1
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Topcu C, Vrancken B, Rodosthenous JH, van de Vijver D, Siakallis G, Lemey P, Kostrikis LG. Mapping Transmission Dynamics and Drug Resistance Surveillance in the Cyprus HIV-1 Epidemic (2017-2021). Viruses 2024; 16:1449. [PMID: 39339925 PMCID: PMC11437465 DOI: 10.3390/v16091449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 09/05/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) epidemic has been a major public health threat on a global scale since the early 1980s. Despite the introduction of combination antiretroviral therapy (cART), the incidence of new HIV-1 infections continues to rise in some regions around the world. Thus, with the continuous transmission of HIV-1 and the lack of a cure, it is imperative for molecular epidemiological studies to be performed, to monitor the infection and ultimately be able to control the spread of this virus. This work provides a comprehensive molecular epidemiological analysis of the HIV-1 infection in Cyprus, through examining 305 HIV-1 sequences collected between 9 March 2017 and 14 October 2021. Employing advanced statistical and bioinformatic techniques, the research delved deeply into understanding the transmission dynamics of the HIV-1 epidemic in Cyprus, as well as the monitoring of HIV-1's genetic diversity and the surveillance of transmitted drug resistance. The characterization of Cyprus's HIV-1 epidemic revealed a diverse landscape, comprising 21 HIV-1 group M pure subtypes and circulating recombinant forms (CRFs), alongside numerous uncharacterized recombinant strains. Subtypes A1 and B emerged as the most prevalent strains, followed by CRF02_AG. The findings of this study also revealed high levels of transmitted drug resistance (TDR) patterns, raising concerns for the efficacy of cART. The demographic profiles of individuals involved in HIV-1 transmission underscored the disproportionate burden borne by young to middle-aged Cypriot males, particularly those in the MSM community, who reported contracting the virus in Cyprus. An assessment of the spatiotemporal evolutionary dynamics illustrated the global interconnectedness of HIV-1 transmission networks, implicating five continents in the dissemination of strains within Cyprus: Europe, Africa, Asia, North America, and Oceania. Overall, this study advances the comprehension of the HIV-1 epidemic in Cyprus and highlights the importance of understanding HIV-1's transmission dynamics through continuous surveillance efforts. Furthermore, this work emphasizes the critical role of state-of-the-art bioinformatics analyses in addressing the challenges posed by HIV-1 transmission globally, laying the groundwork for public health interventions aimed at curbing its spread and improving patient outcomes.
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Affiliation(s)
- Cicek Topcu
- Laboratory of Biotechnology and Molecular Virology, Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
| | - Bram Vrancken
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Johana Hezka Rodosthenous
- Laboratory of Biotechnology and Molecular Virology, Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
| | - David van de Vijver
- Department of Viroscience, Erasmus University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | | | - Philippe Lemey
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Leondios G. Kostrikis
- Laboratory of Biotechnology and Molecular Virology, Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 1011 Nicosia, Cyprus
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2
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Kareinen L, Tammiranta N, Kauppinen A, Zecchin B, Pastori A, Monne I, Terregino C, Giussani E, Kaarto R, Karkamo V, Lähteinen T, Lounela H, Kantala T, Laamanen I, Nokireki T, London L, Helve O, Kääriäinen S, Ikonen N, Jalava J, Kalin-Mänttäri L, Katz A, Savolainen-Kopra C, Lindh E, Sironen T, Korhonen EM, Aaltonen K, Galiano M, Fusaro A, Gadd T. Highly pathogenic avian influenza A(H5N1) virus infections on fur farms connected to mass mortalities of black-headed gulls, Finland, July to October 2023. Euro Surveill 2024; 29:2400063. [PMID: 38904109 PMCID: PMC11191417 DOI: 10.2807/1560-7917.es.2024.29.25.2400063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/06/2024] [Indexed: 06/22/2024] Open
Abstract
Highly pathogenic avian influenza (HPAI) has caused widespread mortality in both wild and domestic birds in Europe 2020-2023. In July 2023, HPAI A(H5N1) was detected on 27 fur farms in Finland. In total, infections in silver and blue foxes, American minks and raccoon dogs were confirmed by RT-PCR. The pathological findings in the animals include widespread inflammatory lesions in the lungs, brain and liver, indicating efficient systemic dissemination of the virus. Phylogenetic analysis of Finnish A(H5N1) strains from fur animals and wild birds has identified three clusters (Finland I-III), and molecular analyses revealed emergence of mutations known to facilitate viral adaptation to mammals in the PB2 and NA proteins. Findings of avian influenza in fur animals were spatially and temporally connected with mass mortalities in wild birds. The mechanisms of virus transmission within and between farms have not been conclusively identified, but several different routes relating to limited biosecurity on the farms are implicated. The outbreak was managed in close collaboration between animal and human health authorities to mitigate and monitor the impact for both animal and human health.
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Affiliation(s)
| | | | | | - Bianca Zecchin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Ambra Pastori
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Edoardo Giussani
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | | | | | | | | | | | | | | | | | - Otto Helve
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Sohvi Kääriäinen
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Niina Ikonen
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Jari Jalava
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Laura Kalin-Mänttäri
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Anna Katz
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Carita Savolainen-Kopra
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Erika Lindh
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Tarja Sironen
- University of Helsinki, Department of Veterinary Biosciences, Helsinki, Finland
| | - Essi M Korhonen
- University of Helsinki, Department of Veterinary Biosciences, Helsinki, Finland
| | - Kirsi Aaltonen
- University of Helsinki, Department of Veterinary Biosciences, Helsinki, Finland
| | - Monica Galiano
- Worldwide Influenza Centre, Francis Crick Institute, London, United Kingdom
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Tuija Gadd
- Finnish Food Authority (FFA), Helsinki, Finland
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3
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Fusaro A, Zecchin B, Giussani E, Palumbo E, Agüero-García M, Bachofen C, Bálint Á, Banihashem F, Banyard AC, Beerens N, Bourg M, Briand FX, Bröjer C, Brown IH, Brugger B, Byrne AMP, Cana A, Christodoulou V, Dirbakova Z, Fagulha T, Fouchier RAM, Garza-Cuartero L, Georgiades G, Gjerset B, Grasland B, Groza O, Harder T, Henriques AM, Hjulsager CK, Ivanova E, Janeliunas Z, Krivko L, Lemon K, Liang Y, Lika A, Malik P, McMenamy MJ, Nagy A, Nurmoja I, Onita I, Pohlmann A, Revilla-Fernández S, Sánchez-Sánchez A, Savic V, Slavec B, Smietanka K, Snoeck CJ, Steensels M, Svansson V, Swieton E, Tammiranta N, Tinak M, Van Borm S, Zohari S, Adlhoch C, Baldinelli F, Terregino C, Monne I. High pathogenic avian influenza A(H5) viruses of clade 2.3.4.4b in Europe-Why trends of virus evolution are more difficult to predict. Virus Evol 2024; 10:veae027. [PMID: 38699215 PMCID: PMC11065109 DOI: 10.1093/ve/veae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/26/2024] [Indexed: 05/05/2024] Open
Abstract
Since 2016, A(H5Nx) high pathogenic avian influenza (HPAI) virus of clade 2.3.4.4b has become one of the most serious global threats not only to wild and domestic birds, but also to public health. In recent years, important changes in the ecology, epidemiology, and evolution of this virus have been reported, with an unprecedented global diffusion and variety of affected birds and mammalian species. After the two consecutive and devastating epidemic waves in Europe in 2020-2021 and 2021-2022, with the second one recognized as one of the largest epidemics recorded so far, this clade has begun to circulate endemically in European wild bird populations. This study used the complete genomes of 1,956 European HPAI A(H5Nx) viruses to investigate the virus evolution during this varying epidemiological outline. We investigated the spatiotemporal patterns of A(H5Nx) virus diffusion to/from and within Europe during the 2020-2021 and 2021-2022 epidemic waves, providing evidence of ongoing changes in transmission dynamics and disease epidemiology. We demonstrated the high genetic diversity of the circulating viruses, which have undergone frequent reassortment events, providing for the first time a complete overview and a proposed nomenclature of the multiple genotypes circulating in Europe in 2020-2022. We described the emergence of a new genotype with gull adapted genes, which offered the virus the opportunity to occupy new ecological niches, driving the disease endemicity in the European wild bird population. The high propensity of the virus for reassortment, its jumps to a progressively wider number of host species, including mammals, and the rapid acquisition of adaptive mutations make the trend of virus evolution and spread difficult to predict in this unfailing evolving scenario.
