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Nelder MP, Schats R, Poinar HN, Cooke A, Brickley MB. Pathogen prospecting of museums: Reconstructing malaria epidemiology. Proc Natl Acad Sci U S A 2024; 121:e2310859121. [PMID: 38527214 PMCID: PMC11009618 DOI: 10.1073/pnas.2310859121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Mark P. Nelder
- Enteric, Zoonotic and Vector-Borne Diseases, Health Protection, Public Health Ontario, Toronto, ONM5G 1M1, Canada
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, 2333 CCLeiden, The Netherlands
| | - Hendrik N. Poinar
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
- Department of Biochemistry, McMaster University, Hamilton, ONL8S 4L9, Canada
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Amanda Cooke
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Megan B. Brickley
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
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2
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Tropini C, Finlay BB, Nichter M, Melby MK, Metcalf JL, Dominguez-Bello MG, Zhao L, McFall-Ngai MJ, Geva-Zatorsky N, Amato KR, Undurraga EA, Poinar HN, Gilbert JA. Time to rethink academic publishing: the peer reviewer crisis. mBio 2023; 14:e0109123. [PMID: 37975666 PMCID: PMC10746150 DOI: 10.1128/mbio.01091-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
There is concern that the time taken to publish academic papers in microbiological science has significantly increased in recent years. While the data do not specifically support this, evidence suggests that editors are having to invite more and more reviewers to identify those willing to perform peer review.
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Affiliation(s)
- Carolina Tropini
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - B. Brett Finlay
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Microbiology and the Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark Nichter
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- School of Anthropology, University of Arizona, Tucson, Arizona, USA
| | - Melissa K. Melby
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Anthropology, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Maria Gloria Dominguez-Bello
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
- Department of Anthropolog, Rutgers University, New Brunswick, New Jersey, USA
| | - Liping Zhao
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Margaret J. McFall-Ngai
- Carnegie Institution for Science, California Institute of Technology, Pasadena, California, USA
| | - Naama Geva-Zatorsky
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa, Israel
| | - Katherine R. Amato
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Eduardo A. Undurraga
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Santiago, Región Metropolitana, Chile
- Research Center for Integrated Disaster Risk Management (CIGIDEN), Santiago, Región Metropolitana, Chile
| | - Hendrik N. Poinar
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Ontario, Canada
| | - Jack A. Gilbert
- Department of Pediatrics, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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3
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Long GS, Hider J, Duggan AT, Klunk J, Eaton K, Karpinski E, Giuffra V, Ventura L, Prowse TL, Fornaciari A, Fornaciari G, Holmes EC, Golding GB, Poinar HN. A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade. PLoS Pathog 2023; 19:e1011538. [PMID: 37523413 PMCID: PMC10414615 DOI: 10.1371/journal.ppat.1011538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 08/10/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.
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Affiliation(s)
- George S. Long
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Jessica Hider
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Jennifer Klunk
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Daicel Arbor Biosciences, Ann Arbor, Michigan, United States of America
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Emil Karpinski
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Luca Ventura
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
- Division of Pathology, San Salvatore Hospital, Coppito, Italy
| | - Tracy L. Prowse
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Antonio Fornaciari
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, Australia
| | | | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
- Department of Biochemistry, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- CIFAR Humans and the Microbiome Program, Toronto, Canada
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4
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Vilgalys TP, Klunk J, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB. Reply to Barton et al: signatures of natural selection during the Black Death. bioRxiv 2023:2023.04.06.535944. [PMID: 37066254 PMCID: PMC10104142 DOI: 10.1101/2023.04.06.535944] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Barton et al.1 raise several statistical concerns regarding our original analyses2 that highlight the challenge of inferring natural selection using ancient genomic data. We show here that these concerns have limited impact on our original conclusions. Specifically, we recover the same signature of enrichment for high FST values at the immune loci relative to putatively neutral sites after switching the allele frequency estimation method to a maximum likelihood approach, filtering to only consider known human variants, and down-sampling our data to the same mean coverage across sites. Furthermore, using permutations, we show that the rs2549794 variant near ERAP2 continues to emerge as the strongest candidate for selection (p = 1.2×10-5), falling below the Bonferroni-corrected significance threshold recommended by Barton et al. Importantly, the evidence for selection on ERAP2 is further supported by functional data demonstrating the impact of the ERAP2 genotype on the immune response to Y. pestis and by epidemiological data from an independent group showing that the putatively selected allele during the Black Death protects against severe respiratory infection in contemporary populations.
