - Jorge Coronel
- grid.11100.310000 0001 0673 9488Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Julia Rios Vidal
- grid.419858.90000 0004 0371 3700Unidad Técnica de Tuberculosis MDR, Ministerio de Salud, Lima, Perú
| | - Cesar Bonilla
- grid.419858.90000 0004 0371 3700Unidad Técnica de Tuberculosis MDR, Ministerio de Salud, Lima, Perú ,grid.441740.20000 0004 0542 2122Universidad Privada San Juan Bautista, Lima, Perú
| | - David A. J. Moore
- grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Robert H. Gilman
- grid.21107.350000 0001 2171 9311Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | | | - Onn Min Kon
- grid.7445.20000 0001 2113 8111Respiratory Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Xavier Didelot
- grid.7372.10000 0000 8809 1613University of Warwick, School of Life Sciences and Department of Statistics, Warwick, UK
| | - Louis Grandjean
- Imperial College London, Department of Infectious Diseases, London, UK. .,UCL Department of Infection, Institute of Child Health, London, UK.
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28
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White AE, de-Dios T, Carrión P, Bonora GL, Llovera L, Cilli E, Lizano E, Khabdulina MK, Tleugabulov DT, Olalde I, Marquès-Bonet T, Balloux F, Pettener D, van Dorp L, Luiselli D, Lalueza-Fox C. Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome. BIOLOGY 2021; 10:biology10121324. [PMID: 34943238 PMCID: PMC8698332 DOI: 10.3390/biology10121324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 11/16/2022]
Abstract
The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.
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Affiliation(s)
- Anna E. White
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Toni de-Dios
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Pablo Carrión
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Gian Luca Bonora
- ISMEO—International Association for Mediterranean and East Studies, 00186 Rome, Italy;
| | - Laia Llovera
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;
| | - Esther Lizano
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Maral K. Khabdulina
- K.A. Akishev Institute of Archaeology, L.N. Gumilev Eurasian National University, Nur-Sultan 010000, Kazakhstan; (M.K.K.); (D.T.T.)
| | - Daniyar T. Tleugabulov
- K.A. Akishev Institute of Archaeology, L.N. Gumilev Eurasian National University, Nur-Sultan 010000, Kazakhstan; (M.K.K.); (D.T.T.)
| | - Iñigo Olalde
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Centro de Investigación “Lascaray” Ikergunea, BIOMICs Research Group, Universidad del País Vasco, 01006 Vitoria-Gasteiz, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, Department of Genetics Evolution & Environment, University College London, London WC1E 6BT, UK;
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics Evolution & Environment, University College London, London WC1E 6BT, UK;
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
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29
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Lima DAR, Zimpel CK, Patané JS, Silva-Pereira TT, Etges RN, Rodrigues RA, Dávila AMR, Ikuta CY, Ferreira Neto JS, Guimarães AMS, Araújo FR. Genomic analysis of an outbreak of bovine tuberculosis in a man-made multi-host species system: A call for action on wildlife in Brazil. Transbound Emerg Dis 2021; 69:e580-e591. [PMID: 34633756 DOI: 10.1111/tbed.14343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 11/26/2022]
Abstract
We report on a 15-year-long outbreak of bovine tuberculosis (bTB) in wildlife from a Brazilian safari park. A timeline of diagnostic events and whole-genome sequencing (WGS) of 21 Mycobacterium bovis isolates from deer and llamas were analyzed. Accordingly, from 2003 to 2018, at least 16 animals, from eight species, died due to TB, which is likely an underestimated number. In three occasions since 2013, the deer presented positive tuberculin tests, leading to the park closure and culling of all deer. WGS indicated that multiple M. bovis strains were circulating, with at least three founding introductions since the park inauguration in 1977. Using a previously sequenced dataset of 71 M. bovis genomes from cattle, we found no recent transmission events between nearby farms and the park based on WGS. Lastly, by discussing socio-economic and environmental factors escaping current regulatory gaps that were determinant of this outbreak, we pledge for the development of a plan to report and control bTB in wildlife in Brazil.