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Affiliation(s)
- Alice Fusaro
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Bianca Zecchin
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Edoardo Giussani
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Elisa Palumbo
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Montserrat Agüero-García
- Ministry of Agriculture, Fisheries and Food, Laboratorio Central de Veterinaria (LCV), Ctra. M-106, Km 1,4 Algete, Madrid 28110, Spain
| | - Claudia Bachofen
- Federal Department of Home Affairs FDHA Institute of Virology and Immunology IVI, Sensemattstrasse 293, Mittelhäusern 3147, Switzerland
| | - Ádám Bálint
- Veterinary Diagnostic Directorate (NEBIH), Laboratory of Virology, National Food Chain Safety Office, Tábornok utca 2, Budapest 1143, Hungary
| | - Fereshteh Banihashem
- Department of Microbiology, National Veterinary Institute (SVA), Travvägen 20, Uppsala 75189, Sweden
| | - Ashley C Banyard
- WOAH/FAO international reference laboratory for Avian Influenza and Newcastle Disease, Virology Department, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, United Kingdom
| | - Nancy Beerens
- Department of Virology Wageningen Bioveterinary Research, Houtribweg 39, Lelystad 8221 RA, The Netherlands
| | - Manon Bourg
- Luxembourgish Veterinary and Food Administration (ALVA), State Veterinary Laboratory, 1 Rue Louis Rech, Dudelange 3555, Luxembourg
| | - Francois-Xavier Briand
- Agence Nationale de Sécurité Sanitaire, de l’Alimentation, de l’Environnement et du Travail, Laboratoire de Ploufragan-Plouzané-Niort, Unité de Virologie, Immunologie, Parasitologie Avaires et Cunicoles, 41 Rue de Beaucemaine – BP 53, Ploufragan 22440, France
| | - Caroline Bröjer
- Department of Pathology and Wildlife Disease, National Veterinary Institute (SVA), Travvägen 20, Uppsala 75189, Sweden
| | - Ian H Brown
- WOAH/FAO international reference laboratory for Avian Influenza and Newcastle Disease, Virology Department, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, United Kingdom
| | - Brigitte Brugger
- Icelandic Food and Veterinary Authority, Austurvegur 64, Selfoss 800, Iceland
| | - Alexander M P Byrne
- WOAH/FAO international reference laboratory for Avian Influenza and Newcastle Disease, Virology Department, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, United Kingdom
| | - Armend Cana
- Kosovo Food and Veterinary Agency, Sector of Serology and Molecular Diagnostics, Kosovo Food and Veterinary Laboratory, Str Lidhja e Pejes, Prishtina 10000, Kosovo
| | - Vasiliki Christodoulou
- Laboratory for Animal Health Virology Section Veterinary Services (1417), 79, Athalassa Avenue Aglantzia, Nicosia 2109, Cyprus
| | - Zuzana Dirbakova
- Department of Animal Health, State Veterinary Institute, Pod Dráhami 918, Zvolen 96086, Slovakia
| | - Teresa Fagulha
- I.P. (INIAV, I.P.), Avenida da República, Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, Oeiras 2780 – 157, Portugal
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, Dr. Molewaterplein 40, Rotterdam 3015 GD, The Netherlands
| | - Laura Garza-Cuartero
- Department of Agriculture, Food and the Marine, Central Veterinary Research Laboratory (CVRL), Backweston Campus, Stacumny Lane, Celbridge, Co. Kildare W23 X3PH, Ireland
| | - George Georgiades
- Thessaloniki Veterinary Centre (TVC), Department of Avian Diseases, 26th October Street 80, Thessaloniki 54627, Greece
| | - Britt Gjerset
- Immunology & Virology department, Norwegian Veterinary Institute, Arboretveien 57, Oslo Pb 64, N-1431 Ås, Norway
| | - Beatrice Grasland
- Agence Nationale de Sécurité Sanitaire, de l’Alimentation, de l’Environnement et du Travail, Laboratoire de Ploufragan-Plouzané-Niort, Unité de Virologie, Immunologie, Parasitologie Avaires et Cunicoles, 41 Rue de Beaucemaine – BP 53, Ploufragan 22440, France
| | - Oxana Groza
- Republican Center for Veterinary Diagnostics (NRL), 3 street Murelor, Chisinau 2051, Republic of Moldova
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Ana Margarida Henriques
- I.P. (INIAV, I.P.), Avenida da República, Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, Oeiras 2780 – 157, Portugal
| | - Charlotte Kristiane Hjulsager
- Department for Virus and Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, Copenhagen DK-2300, Denmark
| | - Emiliya Ivanova
- National Reference Laboratory for Avian Influenza and Newcastle Disease, National Diagnostic and Research Veterinary Medical Institute (NDRVMI), 190 Lomsko Shose Blvd., Sofia 1231, Bulgaria
| | - Zygimantas Janeliunas
- National Food and Veterinary Risk Assessment Institute (NFVRAI), Kairiukscio str. 10, Vilnius 08409, Lithuania
| | - Laura Krivko
- Institute of Food Safety, Animal Health and Environment (BIOR), Laboratory of Microbilogy and Pathology, 3 Lejupes Street, Riga 1076, Latvia
| | - Ken Lemon
- Virological Molecular Diagnostic Laboratory, Veterinary Sciences Division, Department of Virology, Agri-Food and Bioscience Institute (AFBI), Stoney Road, Belfast BT4 3SD, Northern Ireland
| | - Yuan Liang
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, Frederiksberg 1870, Denmark
| | - Aldin Lika
- Animal Health Department, Food Safety and Veterinary Institute, Rruga Aleksandër Moisiu 10, Tirana 1001, Albania
| | - Péter Malik
- Veterinary Diagnostic Directorate (NEBIH), Laboratory of Virology, National Food Chain Safety Office, Tábornok utca 2, Budapest 1143, Hungary
| | - Michael J McMenamy
- Virological Molecular Diagnostic Laboratory, Veterinary Sciences Division, Department of Virology, Agri-Food and Bioscience Institute (AFBI), Stoney Road, Belfast BT4 3SD, Northern Ireland
| | - Alexander Nagy
- Department of Molecular Biology, State Veterinary Institute Prague, Sídlištní 136/24, Praha 6-Lysolaje 16503, Czech Republic
| | - Imbi Nurmoja
- National Centre for Laboratory Research and Risk Assessment (LABRIS), Kreutzwaldi 30, Tartu 51006, Estonia
| | - Iuliana Onita
- Institute for Diagnosis and Animal Health (IDAH), Str. Dr. Staicovici 63, Bucharest 050557, Romania
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Sandra Revilla-Fernández
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control, Robert Koch Gasse 17, Mödling 2340, Austria
| | - Azucena Sánchez-Sánchez
- Ministry of Agriculture, Fisheries and Food, Laboratorio Central de Veterinaria (LCV), Ctra. M-106, Km 1,4 Algete, Madrid 28110, Spain
| | - Vladimir Savic
- Croatian Veterinary Institute, Poultry Centre, Heinzelova 55, Zagreb 10000, Croatia
| | - Brigita Slavec
- University of Ljubljana – Veterinary Faculty/National Veterinary Institute, Gerbičeva 60, Ljubljana 1000, Slovenia
| | - Krzysztof Smietanka
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantow 57, Puławy 24-100, Poland
| | - Chantal J Snoeck
- Luxembourg Institute of Health (LIH), Department of Infection and Immunity, 29 Rue Henri Koch, Esch-sur-Alzette 4354, Luxembourg
| | - Mieke Steensels
- Avian Virology and Immunology, Sciensano, Rue Groeselenberg 99, Ukkel 1180, Ukkel, Belgium
| | - Vilhjálmur Svansson
- Biomedical Center, Institute for Experimental Pathology, University of Iceland, Keldnavegi 3 112 Reykjavík Ssn. 650269 4549, Keldur 851, Iceland
| | - Edyta Swieton
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantow 57, Puławy 24-100, Poland
| | - Niina Tammiranta
- Finnish Food Authority, Animal Health Diagnostic Unit, Veterinary Virology, Mustialankatu 3, Helsinki FI-00790, Finland
| | - Martin Tinak
- Department of Animal Health, State Veterinary Institute, Pod Dráhami 918, Zvolen 96086, Slovakia
| | - Steven Van Borm
- Avian Virology and Immunology, Sciensano, Rue Groeselenberg 99, Ukkel 1180, Ukkel, Belgium
| | - Siamak Zohari
- Department of Microbiology, National Veterinary Institute (SVA), Travvägen 20, Uppsala 75189, Sweden
| | - Cornelia Adlhoch
- European Centre for Disease Prevention and Control, Gustav III:s boulevard 40, Solna 169 73, Sweden
| | | | - Calogero Terregino
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
| | - Isabella Monne
- European Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'universita 10, Legnaro, Padua 35020, Italy
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Zhang G, Cui C, Wangdue S, Lu H, Chen H, Xi L, He W, Yuan H, Tsring T, Chen Z, Yang F, Tsering T, Li S, Tashi N, Yang T, Tong Y, Wu X, Li L, He Y, Cao P, Dai Q, Liu F, Feng X, Wang T, Yang R, Ping W, Zhang M, Gao X, Liu Y, Wang W, Fu Q. Maternal genetic history of ancient Tibetans over the past 4000 years. J Genet Genomics 2023; 50:765-775. [PMID: 36933795 DOI: 10.1016/j.jgg.2023.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians vary over the past 4000 years, with a stronger matrilineal connection between the two during 4000 BP-3000 BP, and a weakened connection after 3000 BP, that are coincident with climate change, followed by a reinforced connection after the Tubo period (1400 BP-1100 BP). Besides, an over 4000-year matrilineal continuity is observed in some of the maternal lineages. We also find the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that are dynamically shaped by geography, climate changes, as well as historical events.
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Affiliation(s)
- Ganyu Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Can Cui
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Hongliang Lu
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Lin Xi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Haibing Yuan
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Feng Yang
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tashi Tsering
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Shuai Li
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Tsho Yang
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Linhui Li
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yuanhong He
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ming Zhang
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Science and Technology Archaeology, National Centre for Archaeology, Beijing 100013, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Qi Zhi Institute, Shanghai 200232, China.
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5
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Jones BR, Joy JB. Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference. Mol Biol Evol 2023; 40:msad156. [PMID: 37421655 PMCID: PMC10411489 DOI: 10.1093/molbev/msad156] [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: 11/18/2022] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV) proviruses archived in the persistent reservoir currently pose the greatest obstacle to HIV cure due to their evasion of combined antiretroviral therapy and ability to reseed HIV infection. Understanding the dynamics of the HIV persistent reservoir is imperative for discovering a durable HIV cure. Here, we explore Bayesian methods using the software BEAST2 to estimate HIV proviral integration dates. We started with within-host longitudinal HIV sequences collected prior to therapy, along with sequences collected from the persistent reservoir during suppressive therapy. We built a BEAST2 model to estimate integration dates of proviral sequences collected during suppressive therapy, implementing a tip date random walker to adjust the sequence tip dates and a latency-specific prior to inform the dates. To validate our method, we implemented it on both simulated and empirical data sets. Consistent with previous studies, we found that proviral integration dates were spread throughout active infection. Path sampling to select an alternative prior for date estimation in place of the latency-specific prior produced unrealistic results in one empirical data set, whereas on another data set, the latency-specific prior was selected as best fitting. Our Bayesian method outperforms current date estimation techniques with a root mean squared error of 0.89 years on simulated data relative to 1.23-1.89 years with previously developed methods. Bayesian methods offer an adaptable framework for inferring proviral integration dates.
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Affiliation(s)
- Bradley R Jones
- Molecular Epidemiology and Evolutionary Genetics, B.C. Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, Canada
| | - Jeffrey B Joy
- Molecular Epidemiology and Evolutionary Genetics, B.C. Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, Canada
- Deparment of Medicine, University of British Columbia, Vancouver, Canada
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6
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Barido-Sottani J, Żyła D, Heath TA. Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process. Syst Biol 2023; 72:466-475. [PMID: 36382797 PMCID: PMC10275547 DOI: 10.1093/sysbio/syac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/04/2022] [Indexed: 02/02/2024] Open
Abstract
Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical data sets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical data set of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical data sets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits. [Bayesian phylogenetic inference; fossil age estimates; fossilized birth-death; Lagerstätte; total-evidence.].
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Affiliation(s)
- Joëlle Barido-Sottani
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, IA 50011, USA
- Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, 75005 Paris, France
| | - Dagmara Żyła
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, IA 50011, USA
- Department of Invertebrate Zoology and Parasitology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
- Museum of Nature Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Tracy A Heath
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, IA 50011, USA
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7
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de Moraes L, Portilho MM, Vrancken B, Van den Broeck F, Santos LA, Cucco M, Tauro LB, Kikuti M, Silva MMO, Campos GS, Reis MG, Barral A, Barral-Netto M, Boaventura VS, Vandamme AM, Theys K, Lemey P, Ribeiro GS, Khouri R. Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas. Viruses 2023; 15:1236. [PMID: 37376536 DOI: 10.3390/v15061236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The Americas, particularly Brazil, were greatly impacted by the widespread Zika virus (ZIKV) outbreak in 2015 and 2016. Efforts were made to implement genomic surveillance of ZIKV as part of the public health responses. The accuracy of spatiotemporal reconstructions of the epidemic spread relies on the unbiased sampling of the transmission process. In the early stages of the outbreak, we recruited patients exhibiting clinical symptoms of arbovirus-like infection from Salvador and Campo Formoso, Bahia, in Northeast Brazil. Between May 2015 and June 2016, we identified 21 cases of acute ZIKV infection and subsequently recovered 14 near full-length sequences using the amplicon tiling multiplex approach with nanopore sequencing. We performed a time-calibrated discrete phylogeographic analysis to trace the spread and migration history of the ZIKV. Our phylogenetic analysis supports a consistent relationship between ZIKV migration from Northeast to Southeast Brazil and its subsequent dissemination beyond Brazil. Additionally, our analysis provides insights into the migration of ZIKV from Brazil to Haiti and the role Brazil played in the spread of ZIKV to other countries, such as Singapore, the USA, and the Dominican Republic. The data generated by this study enhances our understanding of ZIKV dynamics and supports the existing knowledge, which can aid in future surveillance efforts against the virus.