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Affiliation(s)
- Tauras P Vilgalys
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Christian E Demeure
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France
| | - Xiaoheng Cheng
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Mari Shiratori
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Julien Madej
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France
| | - Rémi Beau
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France
| | - Derek Elli
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Maria I Patino
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Rebecca Redfern
- Centre for Human Bioarchaeology, Museum of London, London, UK, EC2Y 5HN
| | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, SC, USA
| | - Julia A Gamble
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, R3T2N2
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark
| | - Ann Carmichael
- History Department, Indiana University, Bloomington, IN, USA
| | - Nükhet Varlik
- Department of History, Rutgers University-Newark, NJ, USA
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada, H1T 1C7
| | - G Brian Golding
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9
| | | | - Jean-Marie Rouillard
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan Ann Arbor, Ann Arbor, MI, USA
| | - Vania Yotova
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada, H3T 1C5
| | - Renata Sindeaux
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada, H3T 1C5
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Matin Bikaran
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Anne Dumaine
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jessica F Brinkworth
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dominique Missiakas
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Guy A Rouleau
- Montreal Neurological Institute-Hospital, McGill University, Montréal, Quebec, Canada, H3A 2B4
| | - Matthias Steinrücken
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Luis B Barreiro
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Centre for Human Bioarchaeology, Museum of London, London, UK, EC2Y 5HN
- Department of Anthropology, University of South Carolina, Columbia, SC, USA
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, R3T2N2
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5
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Eaton K, Sidhu RK, Klunk J, Gamble JA, Boldsen JL, Carmichael AG, Varlık N, Duchene S, Featherstone L, Grimes V, Golding GB, DeWitte SN, Holmes EC, Poinar HN. Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark. Curr Biol 2023; 33:1147-1152.e5. [PMID: 36841239 DOI: 10.1016/j.cub.2023.01.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 02/27/2023]
Abstract
The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.1,2 A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.3 Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.4,5 To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.
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Affiliation(s)
- Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
| | - Ravneet K Sidhu
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON L8S 4E8, Canada
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Daicel Arbor Biosciences, Ann Arbor, MI 48103, USA
| | - Julia A Gamble
- Department of Anthropology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, 5260 Odense, Denmark
| | - Ann G Carmichael
- Department of History, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Nükhet Varlık
- Department of History, Rutgers University - Newark, Newark, NJ 07102, USA
| | - Sebastian Duchene
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3004, Australia
| | - Leo Featherstone
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3004, Australia
| | - Vaughan Grimes
- Department of Archaeology, Memorial University of Newfoundland, St. Johns, SC A1C 5S7, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, ON L8S 4E8, Canada
| | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, SC 29208, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney 2006, Australia
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada; Department of Biochemistry, McMaster University, Hamilton, ON L82 4K1, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada.
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6
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Hider J, Duggan AT, Klunk J, Eaton K, Long GS, Karpinski E, Giuffra V, Ventura L, Fornaciari A, Fornaciari G, Golding GB, Prowse TL, Poinar HN. Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis. Int J Paleopathol 2022; 39:20-34. [PMID: 36174312 DOI: 10.1016/j.ijpp.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 08/05/2022] [Accepted: 08/13/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 th century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis. METHODS Shotgun sequencing data from was examined to determine the presence of Brucella DNA. RESULTS Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7-169), but for many the data quality was insufficient to withstand our identification and authentication criteria. CONCLUSIONS We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification. SIGNIFICANCE Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease. LIMITATIONS Study focuses on pathogen recovery in a single individual. SUGGESTIONS FOR FURTHER RESEARCH Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples.
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Affiliation(s)
- Jessica Hider
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada.
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Daicel Arbor Biosciences, 5840 Interface Drive, Suite 101, Ann Arbor, MI 48103, USA
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - George S Long
- Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, Medical School, via Roma 57, 56126 Pisa, PI, Italy
| | - Luca Ventura
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy; Division of Pathology, San Salvatore Hospital, University of L'Aquila, Coppito, 67100 L'Aquila, AQ, Italy
| | - Antonio Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, Medical School, via Roma 57, 56126 Pisa, PI, Italy
| | - Gino Fornaciari
- Maria Luisa di Borbone Academy, Villa Borbone, viale dei Tigli 32, 55049 Viareggio, LU, Italy
| | - G Brian Golding
- Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Tracy L Prowse
- Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L9, Canada
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7
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Klunk J, Vilgalys TP, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB. Evolution of immune genes is associated with the Black Death. Nature 2022; 611:312-319. [PMID: 36261521 PMCID: PMC9580435 DOI: 10.1038/s41586-022-05349-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/14/2022] [Indexed: 01/10/2023]
Abstract
Infectious diseases are among the strongest selective pressures driving human evolution1,2. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis3. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population4. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.