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Affiliation(s)
- Daiane A R Lima
- Department of Veterinary Medicine, Graduate Program in Veterinary Sciences, School of Veterinary Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Cristina K Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - José S Patané
- Center for Bioinformatics and Computational Biology, Butantan Institute, São Paulo, São Paulo, Brazil
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Rodrigo N Etges
- Livestock and Rural Development, Secretary of Agriculture, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rudielle A Rodrigues
- Department of Veterinary Medicine, Graduate Program in Veterinary Sciences, School of Veterinary Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory and Graduate Program on Biodiversity and Health, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Cássia Y Ikuta
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - José S Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana Marcia S Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Flábio R Araújo
- Embrapa Beef Cattle, Campo Grande, Mato Grosso do Sul, Brazil
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30
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Srihi H, Chatti N, Ben Mhadheb M, Gharbi J, Abid N. Phylodynamic and phylogeographic analysis of the complete genome of the West Nile virus lineage 2 (WNV-2) in the Mediterranean basin. BMC Ecol Evol 2021; 21:183. [PMID: 34579648 PMCID: PMC8477494 DOI: 10.1186/s12862-021-01902-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/12/2021] [Indexed: 11/25/2022] Open
Abstract
Background The West Nile virus is a highly contagious agent for a wide range of hosts. Its spread in the Mediterranean region raises several questions about its origin and the risk factors underlying the virus’s dispersal. Materials and methods The present study aims to reconstruct the temporal and spatial phylodynamics of West Nile virus lineage 2 in the Mediterranean region using 75 complete genome sequences from different host species retrieved from international databases. Results This data set suggests that current strains of WNV-2 began spreading in South Africa or nearby regions in the early twentieth century, and it migrated northwards via at least one route crossing the Mediterranean to reach Hungary in the early 2000s, before spreading throughout Europe. Another introduction event, according to the data set collected and analyses performed, is inferred to have occurred in around 1978. Migratory birds constitute, among others, additional risk factors that enhance the geographical transmission of the infection.
Conclusion Our data underline the importance of the spatial–temporal tracking of migratory birds and phylodynamic reconstruction in setting up an efficient surveillance system for emerging and reemerging zoonoses in the Mediterranean region. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01902-w.
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Affiliation(s)
- Haythem Srihi
- Research Unit UR17ES30 "Genomics, Biotechnology and Antiviral Strategies", Higher Institute of Biotechnology of Monastir, University of Monastir, Tahar Hadded Avenue, PB 74, 5000, Monastir, Tunisia.
| | - Noureddine Chatti
- Research Unit UR17ES30 "Genomics, Biotechnology and Antiviral Strategies", Higher Institute of Biotechnology of Monastir, University of Monastir, Tahar Hadded Avenue, PB 74, 5000, Monastir, Tunisia
| | - Manel Ben Mhadheb
- Research Unit UR17ES30 "Genomics, Biotechnology and Antiviral Strategies", Higher Institute of Biotechnology of Monastir, University of Monastir, Tahar Hadded Avenue, PB 74, 5000, Monastir, Tunisia
| | - Jawhar Gharbi
- Research Unit UR17ES30 "Genomics, Biotechnology and Antiviral Strategies", Higher Institute of Biotechnology of Monastir, University of Monastir, Tahar Hadded Avenue, PB 74, 5000, Monastir, Tunisia.,Department of Biological Sciences, College of Science, King Faisal University, PB 400, Post Code 31982, Al-Ahsa, Saudi Arabia
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Ibn Sina Street, 5000, Monastir, Tunisia. .,High Institute of Biotechnology of Sidi Thabet, Department of Biotechnology, University of Manouba, BiotechPôlet Sidi Thabet, PB 66, 2020, Ariana-Tunis, Tunisia.
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31
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Calland JK, Pascoe B, Bayliss SC, Mourkas E, Berthenet E, Thorpe HA, Hitchings MD, Feil EJ, Corander J, Blaser MJ, Falush D, Sheppard SK. Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages. PLoS Genet 2021; 17:e1009829. [PMID: 34582435 PMCID: PMC8500405 DOI: 10.1371/journal.pgen.1009829] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/08/2021] [Accepted: 09/20/2021] [Indexed: 11/20/2022] Open
Abstract
Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the 'birthday problem'. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10-6 s/s/y) and Campylobacter jejuni (3.4 x 10-6 s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame-analogous to a shared birthday-and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.