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Affiliation(s)
- Laise de Moraes
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Moyra M Portilho
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Department of Biomedical Sciences, Antwerp Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Luciane Amorim Santos
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Escola Bahiana de Medicina e Saúde Pública, Salvador 41150-100, Brazil
| | - Marina Cucco
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Laura B Tauro
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Instituto de Biología Subtropical, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Misiones, Puerto Iguazú N3370, Argentina
| | - Mariana Kikuti
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Monaise M O Silva
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Gúbio S Campos
- Laboratório de Virologia, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador 40231-300, Brazil
| | - Mitermayer G Reis
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Departamento de Patologia e Medicina Legal, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40110-100, Brazil
| | - Aldina Barral
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Manoel Barral-Netto
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Viviane Sampaio Boaventura
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Hospital Santa Izabel, Salvador 40050-410, Brazil
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
| | - Kristof Theys
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| | - Guilherme S Ribeiro
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Departamento de Medicina Preventiva e Social, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40110-100, Brazil
| | - Ricardo Khouri
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
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8
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Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AMA, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 2022; 612:283-291. [PMID: 36477129 PMCID: PMC9729109 DOI: 10.1038/s41586-022-05453-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
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Affiliation(s)
- Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Binia De Cahsan
- Section for Molecular Ecology and Evolution, The Globe Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian S Michelsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karina K Sand
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, Université Gustave Eiffel, ISTerre, Grenoble, France
| | - Anthony H Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Astrid M A Schmidt
- Nordic Foundation for Development and Ecology (NORDECO), Copenhagen, Denmark
- DIS Study Abroad in Scandinavia, University of Copenhagen, Copenhagen, Denmark
| | - Kristian K Kjeldsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Alexey S Tesakov
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Ian Snowball
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - John C Gosse
- Department of Earth and Environmental Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Yucheng Wang
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Ana Prohaska
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jeppe Å Kristensen
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
- Geological Survey of Denmark and Greenland, (GEUS), Copenhagen, Denmark
| | - Morten Bjerager
- Department of Geophysics and Sedimentary Basins, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Eric Coissac
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
- University of Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Alexandra Rouillard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL, Paris, France
| | - Marc Macias-Fauria
- School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alan J Hidy
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew J Collins
- Department of Archaeology, University of Cambridge, Cambridge, UK
- Section for GeoBiology, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolaj K Larsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM, University of Bremen, Bremen, Germany.
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9
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Emergence of a Reassortant 2.3.4.4b Highly Pathogenic H5N1 Avian Influenza Virus Containing H9N2 PA Gene in Burkina Faso, West Africa, in 2021. Viruses 2022; 14:v14091901. [PMID: 36146708 PMCID: PMC9504354 DOI: 10.3390/v14091901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 12/30/2022] Open
Abstract
Since 2006, the poultry population in Burkina Faso has been seriously hit by different waves of Highly Pathogenic Avian Influenza (HPAI) H5N1 epizootics. In December 2021, three distinct regions of Burkina Faso, namely, Gomboussougou, Bonyollo, and Koubri, detected HPAI H5N1 viruses in poultry. Whole genome characterization and statistical phylogenetic approaches were applied to shed light on the potential origin of these viruses and estimate the time of virus emergence. Our results revealed that the HPAI H5N1 viruses reported in the three affected regions of Burkina Faso cluster together within clade 2.3.4.4b, and are closely related to HPAI H5N1 viruses identified in Nigeria and Niger in the period 2021–2022, except for the PA gene, which clusters with H9N2 viruses of the zoonotic G1 lineage collected in West Africa between 2017 and 2020. These reassortant viruses possess several mutations that may be associated with an increased zoonotic potential. Although it is difficult to ascertain where and when the reassortment event occurred, the emergence of a H5N1/H9N2 reassortant virus in a vulnerable region, such as West Africa, raises concerns about its possible impact on animal and human health. These findings also highlight the risk that West Africa may become a new hotspot for the emergence of new genotypes of HPAI viruses.
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10
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Gräf T, Bello G, Naveca FG, Gomes M, Cardoso VLO, da Silva AF, Dezordi FZ, dos Santos MC, Santos KCDO, Batista ÉLR, Magalhães ALÁ, Vinhal F, Miyajima F, Faoro H, Khouri R, Wallau GL, Delatorre E, Siqueira MM, Resende PC. Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil. iScience 2022; 25:104156. [PMID: 35368908 PMCID: PMC8957357 DOI: 10.1016/j.isci.2022.104156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/23/2022] [Accepted: 03/21/2022] [Indexed: 11/03/2022] Open
Abstract
The COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56-3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59-3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil.
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Affiliation(s)
- Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Leônidas e Maria Deane Institute, Fiocruz, Manaus, Brazil
| | - Marcelo Gomes
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Programa de Computação Científica (PROCC), Fiocruz, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | | | - Fábio Miyajima
- Fundação Oswaldo Cruz - Fiocruz Ceará, Fortaleza, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas (ICC), Fiocruz-PR, Curitiba, Parana, Brazil
| | - Ricardo Khouri
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Gabriel Luz Wallau
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Edson Delatorre
- Departamento de Biologia. Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
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11
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Jia S, Long X, Hu W, Zhu J, Jiang Y, Ahmed S, de Hoog GS, Liu W, Jiang Y. The epidemic of the multiresistant dermatophyte Trichophyton indotineae has reached China. Front Immunol 2022; 13:1113065. [PMID: 36874152 PMCID: PMC9978415 DOI: 10.3389/fimmu.2022.1113065] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/28/2022] [Indexed: 02/18/2023] Open
Abstract
Due to its high degree of natural resistance to terbinafine in vitro and its tendency to spread globally from the Indian subcontinent, the emerging dermatophyte Trichophyton indotineae has become a major concern in dermatology. Herein, we present the first report of T. indotineae from mainland China. The transmission of the fungus to Guizhou Province in central China and eventual host susceptibilities were investigated. We studied 31 strains of the T. mentagrophytes complex from outpatient clinics of our hospital collected during the past 5 years. The set comprised four ITS genotypes, two of which were T. mentagrophytes genotype VIII, now known as Trichophyton indotineae; the earliest isolation in the Guiyang area appeared to date back to 2018. The isolate was derived from an Indian patient, while local Chinese patients had no dermatophytosis caused by this genotype. Reports from around the world indicated that almost all of the globally reported T. indotineae cases originated from the Indian subcontinent and surrounding countries without transmission among native populations, suggesting deviating local conditions or racial differences in immunity against this fungus.
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Affiliation(s)
- Songgan Jia
- Department of Dermatology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.,Department of Microbiology, Basic Medical School, Guizhou Medical University, Guiyang, China
| | - Xuemei Long
- Department of Dermatology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Wei Hu
- Department of Dermatology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.,Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Jiali Zhu
- Department of Dermatology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.,Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Yinhui Jiang
- Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Sarah Ahmed
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - G Sybren de Hoog
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Weida Liu
- Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Infectious Dermatology Group, Jiangsu Key Laboratory of Molecular Biology of Skin and STIs, Nanjing, Jiangsu, China
| | - Yanping Jiang
- Department of Dermatology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.,Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, Netherlands
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12
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Lack of evolutionary changes identified in SARS-CoV-2 for the re-emerging outbreak of COVID-19 in Beijing, china. BIOSAFETY AND HEALTH 2021; 4:1-5. [PMID: 34977529 PMCID: PMC8709725 DOI: 10.1016/j.bsheal.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 12/02/2022] Open
Abstract
Although significant achievements have shown that the coronavirus disease 2019 (COVID-19) resurgence in Beijing, China, was initiated by contaminated frozen products and transported via cold chain transportation, international travelers with asymptomatic symptoms or false-negative nucleic acid may have another possible transmission mode that spread the virus to Beijing. One of the key differences between these two assumptions was whether the virus actively replicated since, so far, no reports showed viruses could stop evolution in alive hosts. We studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences in this outbreak by a modified leaf-dating method with the Bayes factor. The numbers of single nucleotide variants (SNVs) found in SARS-CoV-2 sequences were significantly lower than those called from B.1.1 records collected at the matching time worldwide (P = 0.047). In addition, results of the leaf-dating method showed ages of viruses sampled from this outbreak were earlier than their recorded dates of collection (Bayes factors > 10), while control sequences (selected randomly with ten replicates) showed no differences in their collection dates (Bayes factors < 10). Our results which indicated that the re-emergence of SARS-CoV-2 in Beijing in June 2020 was caused by a virus that exhibited a lack of evolutionary changes compared to viruses collected at the corresponding time, provided evolutionary evidence to the contaminated imported frozen food should be responsible for the reappearance of COVID-19 cases in Beijing. The method developed here might also be helpful to provide the very first clues for potential sources of COVID-19 cases in the future.
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13
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Calvignac-Spencer S, Düx A, Gogarten JF, Patrono LV. Molecular archeology of human viruses. Adv Virus Res 2021; 111:31-61. [PMID: 34663498 DOI: 10.1016/bs.aivir.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The evolution of human-virus associations is usually reconstructed from contemporary patterns of genomic diversity. An intriguing, though still rarely implemented, alternative is to search for the genetic material of viruses in archeological and medical archive specimens to document evolution as it happened. In this chapter, we present lessons from ancient DNA research and incorporate insights from virology to explore the potential range of applications and likely limitations of archeovirological approaches. We also highlight the numerous questions archeovirology will hopefully allow us to tackle in the near future, and the main expected roadblocks to these avenues of research.
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Affiliation(s)
- Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany.
| | - Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany
| | - Jan F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany
| | - Livia V Patrono
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany
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14
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Doan K, Niedziałkowska M, Stefaniak K, Sykut M, Jędrzejewska B, Ratajczak-Skrzatek U, Piotrowska N, Ridush B, Zachos FE, Popović D, Baca M, Mackiewicz P, Kosintsev P, Makowiecki D, Charniauski M, Boeskorov G, Bondarev AA, Danila G, Kusak J, Rannamäe E, Saarma U, Arakelyan M, Manaseryan N, Krasnodębski D, Titov V, Hulva P, Bălășescu A, Trantalidou K, Dimitrijević V, Shpansky A, Kovalchuk O, Klementiev AM, Foronova I, Malikov DG, Juras A, Nikolskiy P, Grigoriev SE, Cheprasov MY, Novgorodov GP, Sorokin AD, Wilczyński J, Protopopov AV, Lipecki G, Stanković A. Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b, including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum.