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Affiliation(s)
- Jennifer Klunk
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Tauras P Vilgalys
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Xiaoheng Cheng
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Mari Shiratori
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Julien Madej
- Yersinia Research Unit, Institut Pasteur, Paris, France
| | - Rémi Beau
- Yersinia Research Unit, Institut Pasteur, Paris, France
| | - Derek Elli
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Maria I Patino
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Rebecca Redfern
- Centre for Human Bioarchaeology, Museum of London, London, UK
| | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, SC, USA
| | - Julia A Gamble
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, Denmark
| | - Ann Carmichael
- History Department, Indiana University, Bloomington, IN, USA
| | - Nükhet Varlik
- Department of History, Rutgers University, Newark, NJ, USA
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - G Brian Golding
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada
| | | | - Jean-Marie Rouillard
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, USA
| | - Vania Yotova
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada
| | - Renata Sindeaux
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Matin Bikaran
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Anne Dumaine
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jessica F Brinkworth
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dominique Missiakas
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Guy A Rouleau
- Montreal Neurological Institute-Hospital, McGill University, Montréal, Quebec, Canada
| | - Matthias Steinrücken
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada.
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
| | - Luis B Barreiro
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
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8
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Murchie TJ, Karpinski E, Eaton K, Duggan AT, Baleka S, Zazula G, MacPhee RDE, Froese D, Poinar HN. Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments. Curr Biol 2022; 32:851-860.e7. [PMID: 35016010 DOI: 10.1016/j.cub.2021.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022]
Abstract
Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.1 In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.2 Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia3-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,6-12 in paleodietary reconstructions,13-19 and facilitated genomic reconstructions from cave contexts.8,20-22 Murchie et al.6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.24 Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Sina Baleka
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Box 2703, Whitehorse, YT Y1A 2C6, Canada; Collections and Research, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, ON K1P 6P4, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB T6G 2E3, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; CIFAR, Humans and the Microbiome Program, MaRS Centre, West Tower, 661 University Avenue, Suite 505, Toronto, ON M5G 1M1, Canada.
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9
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Murchie TJ, Monteath AJ, Mahony ME, Long GS, Cocker S, Sadoway T, Karpinski E, Zazula G, MacPhee RDE, Froese D, Poinar HN. Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA. Nat Commun 2021; 12:7120. [PMID: 34880234 PMCID: PMC8654998 DOI: 10.1038/s41467-021-27439-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada.
| | - Alistair J Monteath
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.,School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - Matthew E Mahony
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - George S Long
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Scott Cocker
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Tara Sadoway
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,The Hospital for Sick Children, Toronto, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Whitehorse, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, United States
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada. .,Department of Biochemistry, McMaster University, Hamilton, Canada. .,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. .,CIFAR Humans and the Microbiome Program, Toronto, Canada.
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10
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Duggan AT, Holmes EC, Poinar HN. Response to Brinkmann et al. "Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States". Genome Biol 2020; 21:287. [PMID: 33272282 PMCID: PMC7716422 DOI: 10.1186/s13059-020-02203-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022] Open
Abstract
We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with ancient DNA.
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Affiliation(s)
- Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, L8S 4L9, Canada.
| | - 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 N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, L8S 4L9, Canada.,M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, L8S 4L9, Canada
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Duggan AT, Klunk J, Porter AF, Dhody AN, Hicks R, Smith GL, Humphreys M, McCollum AM, Davidson WB, Wilkins K, Li Y, Burke A, Polasky H, Flanders L, Poinar D, Raphenya AR, Lau TTY, Alcock B, McArthur AG, Golding GB, Holmes EC, Poinar HN. The origins and genomic diversity of American Civil War Era smallpox vaccine strains. Genome Biol 2020; 21:175. [PMID: 32684155 PMCID: PMC7370420 DOI: 10.1186/s13059-020-02079-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.
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Affiliation(s)
- Ana T Duggan
- Department of Anthropology, McMaster University, Hamilton, L8S 4L9, Canada.