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Affiliation(s)
- Jessica K. Calland
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Ben Pascoe
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Sion C. Bayliss
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Evangelos Mourkas
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Elvire Berthenet
- French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, Bordeaux, France
- Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Harry A. Thorpe
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Matthew D. Hitchings
- Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Edward J. Feil
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Daniel Falush
- Centre for Microbes, Development and Health, Institute Pasteur of Shanghai, Shanghai, China
- * E-mail: (DF); (SKS)
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (DF); (SKS)
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32
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Braga J, Samir C, Fradi A, Feunteun Y, Jakata K, Zimmer VA, Zipfel B, Thackeray JF, Macé M, Wood BA, Grine FE. Cochlear shape distinguishes southern African early hominin taxa with unique auditory ecologies. Sci Rep 2021; 11:17018. [PMID: 34426640 PMCID: PMC8382707 DOI: 10.1038/s41598-021-96543-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
Insights into potential differences among the bony labyrinths of Plio-Pleistocene hominins may inform their evolutionary histories and sensory ecologies. We use four recently-discovered bony labyrinths from the site of Kromdraai to significantly expand the sample for Paranthropus robustus. Diffeomorphometry, which provides detailed information about cochlear shape, reveals size-independent differences in cochlear shape between P. robustus and Australopithecus africanus that exceed those among modern humans and the African apes. The cochlea of P. robustus is distinctive and relatively invariant, whereas cochlear shape in A. africanus is more variable, resembles that of early Homo, and shows a degree of morphological polymorphism comparable to that evinced by modern species. The curvature of the P. robustus cochlea is uniquely derived and is consistent with enhanced sensitivity to low-frequency sounds. Combined with evidence for selection, our findings suggest that sound perception shaped distinct ecological adaptations among southern African early hominins.
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Affiliation(s)
- J. Braga
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier Toulouse III, Faculté de Médecine Purpan, 37 allées Jules Guesde, Toulouse, France ,grid.11951.3d0000 0004 1937 1135Evolutionary Studies Institute, University of the Witwatersrand, PO WITS, Johannesburg, 2050 South Africa
| | - C. Samir
- grid.503317.30000 0000 9971 4898LIMOS, UMR 6158 CNRS-Université Clermont Auvergne, 63173 Aubière, France
| | - A. Fradi
- grid.503317.30000 0000 9971 4898LIMOS, UMR 6158 CNRS-Université Clermont Auvergne, 63173 Aubière, France
| | - Y. Feunteun
- grid.503317.30000 0000 9971 4898LIMOS, UMR 6158 CNRS-Université Clermont Auvergne, 63173 Aubière, France
| | - K. Jakata
- grid.11951.3d0000 0004 1937 1135Evolutionary Studies Institute, University of the Witwatersrand, PO WITS, Johannesburg, 2050 South Africa
| | - V. A. Zimmer
- grid.6936.a0000000123222966Faculty of Informatics, Technical University of Munich, Munich, Germany
| | - B. Zipfel
- grid.11951.3d0000 0004 1937 1135Evolutionary Studies Institute, University of the Witwatersrand, PO WITS, Johannesburg, 2050 South Africa
| | - J. F. Thackeray
- grid.11951.3d0000 0004 1937 1135Evolutionary Studies Institute, University of the Witwatersrand, PO WITS, Johannesburg, 2050 South Africa
| | - M. Macé
- Véto 31, 73 Avenue du Général de Gaulle, 47000 Agen, France
| | - B. A. Wood
- grid.253615.60000 0004 1936 9510Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, DC 20052 USA
| | - F. E. Grine
- grid.36425.360000 0001 2216 9681Department of Anthropology, Stony Brook University, Stony Brook, NY 11794 USA ,grid.36425.360000 0001 2216 9681Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY 11794 USA
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33
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Hayman DTS, Knox MA. Estimating the age of the subfamily Orthocoronavirinae using host divergence times as calibration ages at two internal nodes. Virology 2021; 563:20-27. [PMID: 34411808 PMCID: PMC8365511 DOI: 10.1016/j.virol.2021.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022]
Abstract
Viruses of the subfamily Orthocoronavirinae can cause mild to severe disease in people, including COVID-19, MERS and SARS. Their most common natural hosts are bat and bird species, which are mostly split across four virus genera. Molecular clock analyses of orthocoronaviruses suggested the most recent common ancestor of these viruses might have emerged either around 10,000 years ago or, using models accounting for selection, many millions of years. Here, we reassess the evolutionary history of these viruses. We present time-aware phylogenetic analyses of a RNA-dependent RNA polymerase locus from 123 orthocoronaviruses isolated from birds and bats, including those in New Zealand, which were geographically isolated from other bats around 35 million years ago. We used this age, as well as the age of the avian-mammals split, to calibrate the molecular clocks, under the assumption that these ages are applicable to the analyzed viruses. We found that the time to the most recent ancestor common for all orthocoronaviruses is likely 150 or more million years, supporting clock analyses that account for selection.