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Affiliation(s)
- Karolina Doan
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, S. Banacha 2C, 02-097 Warsaw, Poland
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warsaw, Poland
| | | | - Krzysztof Stefaniak
- Department of Palaeozoology, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Maciej Sykut
- Mammal Research Institute Polish Academy of Sciences, Stoczek 1c, 17-230 Białowieża, Poland
| | - Bogumiła Jędrzejewska
- Mammal Research Institute Polish Academy of Sciences, Stoczek 1c, 17-230 Białowieża, Poland
| | | | - Natalia Piotrowska
- Radiocarbon Laboratory Institute of Physics–Center for Science and Education, Silesian University of Technology, Konarskiego 22b,44-100 Gliwice, Poland
| | - Bogdan Ridush
- Department of Physical Geography, Geomorphology and Paleogeography, Yuriy Fedkovych Chernivtsi National University, Kotsubynskogo 2, Chernivtsi 58012, Ukraine
| | - Frank E Zachos
- Natural History Museum Vienna, 1010 Vienna, Austria
- Department of Genetics, University of the Free State, 9301 Bloemfontein, South Africa
- Department of Evolutionary Biology, University of Vienna, 1090 Vienna, Austria
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Mateusz Baca
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta 202, Yekaterinburg 620144, Russia
| | - Daniel Makowiecki
- Nicolaus Copernicus University, Institute of Archaeology, Department of Historical Sciences, Szosa Bydgoska 44/48, 87-100 Toruń, Poland
| | - Maxim Charniauski
- Institute of History of the National Academy of Sciences of Belarus, Academic 1, 220072 Minsk, Belarus
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of Russian Academy of Sciences, Yakutsk, Yakutia, Russian Federation
| | | | - Gabriel Danila
- Universitatea Stefan cel Mare Suceava, Facultatea de Silvicultura, Suceava, Romania
| | - Josip Kusak
- Veterinary Faculty, University of Zagreb, 10000 Zagreb, Croatia
| | - Eve Rannamäe
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Marine Arakelyan
- Yerevan State University, Faculty of Biology, Department of Zoology, Alex Manoogian 1, 0025 Yerevan, Republic of Armenia
| | - Ninna Manaseryan
- The Scientific Center of Zoology and Hydroecology of National Academy of Sciences of Armenia, P. Sevak 7, Yerevan 0014, Republic of Armenia
| | - Dariusz Krasnodębski
- Institute of Archaeology and Ethnology Polish Academy of Sciences, Al. Solidarności 105, 00-140 Warsaw, Poland
| | - Vadim Titov
- Southern Scientific Centre Russian Academy of Sciences, Chekhov 41, Rostov-on-Don 344006, Russian Federation
| | - Pavel Hulva
- Charles University in Prague, Department of Zoology, Viničná 1594/7, 128 00 Nové Město, Prague, Czech Republic
- University of Ostrava, Department of Biology and Ecology, Chittussiho 10, 710 00 Slezská Ostrava, Czech Republic
| | - Adrian Bălășescu
- ’Vasile Pârvan’ Institute of Archaeology, Romanian Academy, Henri Coandă 11, 010667 Bucharest, Romania
| | | | - Vesna Dimitrijević
- Laboratory for Bioarchaeology, Department of Archaeology, Faculty of Philosophy, University of Belgrade, Čika Ljubina 18-20, 11000 Belgrade, Serbia
| | - Andrey Shpansky
- Department of Palaeontology and Historical Geology, Tomsk State University, 634050 Tomsk, Russian Federation
| | - Oleksandr Kovalchuk
- Department of Paleontology, National Museum of Natural History National Academy of Sciences of Ukraine, 15 B. Khmelnytsky 15, Kyiv 01030Ukraine
| | - Alexey M Klementiev
- Institute of the Earth’s Crust, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russian Federation
| | - Irina Foronova
- V. S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Koptyuga pr. 3, Novosibirsk, Russian Federation
| | - Dmitriy G Malikov
- V. S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Koptyuga pr. 3, Novosibirsk, Russian Federation
| | - Anna Juras
- Institute of Human Biology & Evolution, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Pavel Nikolskiy
- Laboratory of Quaternary Stratigraphy, Geological Institute, Russian Academy of Sciences, 119017 Moscow, Russia
| | - Semyon Egorovich Grigoriev
- Laboratory of P. A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University named after M. K. Ammosov, Building of Faculties of Natural Sciences (KFEN), 48 Kulakovsky Str., 677000 Yakutsk, Republic of Sakha (Yakutia), Russian Federation
| | - Maksim Yurievich Cheprasov
- Laboratory of P. A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University named after M. K. Ammosov, Building of Faculties of Natural Sciences (KFEN), 48 Kulakovsky Str., 677000 Yakutsk, Republic of Sakha (Yakutia), Russian Federation
| | - Gavril Petrovich Novgorodov
- Laboratory of P. A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University named after M. K. Ammosov, Building of Faculties of Natural Sciences (KFEN), 48 Kulakovsky Str., 677000 Yakutsk, Republic of Sakha (Yakutia), Russian Federation
| | | | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Cracow, Poland
| | - Albert Vasilievich Protopopov
- Department of Study of Mammoth Fauna, Academy of Science of Sakha Republic (Yakutia), Lenin Avenue 33, Yakutsk, 677027, Republic of Sakha (Yakutia), Russian Federation
| | - Grzegorz Lipecki
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Cracow, Poland
| | - Ana Stanković
- Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
- The Antiquity of Southeastern Europe Research Centre, University of Warsaw, Krakowskie Przedmieście 32, 00-927 Warsaw, Poland
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15
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Chrysostomou AC, Vrancken B, Koumbaris G, Themistokleous G, Aristokleous A, Masia C, Eleftheriou C, Iοannou C, Stylianou DC, Ioannides M, Petrou P, Georgiou V, Hatziyianni A, Lemey P, Vandamme AM, Patsalis PP, Kostrikis LG. A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Viruses 2021; 13:1098. [PMID: 34207490 PMCID: PMC8227210 DOI: 10.3390/v13061098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 12/19/2022] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial outbreak on the island. In this study, we performed a comprehensive retrospective molecular epidemiological analysis (genetic, phylogenetic, phylodynamic and phylogeographic analyses) of SARS-CoV-2 isolates in Cyprus from April 2020 to January 2021, covering the first ten months of the SARS-CoV-2 infection epidemic on the island. The primary aim of this study was to assess the transmissibility of SARS-CoV-2 lineages in Cyprus. Whole SARS-CoV-2 genomic sequences were generated from 596 clinical samples (nasopharyngeal swabs) obtained from community-based diagnostic testing centers and hospitalized patients. The phylogenetic analyses revealed a total of 34 different lineages in Cyprus, with B.1.258, B.1.1.29, B.1.177, B.1.2, B.1 and B.1.1.7 (designated a Variant of Concern 202012/01, VOC) being the most prevalent lineages on the island during the study period. Phylodynamic analysis showed a highly dynamic epidemic of SARS-CoV-2 infection, with three consecutive surges characterized by specific lineages (B.1.1.29 from April to June 2020; B.1.258 from September 2020 to January 2021; and B.1.1.7 from December 2020 to January 2021). Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, ΔH69/V70, S898F, ΔY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. Phylogeographic analysis indicated that the majority of imports and exports were to and from the United Kingdom (UK), although many other regions/countries were identified (southeastern Asia, southern Europe, eastern Europe, Germany, Italy, Brazil, Chile, the USA, Denmark, the Czech Republic, Slovenia, Finland, Switzerland and Pakistan). Taken together, these findings demonstrate that the SARS-CoV-2 infection epidemic in Cyprus is being maintained by a continuous influx of lineages from many countries, resulting in the establishment of an ever-evolving and polyphyletic virus on the island.
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Affiliation(s)
- Andreas C. Chrysostomou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (B.V.); (P.L.); (A.-M.V.)
| | - George Koumbaris
- NIPD Genetics Limited, Nicosia 2409, Cyprus; (G.K.); (M.I.); (P.P.P.)
| | - George Themistokleous
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Christina Masia
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Christina Eleftheriou
- Department of Health and Safety, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus;
| | - Costakis Iοannou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Marios Ioannides
- NIPD Genetics Limited, Nicosia 2409, Cyprus; (G.K.); (M.I.); (P.P.P.)
| | - Panagiotis Petrou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Vasilis Georgiou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
| | - Amalia Hatziyianni
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, Paralimni 5386, Cyprus; (G.T.); (C.M.); (C.I.); (P.P.); (A.H.)
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (B.V.); (P.L.); (A.-M.V.)
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (B.V.); (P.L.); (A.-M.V.)
- Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
| | - Philippos P. Patsalis
- NIPD Genetics Limited, Nicosia 2409, Cyprus; (G.K.); (M.I.); (P.P.P.)
- Medical School, University of Nicosia, Nicosia 2417, Cyprus
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus; (A.C.C.); (A.A.); (D.C.S.); (V.G.)
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16
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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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17
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Jones BR, Joy JB. Simulating within host human immunodeficiency virus 1 genome evolution in the persistent reservoir. Virus Evol 2020; 6:veaa089. [PMID: 34040795 PMCID: PMC8132731 DOI: 10.1093/ve/veaa089] [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: 12/31/2022] Open
Abstract
The complexities of viral evolution can be difficult to elucidate. Software simulating viral evolution provides powerful tools for exploring hypotheses of viral systems, especially in situations where thorough empirical data are difficult to obtain or parameters of interest are difficult to measure. Human immunodeficiency virus 1 (HIV-1) infection has no durable cure; this is primarily due to the virus’ ability to integrate into the genome of host cells, where it can remain in a transcriptionally latent state. An effective cure strategy must eliminate every copy of HIV-1 in this ‘persistent reservoir’ because proviruses can reactivate, even decades later, to resume an active infection. However, many features of the persistent reservoir remain unclear, including the temporal dynamics of HIV-1 integration frequency and the longevity of the resulting reservoir. Thus, sophisticated analyses are required to measure these features and determine their temporal dynamics. Here, we present software that is an extension of SANTA-SIM to include multiple compartments of viral populations. We used the resulting software to create a model of HIV-1 within host evolution that incorporates the persistent HIV-1 reservoir. This model is composed of two compartments, an active compartment and a latent compartment. With this model, we compared five different date estimation methods (Closest Sequence, Clade, Linear Regression, Least Squares, and Maximum Likelihood) to recover the integration dates of genomes in our model’s HIV-1 reservoir. We found that the Least Squares method performed the best with the highest concordance (0.80) between real and estimated dates and the lowest absolute error (all pairwise t tests: P < 0.01). Our software is a useful tool for validating bioinformatics software and understanding the dynamics of the persistent HIV-1 reservoir.
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Affiliation(s)
- Bradley R Jones
- BC Centre for Excellence in HIV/AIDS, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, 608-1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
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18
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Duchêne S, Ho SYW, Carmichael AG, Holmes EC, Poinar H. The Recovery, Interpretation and Use of Ancient Pathogen Genomes. Curr Biol 2020; 30:R1215-R1231. [PMID: 33022266 PMCID: PMC7534838 DOI: 10.1016/j.cub.2020.08.081] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest - pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) - and for three equally important endemic human disease agents - Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.
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Affiliation(s)
- Sebastián Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L9, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada.