| | - Jennifer Klunk
- Department of Biology, McMaster University, Hamilton, L8S 4L9, Canada.,Present address: Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - Ashleigh F Porter
- 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
| | - Anna N Dhody
- Mütter Research Institute, Philadelphia, PA, 19103, USA.,Mütter Museum of The College of Physicians of Philadelphia, Philadelphia, PA, 19103, USA
| | - Robert Hicks
- Mütter Research Institute, Philadelphia, PA, 19103, USA.,Mütter Museum of The College of Physicians of Philadelphia, Philadelphia, PA, 19103, USA
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | | | - Andrea M McCollum
- U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, Atlanta, GA, 30333, USA
| | - Whitni B Davidson
- U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, Atlanta, GA, 30333, USA
| | - Kimberly Wilkins
- U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, Atlanta, GA, 30333, USA
| | - Yu Li
- U.S. Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, Atlanta, GA, 30333, USA
| | - Amanda Burke
- Mütter Museum of The College of Physicians of Philadelphia, Philadelphia, PA, 19103, USA
| | - Hanna Polasky
- Mütter Museum of The College of Physicians of Philadelphia, Philadelphia, PA, 19103, USA
| | - Lowell Flanders
- Mütter Museum of The College of Physicians of Philadelphia, Philadelphia, PA, 19103, USA
| | - Debi Poinar
- Department of Anthropology, McMaster University, Hamilton, L8S 4L9, Canada
| | | | - Tammy T Y Lau
- Present address: BC Cancer Research Centre, Vancouver, V5Z 1G1, Canada.,M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, L8S 4K1, Canada
| | - Brian Alcock
- Present address: BC Cancer Research Centre, Vancouver, V5Z 1G1, Canada
| | - Andrew G McArthur
- Present address: BC Cancer Research Centre, Vancouver, V5Z 1G1, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, L8S 4L9, Canada
| | - 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 N Poinar
- Department of Anthropology, McMaster University, Hamilton, L8S 4L9, Canada.,Present address: BC Cancer Research Centre, Vancouver, V5Z 1G1, Canada.,Department of Biochemistry, McMaster University, Hamilton, L8S 4L9, Canada
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13
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Delsuc F, Kuch M, Gibb GC, Karpinski E, Hackenberger D, Szpak P, Martínez JG, Mead JI, McDonald HG, MacPhee RDE, Billet G, Hautier L, Poinar HN. Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths. Curr Biol 2019; 29:2031-2042.e6. [PMID: 31178321 DOI: 10.1016/j.cub.2019.05.043] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/18/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022]
Abstract
Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history.
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Affiliation(s)
- Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Gillian C Gibb
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France; Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Centennial Drive, Hokowhitu, Palmerston North 4410, New Zealand
| | - Emil Karpinski
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Dirk Hackenberger
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, ON K9L 0G2, Canada
| | - Jorge G Martínez
- Instituto Superior de Estudios Sociales, CONICET-Instituto de Arqueología y Museo, Universidad Nacional de Tucumán, San Martín 1545, CP4000 San Miguel de Tucumán, Argentina
| | - Jim I Mead
- The Mammoth Site, Hot Springs, Hot Springs, SD 57747, USA; East Tennessee State University Natural History Museum, 1212 Suncrest Drive, Johnson City, TN 37615, USA
| | - H Gregory McDonald
- Bureau of Land Management, Utah State Office, 440 West 200 South #500, Salt Lake City, UT 84101, USA
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, Central Park West & 79th Street, New York, NY 10024, USA
| | - Guillaume Billet
- Centre de Recherche en Paléontologie - Paris (CR2P), UMR CNRS 7207, Sorbonne Université, Muséum National d'Histoire Naturelle, 57 Rue Cuvier, 75005 Paris, France
| | - Lionel Hautier
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France; Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
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14
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Klunk J, Duggan AT, Redfern R, Gamble J, Boldsen JL, Golding GB, Walter BS, Eaton K, Stangroom J, Rouillard JM, Devault A, DeWitte SN, Poinar HN. Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark. Am J Phys Anthropol 2019; 169:240-252. [PMID: 30964548 DOI: 10.1002/ajpa.23820] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/08/2019] [Accepted: 03/02/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVES In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isotope data. This study uses ancient DNA (aDNA) isolated from skeletal remains to examine whether evidence for large-scale population movement can be gleaned from the complete mitochondrial genomes of 264 medieval individuals from England (London) and Denmark. MATERIALS AND METHODS Using a novel library-conserving approach to targeted capture, we recovered 264 full mitochondrial genomes from the petrous portion of the temporal bones and teeth and compared genetic diversity across the medieval period within and between English (London) and Danish populations and with contemporary populations through population pairwise ΦST analysis. RESULTS We find no evidence of significant differences in genetic diversity spatially or temporally in our dataset, yet there is a high degree of haplotype diversity in our medieval samples with little exact sequence sharing. DISCUSSION The mitochondrial genomes of both medieval Londoners and medieval Danes suggest high mitochondrial diversity before, during and after the Black Death. While our mitochondrial genomic data lack geographically correlated signals, these data could be the result of high, continual female migration before and after the Black Death or may simply indicate a large female effective population size unaffected by the upheaval of the medieval period. Either scenario suggests a genetic resiliency in areas of northwestern medieval Europe.