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Affiliation(s)
- David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand.
| | - Matthew A Knox
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand
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34
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Guzmán-Solís AA, Villa-Islas V, Bravo-López MJ, Sandoval-Velasco M, Wesp JK, Gómez-Valdés JA, Moreno-Cabrera MDLL, Meraz A, Solís-Pichardo G, Schaaf P, TenOever BR, Blanco-Melo D, Ávila Arcos MC. Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade. eLife 2021; 10:e68612. [PMID: 34350829 PMCID: PMC8423449 DOI: 10.7554/elife.68612] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
After the European colonization of the Americas, there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover the diversity of viral pathogens during this period, we designed an enrichment assay targeting ancient DNA (aDNA) from viruses of clinical importance and applied it to DNA extracts from individuals found in a Colonial hospital and a Colonial chapel (16th-18th century) where records suggest that victims of epidemics were buried during important outbreaks in Mexico City. This allowed us to reconstruct three ancient human parvovirus B19 genomes and one ancient human hepatitis B virus genome from distinct individuals. The viral genomes are similar to African strains, consistent with the inferred morphological and genetic African ancestry of the hosts as well as with the isotopic analysis of the human remains, suggesting an origin on the African continent. This study provides direct molecular evidence of ancient viruses being transported to the Americas during the transatlantic slave trade and their subsequent introduction to New Spain. Altogether, our observations enrich the discussion about the etiology of infectious diseases during the Colonial period in Mexico.
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Affiliation(s)
- Axel A Guzmán-Solís
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoQuerétaroMexico
| | - Viridiana Villa-Islas
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoQuerétaroMexico
| | - Miriam J Bravo-López
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoQuerétaroMexico
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health, University of CopenhagenCopenhagenDenmark
| | - Julie K Wesp
- Department of Sociology and Anthropology, North Carolina State UniversityRaleighUnited States
| | | | | | - Alejandro Meraz
- Instituto Nacional de Antropología e HistoriaMexico CityMexico
| | - Gabriela Solís-Pichardo
- Laboratorio Universitario de Geoquímica Isotópica (LUGIS), Instituto de Geología, Universidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Peter Schaaf
- LUGIS, Instituto de Geofísica, Universidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Benjamin R TenOever
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Daniel Blanco-Melo
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research CenterSeattle, WAUnited States
| | - María C Ávila Arcos
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoQuerétaroMexico
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35
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Campos PE, Groot Crego C, Boyer K, Gaudeul M, Baider C, Richard D, Pruvost O, Roumagnac P, Szurek B, Becker N, Gagnevin L, Rieux A. First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence. PLoS Pathog 2021; 17:e1009714. [PMID: 34324594 PMCID: PMC8320980 DOI: 10.1371/journal.ppat.1009714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/14/2021] [Indexed: 12/30/2022] Open
Abstract
Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.
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Affiliation(s)
- Paola E. Campos
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
- Herbier national (P), Muséum national d’Histoire naturelle, Paris, France
| | - Claudia Baider
- Ministry of Agro Industry and Food Security, Mauritius Herbarium, R.E. Vaughan Building (MSIRI compound), Agricultural Services, Réduit, Mauritius
| | | | | | - Philippe Roumagnac
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
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Roca-Rada X, Politis G, Messineo PG, Scheifler N, Scabuzzo C, González M, Harkins KM, Reich D, Souilmi Y, Teixeira JC, Llamas B, Fehren-Schmitz L. Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America. iScience 2021; 24:102553. [PMID: 34142055 PMCID: PMC8188552 DOI: 10.1016/j.isci.2021.102553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/26/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023] Open
Abstract
The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.