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19
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Karpinski E, Hackenberger D, Zazula G, Widga C, Duggan AT, Golding GB, Kuch M, Klunk J, Jass CN, Groves P, Druckenmiller P, Schubert BW, Arroyo-Cabrales J, Simpson WF, Hoganson JW, Fisher DC, Ho SYW, MacPhee RDE, Poinar HN. American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations. Nat Commun 2020; 11:4048. [PMID: 32873779 PMCID: PMC7463256 DOI: 10.1038/s41467-020-17893-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 07/24/2020] [Indexed: 12/27/2022] Open
Abstract
Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures. Pleistocene population dynamics can inform the consequences of current climate change. This phylogeography of 35 complete American mastodon mitochondrial genomes suggests distinct lineages in this species repeatedly expanded northwards and then went locally extinct in response to glacial cycles.
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Affiliation(s)
- Emil Karpinski
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada. .,Department of Biology, McMaster University, Hamilton, ON, L8S 4L8, Canada.
| | - Dirk Hackenberger
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada.,Department of Biochemistry, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism and Culture, Government of Yukon, Whitehorse, YT, Y1A 2C6, Canada.,Research and Collections, Canadian Museum of Nature, Ottawa, ON, K2P 2R1, Canada
| | - Chris Widga
- Center of Excellence in Paleontology and Department of Geosciences, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada.,Department of Anthropology, McMaster University, Hamilton, ON, L8S 4L9, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada.,Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - Christopher N Jass
- Quaternary Palaeontology Program, Royal Alberta Museum, Edmonton, T5J 0G2, Canada
| | - Pam Groves
- Institute of Arctic Biology, University of Alaska Fairbanks, Alaska, AK, 99775, USA
| | - Patrick Druckenmiller
- Department of Geosciences, University of Alaska Fairbanks, Alaska, AK, 99775, USA.,University of Alaska Museum, University of Alaska Fairbanks, Alaska, AK, 99775, USA
| | - Blaine W Schubert
- Center of Excellence in Paleontology and Department of Geosciences, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoologia, SLAA, Instituto Nacional de Antropología e Historia, Ciudad de México, 06600, México
| | - William F Simpson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, IL, 60605, USA
| | | | - Daniel C Fisher
- Museum of Paleontology and Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Ross D E MacPhee
- Department of Mammalogy/Vertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, ON, L8S 4L9, Canada. .,Department of Biochemistry, McMaster University, Hamilton, ON, L8S 4L8, Canada. .,Department of Anthropology, McMaster University, Hamilton, ON, L8S 4L9, Canada.
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20
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A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue. Proc Natl Acad Sci U S A 2020; 117:12222-12229. [PMID: 32430331 DOI: 10.1073/pnas.1913682117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long prediscovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,645 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Central Africa between 1958 and 1966. We report the near-complete viral genome in one HIV-1 positive specimen from Kinshasa, Democratic Republic of Congo (DRC), from 1966 ("DRC66")-a nonrecombinant sister lineage to subtype C that constitutes the oldest HIV-1 near full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of the DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978 to 2014, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to a time period around the turn of the 20th century (1881 to 1918). In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.
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21
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Faulkner JR, Magee AF, Shapiro B, Minin VN. Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories. Biometrics 2020; 76:677-690. [PMID: 32277713 DOI: 10.1111/biom.13276] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 04/26/2019] [Accepted: 07/09/2019] [Indexed: 11/26/2022]
Abstract
Phylodynamics is an area of population genetics that uses genetic sequence data to estimate past population dynamics. Modern state-of-the-art Bayesian nonparametric methods for recovering population size trajectories of unknown form use either change-point models or Gaussian process priors. Change-point models suffer from computational issues when the number of change-points is unknown and needs to be estimated. Gaussian process-based methods lack local adaptivity and cannot accurately recover trajectories that exhibit features such as abrupt changes in trend or varying levels of smoothness. We propose a novel, locally adaptive approach to Bayesian nonparametric phylodynamic inference that has the flexibility to accommodate a large class of functional behaviors. Local adaptivity results from modeling the log-transformed effective population size a priori as a horseshoe Markov random field, a recently proposed statistical model that blends together the best properties of the change-point and Gaussian process modeling paradigms. We use simulated data to assess model performance, and find that our proposed method results in reduced bias and increased precision when compared to contemporary methods. We also use our models to reconstruct past changes in genetic diversity of human hepatitis C virus in Egypt and to estimate population size changes of ancient and modern steppe bison. These analyses show that our new method captures features of the population size trajectories that were missed by the state-of-the-art methods.
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Affiliation(s)
- James R Faulkner
- Quantitative Ecology and Resource Management, University of Washington, Seattle, Washington.,Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington
| | - Andrew F Magee
- Department of Biology, University of Washington, Seattle, Washington
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department and Genomics Institute, University of California Santa Cruz, Santa Cruz, California.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California
| | - Vladimir N Minin
- Department of Statistics, University of California Irvine, Irvine, California
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22
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Naito YI, Meleg IN, Robu M, Vlaicu M, Drucker DG, Wißing C, Hofreiter M, Barlow A, Bocherens H. Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis. Sci Rep 2020; 10:6612. [PMID: 32313007 PMCID: PMC7170912 DOI: 10.1038/s41598-020-62990-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Heavy reliance on plants is rare in Carnivora and mostly limited to relatively small species in subtropical settings. The feeding behaviors of extinct cave bears living during Pleistocene cold periods at middle latitudes have been intensely studied using various approaches including isotopic analyses of fossil collagen. In contrast to cave bears from all other regions in Europe, some individuals from Romania show exceptionally high δ15N values that might be indicative of meat consumption. Herbivory on plants with high δ15N values cannot be ruled out based on this method, however. Here we apply an approach using the δ15N values of individual amino acids from collagen that offsets the baseline δ15N variation among environments. The analysis yielded strong signals of reliance on plants for Romanian cave bears based on the δ15N values of glutamate and phenylalanine. These results could suggest that the high variability in bulk collagen δ15N values observed among cave bears in Romania reflects niche partitioning but in a general trophic context of herbivory.
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Affiliation(s)
- Yuichi I Naito
- Department of Geosciences, Biogeology, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany.
- Nagoya University Museum, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Ioana N Meleg
- "Emil Racoviță" Institute of Speleology, Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania.
| | - Marius Robu
- "Emil Racoviță" Institute of Speleology, Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania
| | - Marius Vlaicu
- "Emil Racoviță" Institute of Speleology, Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany
| | - Christoph Wißing
- Department of Geosciences, Biogeology, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, OT Golm, Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, OT Golm, Germany
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Hervé Bocherens
- Department of Geosciences, Biogeology, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany
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23
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Wohl S, Metsky HC, Schaffner SF, Piantadosi A, Burns M, Lewnard JA, Chak B, Krasilnikova LA, Siddle KJ, Matranga CB, Bankamp B, Hennigan S, Sabina B, Byrne EH, McNall RJ, Shah RR, Qu J, Park DJ, Gharib S, Fitzgerald S, Barreira P, Fleming S, Lett S, Rota PA, Madoff LC, Yozwiak NL, MacInnis BL, Smole S, Grad YH, Sabeti PC. Combining genomics and epidemiology to track mumps virus transmission in the United States. PLoS Biol 2020; 18:e3000611. [PMID: 32045407 PMCID: PMC7012397 DOI: 10.1371/journal.pbio.3000611] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/03/2020] [Indexed: 01/24/2023] Open
Abstract
Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. We paired epidemiological data from public health investigations with analysis of mumps virus whole genome sequences from 201 infected individuals, focusing on Massachusetts university communities. Our analysis suggests continuous, undetected circulation of mumps locally and nationally, including multiple independent introductions into Massachusetts and into individual communities. Despite the presence of these multiple mumps virus lineages, the genomic data show that one lineage has dominated in the US since at least 2006. Widespread transmission was surprising given high vaccination rates, but we found no genetic evidence that variants arising during this outbreak contributed to vaccine escape. Viral genomic data allowed us to reconstruct mumps transmission links not evident from epidemiological data or standard single-gene surveillance efforts and also revealed connections between apparently unrelated mumps outbreaks.
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Affiliation(s)
- Shirlee Wohl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Hayden C. Metsky
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Stephen F. Schaffner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Anne Piantadosi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Meagan Burns
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Joseph A. Lewnard
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Bridget Chak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Lydia A. Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Christian B. Matranga
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Bettina Bankamp
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Scott Hennigan
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Brandon Sabina
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Elizabeth H. Byrne
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Rebecca J. McNall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rickey R. Shah
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - James Qu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Daniel J. Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Soheyla Gharib
- Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America
| | - Susan Fitzgerald
- Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America
| | - Paul Barreira
- Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America
| | - Stephen Fleming
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Susan Lett
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Paul A. Rota
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lawrence C. Madoff
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nathan L. Yozwiak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Bronwyn L. MacInnis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sandra Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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24
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Thomas JE, Carvalho GR, Haile J, Rawlence NJ, Martin MD, Ho SYW, Sigfússon AÞ, Jósefsson VA, Frederiksen M, Linnebjerg JF, Samaniego Castruita JA, Niemann J, Sinding MHS, Sandoval-Velasco M, Soares AER, Lacy R, Barilaro C, Best J, Brandis D, Cavallo C, Elorza M, Garrett KL, Groot M, Johansson F, Lifjeld JT, Nilson G, Serjeanston D, Sweet P, Fuller E, Hufthammer AK, Meldgaard M, Fjeldså J, Shapiro B, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLife 2019; 8:e47509. [PMID: 31767056 PMCID: PMC6879203 DOI: 10.7554/elife.47509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/22/2019] [Indexed: 01/23/2023] Open
Abstract
The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
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Affiliation(s)
- Jessica E Thomas
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
| | - James Haile
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Michael D Martin
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Simon YW Ho
- School of Life and Environmental SciencesUniversity of SydneySydneyAustralia
| | | | | | | | | | | | - Jonas Niemann
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Mikkel-Holger S Sinding
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Greenland Institute of Natural ResourcesNuukGreenland
| | | | - André ER Soares
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Robert Lacy
- Department of Conservation ScienceChicago Zoological SocietyBrookfieldUnited States
| | | | - Juila Best
- Department of Archaeology, Anthropology and Forensic Science, Faculty of Science and TechnologyBournemouth UniversityPooleUnited Kingdom
- School of History, Archaeology and ReligionCardiff UniversityCardiffUnited Kingdom
| | | | - Chiara Cavallo
- Amsterdam Centre for Ancient Studies and ArchaeologyUniversity of AmsterdamAmsterdamNetherlands
| | - Mikelo Elorza
- Arqueología PrehistóricaSociedad de Ciencias AranzadiSan SebastiánSpain
| | - Kimball L Garrett
- Natural History Museum of Los Angeles CountyLos AngelesUnited States
| | - Maaike Groot
- Institut für Prähistorische ArchäologieFreie Universität BerlinBerlinGermany
| | | | | | - Göran Nilson
- Gothenburg Museum of Natural HistoryGothenburgSweden
| | - Dale Serjeanston
- Humanities ArchaeologyUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Paul Sweet
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkUnited States
| | | | | | | | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural SciencesUniversity of PotsdamPotsdamGermany
| | - John R Stewart
- Faculty of Science and TechnologyBournemouth UniversityDorsetUnited Kingdom
| | - M Thomas P Gilbert
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Michael Knapp
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
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25
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Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza. Nat Commun 2019; 10:5310. [PMID: 31757953 PMCID: PMC6874648 DOI: 10.1038/s41467-019-13287-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022] Open
Abstract
The role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.