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Affiliation(s)
- Jennifer Klunk
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Rebecca Redfern
- Center for Human Bioarchaeology, Museum of London, London, UK
| | - Julia Gamble
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense, Denmark
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Brittany S Walter
- Defense POW/MIA Accounting Agency Laboratory, Offutt AFB, Omaha, Nebraska
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Julianna Stangroom
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Jean-Marie Rouillard
- Arbor Biosciences, Ann Arbor, Michigan.,Department of Chemical Engineering, University of Michigan Ann Arbor, Ann Arbor, Michigan
| | | | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, South Carolina
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Ontario, Canada.,Department of Biology, McMaster University, Hamilton, Ontario, Canada.,Department of Anthropology, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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15
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Delsuc F, Kuch M, Gibb GC, Hughes J, Szpak P, Southon J, Enk J, Duggan AT, Poinar HN. Resolving the phylogenetic position of Darwin's extinct ground sloth ( Mylodon darwinii) using mitogenomic and nuclear exon data. Proc Biol Sci 2019; 285:rspb.2018.0214. [PMID: 29769358 PMCID: PMC5966596 DOI: 10.1098/rspb.2018.0214] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/16/2018] [Indexed: 01/18/2023] Open
Abstract
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12 880-year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient subfossil, probably the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra. Additionally, we enriched over 15 kb of sequence data from seven nuclear exons, using target sequence capture designed against a wide xenarthran dataset. Phylogenetic and dating analyses of the mitogenomic dataset including all extant species of xenarthrans and the assembled nuclear supermatrix unambiguously place Mylodon darwinii as the sister-group of modern two-fingered sloths, from which it diverged around 22 million years ago. These congruent results from both the mitochondrial and nuclear data support the diphyly of the two modern sloth lineages, implying the convergent evolution of their unique suspensory behaviour as an adaption to arboreality. Our results offer promising perspectives for whole-genome sequencing of this emblematic extinct taxon.
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Affiliation(s)
- Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Gillian C Gibb
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Jonathan Hughes
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, ON, Canada
| | - John Southon
- Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, CA, USA
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada.,MYcroarray, Ann Arbor, MI, USA
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
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Harris AJT, Duggan AT, Marciniak S, Marshall I, Fuller BT, Southon J, Poinar HN, Grimes V. Dorset Pre-Inuit and Beothuk foodways in Newfoundland, ca. AD 500-1829. PLoS One 2019; 14:e0210187. [PMID: 30615665 PMCID: PMC6322756 DOI: 10.1371/journal.pone.0210187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022] Open
Abstract
Archaeological research on the Canadian island of Newfoundland increasingly demonstrates that the island's subarctic climate and paucity of terrestrial food resources did not restrict past Pre-Inuit (Dorset) and Native American (Beothuk) hunter-gatherer populations to a single subsistence pattern. This study first sought to characterize hunter-gatherer diets over the past 1500 years; and second, to assess the impact of European colonization on Beothuk lifeways by comparing the bone chemistry of Beothuk skeletal remains before and after the intensification of European settlement in the early 18th century. We employed radiocarbon dating and stable carbon and nitrogen isotope ratio analysis of bulk bone collagen from both Dorset (n = 9) and Beothuk (n = 13) cultures, including a naturally mummified 17th century Beothuk individual. Carbon and nitrogen isotope analysis of 108 faunal samples from Dorset and Beothuk archaeological sites around the island were used as a dietary baseline for the humans. We combined our results with previously published isotope data and radiocarbon dates from Dorset (n = 12) and Beothuk (n = 18) individuals and conducted a palaeodietary analysis using Bayesian modelling, cluster analysis and comparative statistical tests. Dorset diets featured more marine protein than those of the Beothuk, and the diets of Beothuk after the 18th century featured less high trophic level marine protein than those of individuals predating the 18th century. Despite inhabiting the same island, Dorset and Beothuk cultures employed markedly different dietary strategies, consistent with interpretations of other archaeological data. Significantly, European colonization had a profound effect on Beothuk lifeways, as in response to the increasing European presence on the coast, the Beothuk relied more extensively on the limited resources of the island's boreal forests and rivers.
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Affiliation(s)
- Alison J. T. Harris
- Department of Archaeology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Stephanie Marciniak
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Ingeborg Marshall
- Institute of Social and Economic Research, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Benjamin T. Fuller
- Keck Carbon Cycle Accelerator Mass Spectrometry Laboratory, Earth Systems Science Department, University of California Irvine, Irvine, California, United States of America
| | - John Southon
- Keck Carbon Cycle Accelerator Mass Spectrometry Laboratory, Earth Systems Science Department, University of California Irvine, Irvine, California, United States of America
| | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
- Michael D. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Humans & the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Vaughan Grimes
- Department of Archaeology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
- Department of Earth Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