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Affiliation(s)
- Xavier Roca-Rada
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Pablo G. Messineo
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
| | - Nahuel Scheifler
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
| | - Clara Scabuzzo
- CICYTTP-CONICET, Provincia de Entre Ríos-UADER-División Arqueología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata. Dr. Materi y España (3105), Diamante, Entre Ríos Argentina
| | - Mariela González
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
| | - Kelly M. Harkins
- UCSC Paleogenomics Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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Featherstone LA, Di Giallonardo F, Holmes EC, Vaughan TG, Duchêne S. Infectious disease phylodynamics with occurrence data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13620] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Leo A. Featherstone
- Department of Microbiology and Immunology Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Vic. Australia
| | | | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and BiosecurityThe University of Sydney Sydney NSW Australia
- Charles Perkins Centre School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
- School of Medical Sciences The University of Sydney Sydney NSW Australia
| | - Timothy G. Vaughan
- Department of Biosystems Science and Engineering ETH Zurich Basel Switzerland
- Swiss Institute of Bioinformatics (SIB) Lausanne Switzerland
| | - Sebastián Duchêne
- Department of Microbiology and Immunology Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Vic. Australia
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38
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Duchene S, Lemey P, Stadler T, Ho SYW, Duchene DA, Dhanasekaran V, Baele G. Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations. Mol Biol Evol 2021; 37:3363-3379. [PMID: 32895707 PMCID: PMC7454806 DOI: 10.1093/molbev/msaa163] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here, we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) sampling times, and a model in which the samples are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behavior of this classification in analyses of five empirical data sets: modern samples of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus, and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.
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Affiliation(s)
- Sebastian Duchene
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | - Simon Y W Ho
- Swiss Institute of Bioinformatics, Basel, Switzerland.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - David A Duchene
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Vijaykrishna Dhanasekaran
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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Ingle DJ, Howden BP, Duchene S. Development of Phylodynamic Methods for Bacterial Pathogens. Trends Microbiol 2021; 29:788-797. [PMID: 33736902 DOI: 10.1016/j.tim.2021.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 11/30/2022]
Abstract
Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases. To date, the field has centered on viruses. Bacterial pathogens are seldom analyzed under such phylodynamic frameworks, due to their complex genome evolution and, until recently, a paucity of whole-genome sequence data sets with rich associated metadata. We posit that the increasing availability of bacterial genomes and epidemiological data means that the field is now ripe to lay the foundations for applying phylodynamics to bacterial pathogens. The development of new methods that integrate more complex genomic and ecological data will help to inform public heath surveillance and control strategies for bacterial pathogens that represent serious threats to human health.
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Affiliation(s)
- Danielle J Ingle
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
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Ghosh PN, Brookes LM, Edwards HM, Fisher MC, Jervis P, Kappel D, Sewell TR, Shelton JM, Skelly E, Rhodes JL. Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections. Life (Basel) 2020; 10:E315. [PMID: 33260763 PMCID: PMC7761180 DOI: 10.3390/life10120315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022] Open
Abstract
Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future.