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26
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Hostager R, Ragonnet-Cronin M, Murrell B, Hedskog C, Osinusi A, Susser S, Sarrazin C, Svarovskaia E, Wertheim JO. Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage. Virus Evol 2019; 5:vez041. [PMID: 31616569 PMCID: PMC6785677 DOI: 10.1093/ve/vez041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recombination is an important driver of genetic diversity, though it is relatively uncommon in hepatitis C virus (HCV). Recent investigation of sequence data acquired from HCV clinical trials produced twenty-one full-genome recombinant viruses belonging to three putative inter-subtype forms 2b/1a, 2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating recombinant form (CRF), provoking interest in its genetic structure and origin. Discovered in Russia in 1999, 2k/1b cases have since been detected throughout the former Soviet Union, Western Europe, and North America. Although 2k/1b prevalence is highest in the Caucasus mountain region (i.e., Armenia, Azerbaijan, and Georgia), the origin and migration patterns of CRF 2k/1b have remained obscure due to a paucity of available sequences. We assembled an alignment which spans the entire coding region of the HCV genome containing all available 2k/1b sequences (>500 nucleotides; n = 109) sampled in ninteen countries from public databases (102 individuals), additional newly sequenced genomic regions (from 48 of these 102 individuals), unpublished isolates with newly sequenced regions (5 additional individuals), and novel complete genomes (2 additional individuals) generated in this study. Analysis of this expanded dataset reconfirmed the monophyletic origin of 2k/1b with a recombination breakpoint at position 3,187 (95% confidence interval: 3,172–3,202; HCV GT1a reference strain H77). Phylogeography is a valuable tool used to reveal viral migration dynamics. Inference of the timed history of spread in a Bayesian framework identified Russia as the ancestral source of the CRF 2k/1b clade. Further, we found evidence for migration routes leading out of Russia to other former Soviet Republics or countries under the Soviet sphere of influence. These findings suggest an interplay between geopolitics and the historical spread of CRF 2k/1b.
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Affiliation(s)
- Reilly Hostager
- Department of Medicine, University of California, San Diego, CA, USA
| | | | - Ben Murrell
- Department of Medicine, University of California, San Diego, CA, USA
| | | | | | - Simone Susser
- Goethe-University Hospital, Medical Clinic, Frankfurt, Germany
| | - Christoph Sarrazin
- Gilead Sciences, Foster City, CA, USA.,St. Josefs-Hospital, Medical Clinic 2, Wiesbaden, Germany
| | | | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA, USA
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27
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Yuen LKW, Littlejohn M, Duchêne S, Edwards R, Bukulatjpi S, Binks P, Jackson K, Davies J, Davis JS, Tong SYC, Locarnini S. Tracing Ancient Human Migrations into Sahul Using Hepatitis B Virus Genomes. Mol Biol Evol 2019; 36:942-954. [PMID: 30856252 DOI: 10.1093/molbev/msz021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The entry point and timing of ancient human migration into continental Sahul (the combined landmass of Australia, New Guinea, and Tasmania) are subject to debate. Unique strains of hepatitis B virus (HBV) are endemic among modern-day Australian Aboriginals (HBV/C4) and Indigenous Melanesians (HBV/C3). We postulated that HBV genomes could be used to infer human population movements because the main HBV transmission route in endemic populations is via mother-to-child for genotypes B and C infections. Phylogenetic and phylogeographic analyses of HBV genomes inferred the origin of HBV/C4 to be >59 thousand years ago (ka) (95% HPD: 34-85 ka), and most likely to have occurred on the Sunda Shelf (southeast extension of the continental shelf of Southeast Asia). Our analysis further suggested an age of >51 ka (95% Highest Posterior Density (HPD): 36-67 ka) for the most recent common ancestor of HBV/C4 in Australia, correlating with the arrival time of anatomically modern humans into Australia, with the entry point suggested along a southern route via Timor. While we also inferred the origin of HBC/C3 to be on the Sunda Shelf, our analyses suggested that it was carried into Melanesia by Indigenous Melanesians who migrated through New Guinea north of the highlands. These findings reveal that HBV genomes can be used to infer ancient human population movements.
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Affiliation(s)
- Lilly K W Yuen
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Rosalind Edwards
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Sarah Bukulatjpi
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,Ngalkanbuy Clinic, Galiwin'ku, Australia
| | - Paula Binks
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Kathy Jackson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Jane Davies
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Australia
| | - Joshua S Davis
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,John Hunter Hospital, Newcastle, Australia
| | - Steven Y C Tong
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Australia.,Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Stephen Locarnini
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
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28
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Bletsa M, Suchard MA, Ji X, Gryseels S, Vrancken B, Baele G, Worobey M, Lemey P. Divergence dating using mixed effects clock modelling: An application to HIV-1. Virus Evol 2019; 5:vez036. [PMID: 31720009 PMCID: PMC6830409 DOI: 10.1093/ve/vez036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The need to estimate divergence times in evolutionary histories in the presence of various sources of substitution rate variation has stimulated a rich development of relaxed molecular clock models. Viral evolutionary studies frequently adopt an uncorrelated clock model as a generic relaxed molecular clock process, but this may impose considerable estimation bias if discrete rate variation exists among clades or lineages. For HIV-1 group M, rate variation among subtypes has been shown to result in inconsistencies in time to the most recent common ancestor estimation. Although this calls into question the adequacy of available molecular dating methods, no solution to this problem has been offered so far. Here, we investigate the use of mixed effects molecular clock models, which combine both fixed and random effects in the evolutionary rate, to estimate divergence times. Using simulation, we demonstrate that this model outperforms existing molecular clock models in a Bayesian framework for estimating time-measured phylogenies in the presence of mixed sources of rate variation, while also maintaining good performance in simpler scenarios. By analysing a comprehensive HIV-1 group M complete genome data set we confirm considerable rate variation among subtypes that is not adequately modelled by uncorrelated relaxed clock models. The mixed effects clock model can accommodate this rate variation and results in a time to the most recent common ancestor of HIV-1 group M of 1920 (1915-25), which is only slightly earlier than the uncorrelated relaxed clock estimate for the same data set. The use of complete genome data appears to have a more profound impact than the molecular clock model because it reduces the credible intervals by 50 per cent relative to similar estimates based on short envelope gene sequences.
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Affiliation(s)
- Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
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29
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Xavier J, Giovanetti M, Fonseca V, Thézé J, Gräf T, Fabri A, Goes de Jesus J, Lima de Mendonça MC, Damasceno dos Santos Rodrigues C, Mares-Guia MA, Cardoso dos Santos C, Fraga de Oliveira Tosta S, Candido D, Ribeiro Nogueira RM, Luiz de Abreu A, Kleber Oliveira W, Campelo de Albuquerque CF, Chieppe A, de Oliveira T, Brasil P, Calvet G, Carvalho Sequeira P, Rodrigues Faria N, Bispo de Filippis AM, Alcantara LCJ. Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil. PLoS One 2019; 14:e0217871. [PMID: 31185030 PMCID: PMC6559644 DOI: 10.1371/journal.pone.0217871] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/20/2019] [Indexed: 12/14/2022] Open
Abstract
The emergence of chikungunya virus (CHIKV) has raised serious concerns due to the virus' rapid dissemination into new geographic areas and the clinical features associated with infection. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. To better understand CHIKV dynamics in Rio de Janeiro, we generated 11 near-complete genomes by means of real-time portable nanopore sequencing of virus isolates obtained directly from clinical samples. Our phylogenetic reconstructions indicated the circulation of the East-Central-South-African (ECSA) lineage in Rio de Janeiro. Time-measured phylogenetic analysis combined with CHIKV notified case numbers revealed the ECSA lineage was introduced in Rio de Janeiro around June 2015 (95% Bayesian credible interval: May to July 2015) indicating the virus was circulating unnoticed for 5 months before the first reports of CHIKV autochthonous transmissions in Rio de Janeiro, in November 2015. These findings reinforce that continued genomic surveillance strategies are needed to assist in the monitoring and understanding of arbovirus epidemics, which might help to attenuate public health impact of infectious diseases.
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Affiliation(s)
- Joilson Xavier
- Laboratório de Patologia Experimental, Instituto Gonçalo Moniz/Fiocruz, Salvador, Bahia, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Tiago Gräf
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Allison Fabri
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Jaqueline Goes de Jesus
- Laboratório de Patologia Experimental, Instituto Gonçalo Moniz/Fiocruz, Salvador, Bahia, Brazil
| | | | | | | | | | - Stephane Fraga de Oliveira Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Darlan Candido
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - André Luiz de Abreu
- Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | | | | | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Patrícia Brasil
- Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, Brazil
| | - Guilherme Calvet
- Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, Brazil
| | | | | | | | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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30
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Rey-Iglesia A, García-Vázquez A, Treadaway EC, van der Plicht J, Baryshnikov GF, Szpak P, Bocherens H, Boeskorov GG, Lorenzen ED. Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains. Sci Rep 2019; 9:4462. [PMID: 30872771 PMCID: PMC6418263 DOI: 10.1038/s41598-019-40168-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/04/2019] [Indexed: 12/24/2022] Open
Abstract
Over 60% of the modern distribution range of brown bears falls within Russia, yet palaeoecological data from the region remain scarce. Complete modern Russian brown bear mitogenomes are abundant in the published literature, yet examples of their ancient counterparts are absent. Similarly, there is only limited stable isotopic data of prehistoric brown bears from the region. We used ancient DNA and stable carbon (δ13C) and nitrogen (δ15N) isotopes retrieved from five Pleistocene Yakutian brown bears (one Middle Pleistocene and four Late Pleistocene), to elucidate the evolutionary history and palaeoecology of the species in the region. We were able to reconstruct the complete mitogenome of one of the Late Pleistocene specimens, but we were unable to assign it to any of the previously published brown bear mitogenome clades. A subsequent analysis of published mtDNA control region sequences, which included sequences of extinct clades from other geographic regions, assigned the ancient Yakutian bear to the extinct clade 3c; a clade previously identified from Late Quaternary specimens from Eastern Beringia and Northern Spain. Our analyses of stable isotopes showed relatively high δ15N values in the Pleistocene Yakutian brown bears, suggesting a more carnivorous diet than contemporary brown bears from Eastern Beringia.
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Affiliation(s)
- Alba Rey-Iglesia
- Natural History Museum of Denmark, University of Copenhagen, DK-1350, Copenhagen K, Denmark.
| | - Ana García-Vázquez
- Instituto de Xeoloxía Isidro Parga Pondal, ESCI, Campus de Elviña, Universidade da Coruña, 15071A, Coruña, Spain
| | - Eve C Treadaway
- Natural History Museum of Denmark, University of Copenhagen, DK-1350, Copenhagen K, Denmark
| | | | | | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, Ontario, K9L 0G2, Canada
| | - Hervé Bocherens
- Department of Geosciences, Tübingen University, 72074, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, 72074, Tübingen, Germany
| | - Gennady G Boeskorov
- Diamond and Precious Metals Geology Institute, Siberian Branch of Russian Academy of Sciences, 677980, Yakutsk, Russia
| | - Eline D Lorenzen
- Natural History Museum of Denmark, University of Copenhagen, DK-1350, Copenhagen K, Denmark.