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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. Correction: The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathog 2018; 14:e1006887. [PMID: 29425240 PMCID: PMC5806894 DOI: 10.1371/journal.ppat.1006887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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. Hepatitis B virus (HBV) exerts formidable morbidity and mortality in humans. We used ancient DNA techniques to recover the complete genome sequence of an HBV from the mummified remains of a child discovered in the 16th century from Naples, Italy. Strikingly, our analysis of this specimen resulted in two contrasting findings: while the damage patterns lend credence to this HBV sequence being authentically 16th century, phylogenetic analysis revealed a close relationship to recently sampled viruses as expected if the sequence were a modern contaminant. We reconcile these two observations by showing that HBV evolution over the last ~450 years is characterized by a marked lack of temporal structure that hinders attempts to resolve the evolutionary time-scale of this important human 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
- * E-mail: (ECH); (HNP)
| | - 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
- * E-mail: (ECH); (HNP)
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Mortimer TD, Annis DS, O’Neill MB, Bohr LL, Smith TM, Poinar HN, Mosher DF, Pepperell CS. Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus. mSphere 2017; 2:e00511-17. [PMID: 29202045 PMCID: PMC5705806 DOI: 10.1128/msphere.00511-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/13/2017] [Indexed: 12/18/2022] Open
Abstract
Human-pathogenic bacteria are found in a variety of niches, including free-living, zoonotic, and microbiome environments. Identifying bacterial adaptations that enable invasive disease is an important means of gaining insight into the molecular basis of pathogenesis and understanding pathogen emergence. Staphylococcus saprophyticus, a leading cause of urinary tract infections, can be found in the environment, food, animals, and the human microbiome. We identified a selective sweep in the gene encoding the Aas adhesin, a key virulence factor that binds host fibronectin. We hypothesize that the mutation under selection (aas_2206A>C) facilitates colonization of the urinary tract, an environment where bacteria are subject to strong shearing forces. The mutation appears to have enabled emergence and expansion of a human-pathogenic lineage of S. saprophyticus. These results demonstrate the power of evolutionary genomic approaches in discovering the genetic basis of virulence and emphasize the pleiotropy and adaptability of bacteria occupying diverse niches. IMPORTANCEStaphylococcus saprophyticus is an important cause of urinary tract infections (UTI) in women; such UTI are common, can be severe, and are associated with significant impacts to public health. In addition to being a cause of human UTI, S. saprophyticus can be found in the environment, in food, and associated with animals. After discovering that UTI strains of S. saprophyticus are for the most part closely related to each other, we sought to determine whether these strains are specially adapted to cause disease in humans. We found evidence suggesting that a mutation in the gene aas is advantageous in the context of human infection. We hypothesize that the mutation allows S. saprophyticus to survive better in the human urinary tract. These results show how bacteria found in the environment can evolve to cause disease.
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Affiliation(s)
- Tatum D. Mortimer
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Douglas S. Annis
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Mary B. O’Neill
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Lindsey L. Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Tracy M. Smith
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Deane F. Mosher
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
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Porter AF, Duggan AT, Poinar HN, Holmes EC. Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum. Viruses 2017; 9:v9100276. [PMID: 28956829 PMCID: PMC5691628 DOI: 10.3390/v9100276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 01/17/2023] Open
Abstract
The complete genome sequences of two strains of variola virus (VARV) sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD.
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Affiliation(s)
- Ashleigh F Porter
- 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, NSW 2006, Australia.
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry, McMaster University, Hamilton, ON L8S 4L8, Canada.
| | - 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, NSW 2006, Australia.
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Devault AM, Mortimer TD, Kitchen A, Kiesewetter H, Enk JM, Golding GB, Southon J, Kuch M, Duggan AT, Aylward W, Gardner SN, Allen JE, King AM, Wright G, Kuroda M, Kato K, Briggs DE, Fornaciari G, Holmes EC, Poinar HN, Pepperell CS. A molecular portrait of maternal sepsis from Byzantine Troy. eLife 2017; 6. [PMID: 28072390 PMCID: PMC5224923 DOI: 10.7554/elife.20983] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/24/2016] [Indexed: 12/14/2022] Open
Abstract
Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman’s remains. Scanning electron microscopy of the tissue revealed ‘ghost cells’, resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed that G. vaginalis Troy fell within contemporary genetic diversity, whereas S. saprophyticus Troy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology of S. saprophyticus infection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. These results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections. DOI:http://dx.doi.org/10.7554/eLife.20983.001 Why and how have some bacteria evolved to cause illness in humans? One way to study bacterial evolution is to search for ancient samples of bacteria and use DNA sequencing technology to investigate how modern bacteria have changed from their ancestors. Understanding the evolution process may help researchers to understand how some bacteria become resistant to the antibiotics designed to kill them. Complications that occur during pregnancy, including bacterial infections, have long been a major cause of death for women. Now, Devault, Mortimer et al. have been able to sequence the DNA of bacteria found in tissue collected from a woman buried 800 years ago in a cemetery in Troy. Some of the woman’s tissues had been well preserved because they had calcified (probably as the result of infection), which preserved their structure in a mineralized layer. Two mineralized “nodules” in the body appear to be the remains of abscesses. Some of the human DNA in the nodules came from a male, suggesting that the woman was pregnant with a boy and that the abscesses formed in placental tissue. Sequencing the DNA of the bacteria in the abscess allowed Devault, Mortimer et al. to diagnose the woman’s infection, which was caused by two types of bacteria. One species, called Gardnerella vaginalis, is found in modern pregnancy-related infections. The DNA of the ancient samples was similar to that of modern bacteria. The other bacteria species was an ancient form of Staphylococcus saprophyticus, a type of bacteria that causes urinary tract infections. However, the DNA of the ancient S. saprophyticus bacteria is quite different to that of the bacteria found in modern humans. Instead, their DNA sequence appears more similar to forms of the bacteria that infect currently livestock. As humans lived closely with their livestock at the time the woman lived, her infection may be due to a type of bacteria that passed easily between humans and animals. Overall, the results suggest that the disease-causing properties of bacteria can arise from a wide range of sources. In addition, Devault, Mortimer et al. have demonstrated that certain types of tissue found in archeological remains are a potential gold mine of information about the evolution of bacteria and other microbes found in the human body. DOI:http://dx.doi.org/10.7554/eLife.20983.002