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Affiliation(s)
- Pria N. Ghosh
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Lola M. Brookes
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
- Royal Veterinary College, Hawkshead Lane, North Mymms, Herts AL9 7TA, UK
| | - Hannah M. Edwards
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Phillip Jervis
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Dana Kappel
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Thomas R. Sewell
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Jennifer M.G. Shelton
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- UK Centre for Ecology & Hydrology, Wallingford OX10 8BB, UK
| | - Emily Skelly
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Johanna L. Rhodes
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
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Vandelannoote K, Pluschke G, Bolz M, Bratschi MW, Kerber S, Stinear TP, de Jong BC. Introduction of Mycobacterium ulcerans disease in the Bankim Health District of Cameroon follows damming of the Mapé River. PLoS Negl Trop Dis 2020; 14:e0008501. [PMID: 32886658 PMCID: PMC7473558 DOI: 10.1371/journal.pntd.0008501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/19/2020] [Indexed: 11/18/2022] Open
Abstract
Buruli ulcer (BU) is an emerging ulcerative skin disease caused by infection with Mycobacterium ulcerans. Efforts to control its spread have been hampered by our limited understanding of M. ulcerans reservoirs and transmission, and the factors leading to the emergence of BU disease in a particular region. In this report we investigate an anecdotal link between damming the Mapé River in Cameroon and the emergence of BU in the Health Districts bordering Lake Bankim, the impoundment created by the Mapé dam. We used bacterial population genomics and molecular dating to find compelling support for a 2000 M. ulcerans introduction event that followed about 10 years after the filling of the newly created impoundment in 1988. We compared the genomic reconstructions with high-resolution satellite imagery to investigate what major environmental alterations might have driven the emergence of the new focus.
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Affiliation(s)
- Koen Vandelannoote
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Gerd Pluschke
- Molecular Immunology, Swiss Tropical Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Miriam Bolz
- Molecular Immunology, Swiss Tropical Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Martin W. Bratschi
- Molecular Immunology, Swiss Tropical Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah Kerber
- Molecular Immunology, Swiss Tropical Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Bouke C. de Jong
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
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Majander K, Pfrengle S, Kocher A, Neukamm J, du Plessis L, Pla-Díaz M, Arora N, Akgül G, Salo K, Schats R, Inskip S, Oinonen M, Valk H, Malve M, Kriiska A, Onkamo P, González-Candelas F, Kühnert D, Krause J, Schuenemann VJ. Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe. Curr Biol 2020; 30:3788-3803.e10. [PMID: 32795443 DOI: 10.1016/j.cub.2020.07.058] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/24/2020] [Accepted: 07/16/2020] [Indexed: 12/30/2022]
Abstract
Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15th century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.
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Affiliation(s)
- Kerttu Majander
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland.
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany
| | - Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | | | - Marta Pla-Díaz
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zurich, Switzerland
| | - Gülfirde Akgül
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kati Salo
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland; Archaeology, Faculty of Arts, University of Helsinki, Unioninkatu 38F, 00014 Helsinki, Finland
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333CC Leiden, the Netherlands
| | - Sarah Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Markku Oinonen
- Laboratory of Chronology, Finnish Museum of Natural History, University of Helsinki, Gustaf Hällströmin katu 2, 00560 Helsinki, Finland
| | - Heiki Valk
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Tartumaa, Estonia
| | - Martin Malve
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Tartumaa, Estonia
| | - Aivar Kriiska
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Tartumaa, Estonia
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland; Department of Biology, University of Turku, Vesilinnantie 5, 20500 Turku, Finland
| | - Fernando González-Candelas
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Tübingen, Germany.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Tübingen, Germany.
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Kamau E, Otieno JR, Murunga N, Oketch JW, Ngoi JM, de Laurent ZR, Mwema A, Nyiro JU, Agoti CN, Nokes DJ. Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17. Virus Evol 2020; 6:veaa050. [PMID: 32913665 PMCID: PMC7474930 DOI: 10.1093/ve/veaa050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) circulates worldwide, occurring seasonally in communities, and is a leading cause of acute respiratory illness in young children. There is paucity of genomic data from purposively sampled populations by which to investigate evolutionary dynamics and transmission patterns of RSV. Here we present an analysis of 295 RSV group B (RSVB) genomes from Kilifi, coastal Kenya, sampled from individuals seeking outpatient care in nine health facilities across a defined geographical area (∼890 km2), over two RSV epidemics between 2015 and 2017. RSVB diversity was characterized by multiple virus introductions into the area and co-circulation of distinct genetic clusters, which transmitted and diversified locally with varying frequency. Increase in relative genetic diversity paralleled seasonal virus incidence. Importantly, we identified a cluster of viruses that emerged in the 2016/17 epidemic, carrying distinct amino-acid signatures including a novel nonsynonymous change (K68Q) in antigenic site ∅ in the Fusion protein. RSVB diversity was additionally marked by signature nonsynonymous substitutions that were unique to particular genomic clusters, some under diversifying selection. Our findings provide insights into recent evolutionary and epidemiological behaviors of RSVB, and highlight possible emergence of a novel antigenic variant, which has implications on current prophylactic strategies in development.