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31
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Vai S, Sarno S, Lari M, Luiselli D, Manzi G, Gallinaro M, Mataich S, Hübner A, Modi A, Pilli E, Tafuri MA, Caramelli D, di Lernia S. Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara. Sci Rep 2019; 9:3530. [PMID: 30837540 PMCID: PMC6401177 DOI: 10.1038/s41598-019-39802-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/30/2019] [Indexed: 11/16/2022] Open
Abstract
Because Africa's climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. These individuals carry a novel mutation motif linked to the haplogroup N root. Our result demonstrates the presence of an ancestral lineage of the N haplogroup in the Holocene "Green Sahara", associated to a Middle Pastoral (Neolithic) context.
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Affiliation(s)
- Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Giorgio Manzi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Marina Gallinaro
- Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy
| | - Safaa Mataich
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Alexander Hübner
- Max-Planck-Institute for Evolutionary Anthropology, Department Evolutionary Genetics, Leipzig, Germany
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy
| | - Elena Pilli
- Department of Biology, University of Florence, Florence, Italy
| | - Mary Anne Tafuri
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy.
| | - Savino di Lernia
- Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy.
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa.
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32
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Devièse T, Massilani D, Yi S, Comeskey D, Nagel S, Nickel B, Ribechini E, Lee J, Tseveendorj D, Gunchinsuren B, Meyer M, Pääbo S, Higham T. Compound-specific radiocarbon dating and mitochondrial DNA analysis of the Pleistocene hominin from Salkhit Mongolia. Nat Commun 2019; 10:274. [PMID: 30700710 PMCID: PMC6353915 DOI: 10.1038/s41467-018-08018-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/04/2018] [Indexed: 12/04/2022] Open
Abstract
A skullcap found in the Salkhit Valley in northeast Mongolia is, to our knowledge, the only Pleistocene hominin fossil found in the country. It was initially described as an individual with possible archaic affinities, but its ancestry has been debated since the discovery. Here, we determine the age of the Salkhit skull by compound-specific radiocarbon dating of hydroxyproline to 34,950-33,900 Cal. BP (at 95% probability), placing the Salkhit individual in the Early Upper Paleolithic period. We reconstruct the complete mitochondrial genome (mtDNA) of the specimen. It falls within a group of modern human mtDNAs (haplogroup N) that is widespread in Eurasia today. The results now place the specimen into its proper chronometric and biological context and allow us to begin integrating it with other evidence for the human occupation of this region during the Paleolithic, as well as wider Pleistocene sequences across Eurasia.
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Affiliation(s)
- Thibaut Devièse
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK.
| | - Diyendo Massilani
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
| | - Seonbok Yi
- Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Korea
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK
| | - Sarah Nagel
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Birgit Nickel
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Erika Ribechini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Jungeun Lee
- Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Korea
| | - Damdinsuren Tseveendorj
- Institute of History and Archaeology, Mongolian Academy of Sciences, Jucov St 77, Ulaanbaatar, 13343, Mongolia
| | - Byambaa Gunchinsuren
- Institute of History and Archaeology, Mongolian Academy of Sciences, Jucov St 77, Ulaanbaatar, 13343, Mongolia
| | - Matthias Meyer
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Svante Pääbo
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK
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33
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Phylogenetic approach to recover integration dates of latent HIV sequences within-host. Proc Natl Acad Sci U S A 2018; 115:E8958-E8967. [PMID: 30185556 PMCID: PMC6156657 DOI: 10.1073/pnas.1802028115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Given that HIV evolution and latent reservoir establishment occur continually within-host, and that latently infected cells can persist long-term, the HIV reservoir should comprise a genetically heterogeneous archive recapitulating within-host HIV evolution. However, this has yet to be conclusively demonstrated, in part due to the challenges of reconstructing within-host reservoir establishment dynamics over long timescales. We developed a phylogenetic framework to reconstruct the integration dates of individual latent HIV lineages. The framework first involves inference and rooting of a maximum-likelihood phylogeny relating plasma HIV RNA sequences serially sampled before the initiation of suppressive antiretroviral therapy, along with putative latent sequences sampled thereafter. A linear model relating root-to-tip distances of plasma HIV RNA sequences to their sampling dates is used to convert root-to-tip distances of putative latent lineages to their establishment (integration) dates. Reconstruction of the ages of putative latent sequences sampled from chronically HIV-infected individuals up to 10 y following initiation of suppressive therapy revealed a genetically heterogeneous reservoir that recapitulated HIV's within-host evolutionary history. Reservoir sequences were interspersed throughout multiple within-host lineages, with the oldest dating to >20 y before sampling; historic genetic bottleneck events were also recorded therein. Notably, plasma HIV RNA sequences isolated from a viremia blip in an individual receiving otherwise suppressive therapy were highly genetically diverse and spanned a 20-y age range, suggestive of spontaneous in vivo HIV reactivation from a large latently infected cell pool. Our framework for reservoir dating provides a potentially powerful addition to the HIV persistence research toolkit.
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34
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Phylogeny, ecology and taxonomy of systemic pathogens and their relatives in Ajellomycetaceae (Onygenales): Blastomyces, Emergomyces, Emmonsia, Emmonsiellopsis. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0403-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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35
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Tong KJ, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW. A comparison of methods for estimating substitution rates from ancient DNA sequence data. BMC Evol Biol 2018; 18:70. [PMID: 29769015 PMCID: PMC5956955 DOI: 10.1186/s12862-018-1192-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/04/2018] [Indexed: 12/02/2022] Open
Abstract
Background Phylogenetic analysis of DNA from modern and ancient samples allows the reconstruction of important demographic and evolutionary processes. A critical component of these analyses is the estimation of evolutionary rates, which can be calibrated using information about the ages of the samples. However, the reliability of these rate estimates can be negatively affected by among-lineage rate variation and non-random sampling. Using a simulation study, we compared the performance of three phylogenetic methods for inferring evolutionary rates from time-structured data sets: regression of root-to-tip distances, least-squares dating, and Bayesian inference. We also applied these three methods to time-structured mitogenomic data sets from six vertebrate species. Results Our results from 12 simulation scenarios show that the three methods produce reliable estimates when the substitution rate is high, rate variation is low, and samples of similar ages are not all grouped together in the tree (i.e., low phylo-temporal clustering). The interaction of these factors is particularly important for least-squares dating and Bayesian estimation of evolutionary rates. The three estimation methods produced consistent estimates of rates across most of the six mitogenomic data sets, with sequence data from horses being an exception. Conclusions We recommend that phylogenetic studies of ancient DNA sequences should use multiple methods of inference and test for the presence of temporal signal, among-lineage rate variation, and phylo-temporal clustering in the data. Electronic supplementary material The online version of this article (10.1186/s12862-018-1192-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- K Jun Tong
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
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36
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Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas. Sci Rep 2018; 8:6551. [PMID: 29695730 PMCID: PMC5917027 DOI: 10.1038/s41598-018-24497-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 04/03/2018] [Indexed: 12/12/2022] Open
Abstract
Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.
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37
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN. The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathog 2018; 14:e1006750. [PMID: 29300782 PMCID: PMC5754119 DOI: 10.1371/journal.ppat.1006750] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox), showed no DNA reads for VARV yet did for hepatitis B virus (HBV). Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles. We attempted to enrich and sequence for both VARV and HBV DNA. Although we did not recover any reads identified as VARV, we were successful in reconstructing an HBV genome at 163.8X coverage. Strikingly, both the HBV sequence and that of the associated host mitochondrial DNA displayed a nearly identical cytosine deamination pattern near the termini of DNA fragments, characteristic of an ancient origin. In contrast, phylogenetic analyses revealed a close relationship between the putative ancient virus and contemporary HBV strains (of genotype D), at first suggesting contamination. In addressing this paradox we demonstrate that HBV evolution is characterized by a marked lack of temporal structure. This confounds attempts to use molecular clock-based methods to date the origin of this virus over the time-frame sampled so far, and means that phylogenetic measures alone cannot yet be used to determine HBV sequence authenticity. If genuine, this phylogenetic pattern indicates that the genotypes of HBV diversified long before the 16th century, and enables comparison of potential pathogenic similarities between modern and ancient HBV. These results have important implications for our understanding of the emergence and evolution of this common viral pathogen.
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Affiliation(s)
- Zoe Patterson Ross
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Gino Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Sebastian Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Debi Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Mark W. Douglas
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry, McMaster University, Hamilton, ON, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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Bromham L, Duchêne S, Hua X, Ritchie AM, Duchêne DA, Ho SYW. Bayesian molecular dating: opening up the black box. Biol Rev Camb Philos Soc 2017; 93:1165-1191. [DOI: 10.1111/brv.12390] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 11/13/2017] [Accepted: 11/17/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Lindell Bromham
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Melbourne VIC 3010 Australia
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Xia Hua
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
| | - Andrew M. Ritchie
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - David A. Duchêne
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
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40
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Li J, Zeng W, Zhang Y, Ko AMS, Li C, Zhu H, Fu Q, Zhou H. Ancient DNA reveals genetic connections between early Di-Qiang and Han Chinese. BMC Evol Biol 2017; 17:239. [PMID: 29202706 PMCID: PMC5716020 DOI: 10.1186/s12862-017-1082-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 11/17/2017] [Indexed: 12/04/2022] Open
Abstract
Background Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~4000 years old) and compared them to other ancient DNA across China, including an early Han-related site (Hengbei site dated ~3000 years old) to establish the underlying genetic relationship between the Di-Qiang and ancestors of Han Chinese. Results We found Mogou mtDNA haplogroups were highly diverse, comprising 14 haplogroups: A, B, C, D (D*, D4, D5), F, G, M7, M8, M10, M13, M25, N*, N9a, and Z. In contrast, Mogou males were all Y-DNA haplogroup O3a2/P201; specifically one male was further assigned to O3a2c1a/M117 using targeted unique regions on the non-recombining region of the Y-chromosome. We compared Mogou to 7 other ancient and 38 modern Chinese groups, in a total of 1793 individuals, and found that Mogou shared close genetic distances with Taojiazhai (a more recent Di-Qiang population), Hengbei, and Northern Han. We modeled their interactions using Approximate Bayesian Computation, and support was given to a potential admixture of ~13-18% between the Mogou and Northern Han around 3300–3800 years ago. Conclusions Mogou harbors the earliest genetically identifiable Di-Qiang, ancestral to the Taojiazhai, and up to ~33% paternal and ~70% of its maternal haplogroups could be found in present-day Northern Han Chinese. Electronic supplementary material The online version of this article (10.1186/s12862-017-1082-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiawei Li
- College of Life Science, Jilin University, Changchun, 130023, People's Republic of China
| | - Wen Zeng
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, People's Republic of China
| | - Ye Zhang
- College of Life Science, Jilin University, Changchun, 130023, People's Republic of China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, 100044, People's Republic of China
| | - Chunxiang Li
- College of Life Science, Jilin University, Changchun, 130023, People's Republic of China
| | - Hong Zhu
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, People's Republic of China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, 100044, People's Republic of China.
| | - Hui Zhou
- College of Life Science, Jilin University, Changchun, 130023, People's Republic of China. .,Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, People's Republic of China.