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Affiliation(s)
- Alison M Devault
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,MYcroarray, Ann Arbor, United States
| | - Tatum D Mortimer
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, United States
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, United States
| | - Henrike Kiesewetter
- Project Troia, Institute of Prehistory, Early History, and Medieval Archaeology, Tübingen University, Tübingen, Germany
| | - Jacob M Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,MYcroarray, Ann Arbor, United States
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Canada
| | - John Southon
- Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, United States
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - William Aylward
- Molecular Archaeology Laboratory, Biotechnology Center, University of Wisconsin-Madison, Madison, United States.,Department of Classics and Ancient Near Eastern Studies, University of Wisconsin-Madison, Madison, United States
| | - Shea N Gardner
- Lawrence Livermore National Laboratory, Livermore, United States
| | - Jonathan E Allen
- Lawrence Livermore National Laboratory, Livermore, United States
| | - Andrew M King
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Gerard Wright
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kengo Kato
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Derek Eg Briggs
- Department of Geology and Geophysics, Yale University, New Haven, United States
| | - Gino Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - 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, Australia
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States.,Molecular Archaeology Laboratory, Biotechnology Center, University of Wisconsin-Madison, Madison, United States.,Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
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Delsuc F, Gibb GC, Kuch M, Billet G, Hautier L, Southon J, Rouillard JM, Fernicola JC, Vizcaíno SF, MacPhee RD, Poinar HN. The phylogenetic affinities of the extinct glyptodonts. Curr Biol 2016; 26:R155-6. [DOI: 10.1016/j.cub.2016.01.039] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Bos KI, Herbig A, Sahl J, Waglechner N, Fourment M, Forrest SA, Klunk J, Schuenemann VJ, Poinar D, Kuch M, Golding GB, Dutour O, Keim P, Wagner DM, Holmes EC, Krause J, Poinar HN. Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. eLife 2016; 5:e12994. [PMID: 26795402 PMCID: PMC4798955 DOI: 10.7554/elife.12994] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/19/2016] [Indexed: 12/30/2022] Open
Abstract
The 14th–18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague’s persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death. DOI:http://dx.doi.org/10.7554/eLife.12994.001 A bacterium called Yersina pestis is responsible for numerous human outbreaks of plague throughout history. It is carried by rats and other rodents and can spread to humans causing what we conventionally refer to as plague. The most notorious of these plague outbreaks – the Black Death – claimed millions of lives in Europe in the mid-14th century. Several other plague outbreaks emerged in Europe over the next 400 years. Then, there was a large gap before the plague re-emerged as threat in the 19th century and it continues to infect humans today, though on a smaller scale. Scientists have extensively studied Y. pestis to understand its origin and how it evolved to become such a deadly threat. These studies led to the assumption that the plague outbreaks of the 14–18th centuries likely originated in rodents in Asia and spread along trade routes to other parts of the world. However, it is not clear why the plague persisted in Europe for 400 years after the Black Death. Could the bacteria have gained a foothold in local rodents instead of being reintroduced from Asia each time? If it did, why did it then disappear for such a long period from the end of the 18th century? To help answer these questions, Bos, Herbig et al. sequenced the DNA of Y. pestis samples collected from the teeth of five individuals who died of plague during the last major European outbreak of plague in 1722 in Marseille, France. The DNA sequences of these bacterial samples were then compared with the DNA sequences of modern day Y. pestis and other historical samples of the bacteria. The results showed the bacteria in the Marseille outbreak likely evolved from the strain that caused the Black Death back in the 14th century. The comparisons showed that the strain isolated from the teeth is not found today, and may be extinct. This suggests that a historical reservoir for plague existed somewhere, perhaps in Asia, or perhaps in Europe itself, and was able to cause outbreaks up until the 18th century.Bos, Herbig et al.’s findings may help researchers trying to control the current outbreaks of the plague in Madagascar and other places. DOI:http://dx.doi.org/10.7554/eLife.12994.002
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Affiliation(s)
- Kirsten I Bos
- Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jason Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States
| | - Nicholas Waglechner
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Mathieu Fourment
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Stephen A Forrest
- Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | | | - Debi Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Canada
| | - Olivier Dutour
- Laboratoire d'anthropologie biologique Paul Broca, Ecole Pratique des Hautes Etudes, PACEA, Université Bordeaux, Bordeaux, France
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Johannes Krause
- Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hendrik N Poinar
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada.,Department of Biochemistry, McMaster University, Hamilton, Canada
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Gibb GC, Condamine FL, Kuch M, Enk J, Moraes-Barros N, Superina M, Poinar HN, Delsuc F. Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans. Mol Biol Evol 2015; 33:621-42. [PMID: 26556496 PMCID: PMC4760074 DOI: 10.1093/molbev/msv250] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.