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Affiliation(s)
- Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - James R Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - John W Oketch
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce M Ngoi
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anthony Mwema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce U Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
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44
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Affiliation(s)
- Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
| | - Sebastián Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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45
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Dobelmann J, Felden A, Lester PJ. Genetic Strain Diversity of Multi-Host RNA Viruses that Infect a Wide Range of Pollinators and Associates is Shaped by Geographic Origins. Viruses 2020; 12:E358. [PMID: 32213950 PMCID: PMC7150836 DOI: 10.3390/v12030358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/16/2020] [Accepted: 03/21/2020] [Indexed: 01/29/2023] Open
Abstract
Emerging viruses have caused concerns about pollinator population declines, as multi-host RNA viruses may pose a health threat to pollinators and associated arthropods. In order to understand the ecology and impact these viruses have, we studied their host range and determined to what extent host and spatial variation affect strain diversity. Firstly, we used RT-PCR to screen pollinators and associates, including honey bees (Apis mellifera) and invasive Argentine ants (Linepithema humile), for virus presence and replication. We tested for the black queen cell virus (BQCV), deformed wing virus (DWV), and Kashmir bee virus (KBV) that were initially detected in bees, and the two recently discovered Linepithema humile bunya-like virus 1 (LhuBLV1) and Moku virus (MKV). DWV, KBV, and MKV were detected and replicated in a wide range of hosts and commonly co-infected hymenopterans. Secondly, we placed KBV and DWV in a global phylogeny with sequences from various countries and hosts to determine the association of geographic origin and host with shared ancestry. Both phylogenies showed strong geographic rather than host-specific clustering, suggesting frequent inter-species virus transmission. Transmission routes between hosts are largely unknown. Nonetheless, avoiding the introduction of non-native species and diseased pollinators appears important to limit spill overs and disease emergence.
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Affiliation(s)
- Jana Dobelmann
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; (A.F.); (P.J.L.)
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46
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van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Mol Biol Evol 2020; 37:773-785. [PMID: 31697387 PMCID: PMC7038659 DOI: 10.1093/molbev/msz264] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Adrien Rieux
- CIRAD, UMR PVBMT, St. Pierre de la Réunion, France
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Fregel
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Spain
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Population Health and Immunity Division, Walter & Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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Abstract
Discovering that chytrid fungi cause chytridiomycosis in amphibians represented a paradigm shift in our understanding of how emerging infectious diseases contribute to global patterns of biodiversity loss. In this Review we describe how the use of multidisciplinary biological approaches has been essential to pinpointing the origins of amphibian-parasitizing chytrid fungi, including Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, as well as to timing their emergence, tracking their cycles of expansion and identifying the core mechanisms that underpin their pathogenicity. We discuss the development of the experimental methods and bioinformatics toolkits that have provided a fuller understanding of batrachochytrid biology and informed policy and control measures.