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41
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Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
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Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
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42
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Rieux A, Khatchikian CE. tipdatingbeast: an r package to assist the implementation of phylogenetic tip-dating tests using beast. Mol Ecol Resour 2017; 17:608-613. [PMID: 27717245 DOI: 10.1111/1755-0998.12603] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 09/10/2016] [Accepted: 09/16/2016] [Indexed: 11/26/2022]
Abstract
Molecular tip dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to coestimate the timing of evolutionary events with rates of molecular evolution. In this context, beast, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce tipdatingbeast, an r package built to assist the implementation of various phylogenetic tip-dating tests using beast. tipdatingbeast currently contains two main functions. The first one allows preparing date-randomization analyses, which assess the temporal signal of a data set. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical data set and supply practical guidance for results interpretation.
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Affiliation(s)
- Adrien Rieux
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
| | - Camilo E Khatchikian
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA, 19104, USA
- Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave, Bioscience Research Bldg. Room 2.120, EL Paso, TX, 79968, USA
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43
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Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC. Zika virus evolution and spread in the Americas. Nature 2017; 546:411-415. [PMID: 28538734 PMCID: PMC5563848 DOI: 10.1038/nature22402] [Citation(s) in RCA: 264] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/02/2017] [Indexed: 12/22/2022]
Abstract
Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests.
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Affiliation(s)
- Hayden C Metsky
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Shirlee Wohl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Stephen F Schaffner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Catherine A Freije
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sarah M Winnicki
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kendra West
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - James Qu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Aaron E Lin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | | | - Simon H Ye
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Cynthia Y Luo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Rickey R Shah
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard University Extension School, Cambridge, Massachusetts, USA
| | - Bridget Chak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Giselle Barbosa-Lima
- National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasmine R Vieira
- National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Amanda L Tan
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Carolyn M Barcellona
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | | | | | - Andrew C Cannons
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA
| | - Marshall R Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA
| | - Kelly N Hogan
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA
| | - Edgar W Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA
| | - Joshua J Anzinger
- Department of Microbiology, The University of the West Indies, Mona, Kingston, Jamaica
| | - Kimberly F Garcia
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Leda A Parham
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Rosa M Gélvez Ramírez
- Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
| | | | - Diana P Rojas
- Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Catherine M Brown
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Scott Hennigan
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Brandon Sabina
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Sarah Scotland
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - Glenn Oliveira
- Scripps Translational Science Institute, La Jolla, California, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sandra Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Luis Villar
- Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Salim Mattar
- Institute for Tropical Biology Research, Universidad de Córdoba, Montería, Córdoba, Colombia
| | - Ivette Lorenzana
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Jose Cerbino-Neto
- National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarissa Valim
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, Michegan, USA
| | - Wim Degrave
- FIOCRUZ, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia T Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kristian G Andersen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
- Scripps Translational Science Institute, La Jolla, California, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Sharon Isern
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Fernando A Bozza
- National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
- D'Or Institute for Research and Education, Rio de Janeiro, Brazil
| | - Thiago M L Souza
- National Institute for Science and Technology on Innovation on Neglected Diseases, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- Center for Technological Development in Health, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Irene Bosch
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nathan L Yozwiak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Fossil and genomic evidence constrains the timing of bison arrival in North America. Proc Natl Acad Sci U S A 2017; 114:3457-3462. [PMID: 28289222 DOI: 10.1073/pnas.1620754114] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada's Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf. priscus We extracted and sequenced mitochondrial genomes from both this bison and from the remains of a recently discovered, ∼120,000-y-old giant long-horned bison, Bison latifrons, from Snowmass, Colorado. We analyzed these and 44 other bison mitogenomes with ages that span the Late Pleistocene, and identified two waves of bison dispersal into North America from Asia, the earliest of which occurred ∼195-135 thousand y ago and preceded the morphological diversification of North American bison, and the second of which occurred during the Late Pleistocene, ∼45-21 thousand y ago. This chronological arc establishes that bison first entered North America during the sea level lowstand accompanying marine isotope stage 6, rejecting earlier records of bison in North America. After their invasion, bison rapidly colonized North America during the last interglaciation, spreading from Alaska through continental North America; they have been continuously resident since then.
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45
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Baele G, Suchard MA, Rambaut A, Lemey P. Emerging Concepts of Data Integration in Pathogen Phylodynamics. Syst Biol 2017; 66:e47-e65. [PMID: 28173504 PMCID: PMC5837209 DOI: 10.1093/sysbio/syw054] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 06/02/2016] [Indexed: 12/24/2022] Open
Abstract
Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.
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Affiliation(s)
- Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3FL, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Edinburgh EH9 3FL, UK
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
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46
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Abstract
The molecular clock is a valuable and widely used tool for estimating evolutionary rates and timescales in biological research. There has been considerable progress in the theory and practice of molecular clocks over the past five decades. Although the idea of a molecular clock was originally put forward in the context of protein evolution and advanced using various biochemical techniques, it is now primarily applied to analyses of DNA sequences. An interesting but very underappreciated aspect of molecular clocks is that they can be based on genetic data other than DNA or protein sequences. For example, evolutionary timescales can be estimated using microsatellites, protein folds, and even the extent of recombination. These genome features hold great potential for molecular dating, particularly in cases where nucleotide sequences might be uninformative or unreliable. Here we present an outline of the different genetic data types that have been used for molecular dating, and we describe the features that good molecular clocks should possess. We hope that our article inspires further work on the genome as an evolutionary timepiece.
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Affiliation(s)
- Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Amanda X Y Chen
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Luana S F Lins
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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47
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Fortes GG, Grandal-d'Anglade A, Kolbe B, Fernandes D, Meleg IN, García-Vázquez A, Pinto-Llona AC, Constantin S, de Torres TJ, Ortiz JE, Frischauf C, Rabeder G, Hofreiter M, Barlow A. Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears. Mol Ecol 2016; 25:4907-18. [DOI: 10.1111/mec.13800] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 08/04/2016] [Accepted: 08/08/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Gloria G. Fortes
- Institute for Biochemistry and Biology; University of Potsdam; 14476 Potsdam OT Golm Germany
- Department of Biology and Evolution; University of Ferrara; I-44121 Ferrara Italy
- Instituto Universitario de Xeoloxía; Universidade da Coruña; 15081 A Coruña Spain
| | | | - Ben Kolbe
- Institute for Biochemistry and Biology; University of Potsdam; 14476 Potsdam OT Golm Germany
| | - Daniel Fernandes
- School of Archaeology and Earth Institute; University College Dublin; Dublin 4 Ireland
| | - Ioana N. Meleg
- “Emil Racoviță” Institute of Speleology; 050711 Bucharest Romania
| | - Ana García-Vázquez
- Instituto Universitario de Xeoloxía; Universidade da Coruña; 15081 A Coruña Spain
| | - Ana C. Pinto-Llona
- c/o J. Villarías Instituto de Historia, Consejo Superior de Investigaciones Científicas; 28037 Madrid Spain
| | | | - Trino J. de Torres
- Depto. de Ingeniería Geológica y Minera; Universidad Politécnica de Madrid; 28003 Madrid Spain
| | - Jose E. Ortiz
- Depto. de Ingeniería Geológica y Minera; Universidad Politécnica de Madrid; 28003 Madrid Spain
| | | | - Gernot Rabeder
- Institute of Palaeontology; University of Vienna; A-1090 Vienna Austria
| | - Michael Hofreiter
- Institute for Biochemistry and Biology; University of Potsdam; 14476 Potsdam OT Golm Germany
- Department of Biology; The University of York; York YO10 5DD UK
| | - Axel Barlow
- Institute for Biochemistry and Biology; University of Potsdam; 14476 Potsdam OT Golm Germany
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48
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Drummond AJ, Stadler T. Bayesian phylogenetic estimation of fossil ages. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150129. [PMID: 27325827 PMCID: PMC4920331 DOI: 10.1098/rstb.2015.0129] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 12/26/2022] Open
Abstract
Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Alexei J Drummond
- Department of Computer Science, University of Auckland, Auckland 1010, New Zealand Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, 4058 Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, 4058 Basel, Switzerland Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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49
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Rieux A, Balloux F. Inferences from tip-calibrated phylogenies: a review and a practical guide. Mol Ecol 2016; 25:1911-24. [PMID: 26880113 PMCID: PMC4949988 DOI: 10.1111/mec.13586] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 12/25/2022]
Abstract
Molecular dating of phylogenetic trees is a growing discipline using sequence data to co‐estimate the timing of evolutionary events and rates of molecular evolution. All molecular‐dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast‐evolving genomes such as viruses and some bacteria, the time span over which samples were collected may cover a significant proportion of the time since they last shared a common ancestor. This situation allows phylogenetic trees to be calibrated by associating sampling dates directly to the sequences representing the tips (terminal nodes) of the tree. The increasing availability of genomic data from ancient DNA extends the applicability of such tip‐based calibration to a variety of taxa including humans, extinct megafauna and various microorganisms which typically have a scarce fossil record. The development of statistical models accounting for heterogeneity in different aspects of the evolutionary process while accommodating very large data sets (e.g. whole genomes) has allowed using tip‐dating methods to reach inferences on divergence times, substitution rates, past demography or the age of specific mutations on a variety of spatiotemporal scales. In this review, we summarize the current state of the art of tip dating, discuss some recent applications, highlight common pitfalls and provide a ‘how to’ guide to thoroughly perform such analyses.
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Affiliation(s)
- Adrien Rieux
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| | - François Balloux
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
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50
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Abstract
Molecular dating has become central to placing a temporal dimension on the tree of life. Methods for estimating divergence times have been developed for over 50 years, beginning with the proposal of molecular clock in 1962. We categorize the chronological development of these methods into four generations based on the timing of their origin. In the first generation approaches (1960s-1980s), a strict molecular clock was assumed to date divergences. In the second generation approaches (1990s), the equality of evolutionary rates between species was first tested and then a strict molecular clock applied to estimate divergence times. The third generation approaches (since ∼2000) account for differences in evolutionary rates across the tree by using a statistical model, obviating the need to assume a clock or to test the equality of evolutionary rates among species. Bayesian methods in the third generation require a specific or uniform prior on the speciation-process and enable the inclusion of uncertainty in clock calibrations. The fourth generation approaches (since 2012) allow rates to vary from branch to branch, but do not need prior selection of a statistical model to describe the rate variation or the specification of speciation model. With high accuracy, comparable to Bayesian approaches, and speeds that are orders of magnitude faster, fourth generation methods are able to produce reliable timetrees of thousands of species using genome scale data. We found that early time estimates from second generation studies are similar to those of third and fourth generation studies, indicating that methodological advances have not fundamentally altered the timetree of life, but rather have facilitated time estimation by enabling the inclusion of more species. Nonetheless, we feel an urgent need for testing the accuracy and precision of third and fourth generation methods, including their robustness to misspecification of priors in the analysis of large phylogenies and data sets.
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Affiliation(s)
- Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University Center for Biodiversity, Temple University Department of Biology, Temple University
| | - S Blair Hedges
- Institute for Genomics and Evolutionary Medicine, Temple University Center for Biodiversity, Temple University Department of Biology, Temple University
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