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48
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Miura S, Tamura K, Tao Q, Huuki LA, Kosakovsky Pond SL, Priest J, Deng J, Kumar S. A new method for inferring timetrees from temporally sampled molecular sequences. PLoS Comput Biol 2020; 16:e1007046. [PMID: 31951607 PMCID: PMC7018096 DOI: 10.1371/journal.pcbi.1007046] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 02/13/2020] [Accepted: 12/09/2019] [Indexed: 12/11/2022] Open
Abstract
Pathogen timetrees are phylogenies scaled to time. They reveal the temporal history of a pathogen spread through the populations as captured in the evolutionary history of strains. These timetrees are inferred by using molecular sequences of pathogenic strains sampled at different times. That is, temporally sampled sequences enable the inference of sequence divergence times. Here, we present a new approach (RelTime with Dated Tips [RTDT]) to estimating pathogen timetrees based on a relative rate framework underlying the RelTime approach that is algebraic in nature and distinct from all other current methods. RTDT does not require many of the priors demanded by Bayesian approaches, and it has light computing requirements. In analyses of an extensive collection of computer-simulated datasets, we found the accuracy of RTDT time estimates and the coverage probabilities of their confidence intervals (CIs) to be excellent. In analyses of empirical datasets, RTDT produced dates that were similar to those reported in the literature. In comparative benchmarking with Bayesian and non-Bayesian methods (LSD, TreeTime, and treedater), we found that no method performed the best in every scenario. So, we provide a brief guideline for users to select the most appropriate method in empirical data analysis. RTDT is implemented for use via a graphical user interface and in high-throughput settings in the newest release of cross-platform MEGA X software, freely available from http://www.megasoftware.net. Pathogen timetrees trace the origins and evolutionary histories of strains in populations, hosts, and outbreaks. The tips of these molecular phylogenies often contain sampling time information because the sequences were generally obtained at different times during the disease outbreaks and propagation. We have developed a new method for inferring divergence times and confidence intervals for phylogenies with tip dates. The new Relative Times with Dated Tips (RTDT) methods showed excellent performance in the analysis of computer-simulated datasets, producing similar or better results in several evolutionary scenarios as compared to other fast, non-Bayesian methods. The new method is available in the cross-platform MEGA software package (version 10.1 and higher) that provides a graphical user interface and allows usage via a command line in scripting and high throughput analysis (www.megasoftware.net).
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Affiliation(s)
- Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Louise A. Huuki
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jessica Priest
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jiamin Deng
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
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49
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Jeong K, Muñoz-Bodnar A, Arias Rojas N, Poulin L, Rodriguez-R LM, Gagnevin L, Vernière C, Pruvost O, Koebnik R. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri. BMC Genomics 2019; 20:917. [PMID: 31791238 PMCID: PMC6889575 DOI: 10.1186/s12864-019-6267-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/06/2019] [Indexed: 12/26/2022] Open
Abstract
Background Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. Results We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. Conclusions CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.
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Affiliation(s)
- Kwanho Jeong
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Alejandra Muñoz-Bodnar
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Current address: Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Lucie Poulin
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Laboratoire de Biologie et de Pathologie Végétales, Université de Nantes, Nantes, France
| | - Luis Miguel Rodriguez-R
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Lionel Gagnevin
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,CIRAD, UMR PVBMT, 97410, Saint Pierre, La Réunion, France
| | - Christian Vernière
- CIRAD, UMR PVBMT, 97410, Saint Pierre, La Réunion, France.,CIRAD, UMR BGPI, 34398, Montpellier, France
| | | | - Ralf Koebnik
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.
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50
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Fang Y, Liu C, Lin J, Li X, Alavian KN, Yang Y, Niu Y. PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees. BMC Evol Biol 2019; 19:219. [PMID: 31791235 PMCID: PMC6889546 DOI: 10.1186/s12862-019-1541-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/13/2019] [Indexed: 02/05/2023] Open
Abstract
Background Phylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediate steps, such as processing extremely large sequences and preparing configure files to connect multiple software. When the species number is large, the intermediate steps become a bottleneck that may seriously affect the efficiency of tree building. Results Here, we present an easy-to-use pipeline named PhySpeTree to facilitate the reconstruction of species trees across bacterial, archaeal, and eukaryotic organisms. Users need only to input the abbreviations of species names; PhySpeTree prepares complex configure files for different software, then automatically downloads genomic data, cleans sequences, and builds trees. PhySpeTree allows users to perform critical steps such as sequence alignment and tree construction by adjusting advanced options. PhySpeTree provides two parallel pipelines based on concatenated highly conserved proteins and small subunit ribosomal RNA sequences, respectively. Accessory modules, such as those for inserting new species, generating visualization configurations, and combining trees, are distributed along with PhySpeTree. Conclusions Together with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). The source code is freely available with detailed documentation (https://github.com/yangfangs/physpetools).
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Affiliation(s)
- Yang Fang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases &Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiangyi Lin
- Wu YuZhang Honors College of Sichuan University, Chengdu, People's Republic of China
| | - Xufeng Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Kambiz N Alavian
- Department of Medicine, Division of Brain Sciences, Imperial College London, London, UK.,Department of Internal Medicine, Endocrinology, Yale University, New Haven, USA
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China.
| | - Yulong Niu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China.
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