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Affiliation(s)
- Gillian C Gibb
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden Department of Biological Sciences, University of Alberta, Edmonton, AL, Canada
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology and Biology, McMaster University, Hamilton, ON, Canada
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology and Biology, McMaster University, Hamilton, ON, Canada
| | - Nadia Moraes-Barros
- Cibio/Inbio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal Laboratório de Biologia Evolutiva e Conservação de Vertebrados (Labec), Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mariella Superina
- Laboratorio de Endocrinología de la Fauna Silvestre, IMBECU, CCT CONICET Mendoza, Mendoza, Argentina
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology and Biology, McMaster University, Hamilton, ON, Canada
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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Gutiérrez-García TA, Vázquez-Domínguez E, Arroyo-Cabrales J, Kuch M, Enk J, King C, Poinar HN. Correction to 'Ancient DNA and the tropics: a rodent's tale'. Biol Lett 2015; 11:rsbl.2015.0111. [PMID: 25808000 DOI: 10.1098/rsbl.2015.0111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The present erratum is in regards to our article entitled ‘Ancient DNA and the tropics: a rodent's tale’. We were made aware of problems with some of the ancient sequences submitted to GenBank and conducted a systematic review of all the files used in our study. We discovered that, unfortunately, an incorrect file was sent to GenBank and was also used in some of our downstream analyses. We immediately contacted GenBank, explained the situation and corrected the file. We have redone some analyses with the correct file and describe these changes below.
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Gutiérrez-García TA, Vázquez-Domínguez E, Arroyo-Cabrales J, Kuch M, Enk J, King C, Poinar HN. Ancient DNA and the tropics: a rodent's tale. Biol Lett 2015; 10:rsbl.2014.0224. [PMID: 24899682 DOI: 10.1098/rsbl.2014.0224] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient DNA from rodent jawbones identified as Ototylomys phyllotis, found in Holocene and Late Pleistocene stratigraphic layers from Loltún, a humid tropical cave located in the Yucatan peninsula. We extracted DNA and amplified six short overlapping fragments of the cytochrome b gene, totalling 666 bp, which represents an unprecedented success considering tropical ancient DNA samples. We performed genetic, phylogenetic and divergence time analyses, combining sequences from ancient and modern O. phyllotis, in order to assess the ancestry of the Loltún samples. Results show that all ancient samples fall into a unique clade that diverged prior to the divergence of the modern O. phyllotis, supporting it as a distinct Pleistocene form of the Ototylomys genus. Hence, this rodent's tale suggests that the sister group to modern O. phyllotis arose during the Miocene-Pliocene, diversified during the Pleistocene and went extinct in the Holocene.
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Affiliation(s)
- Tania A Gutiérrez-García
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ap. Postal 70-275, Ciudad Universitaria 04510, México
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ap. Postal 70-275, Ciudad Universitaria 04510, México
| | - Joaquín Arroyo-Cabrales
- Laboratorio de Arqueozoología, Instituto Nacional de Antropología e Historia, Moneda no. 16, Centro 06060, Distrito Federal, México
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
| | - Christine King
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
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Marciniak S, Klunk J, Devault A, Enk J, Poinar HN. Ancient human genomics: the methodology behind reconstructing evolutionary pathways. J Hum Evol 2015; 79:21-34. [PMID: 25601038 DOI: 10.1016/j.jhevol.2014.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 09/09/2014] [Accepted: 11/07/2014] [Indexed: 11/15/2022]
Abstract
High-throughput sequencing (HTS) has radically altered approaches to human evolutionary research. Recent contributions highlight that HTS is able to reach depths of the human lineage previously thought to be impossible. In this paper, we outline the methodological advances afforded by recent developments in DNA recovery, data output, scalability, speed, and resolution of the current sequencing technology. We review and critically evaluate the 'DNA pipeline' for ancient samples: from DNA extraction, to constructing immortalized sequence libraries, to enrichment strategies (e.g., polymerase chain reaction [PCR] and hybridization capture), and finally, to bioinformatic analyses of sequence data. We argue that continued evaluations and improvements to this process are essential to ensure sequence data validity. Also, we highlight the role of contamination and authentication in ancient DNA-HTS, which is particularly relevant to ancient human genomics, since sequencing the genomes of hominins such as Homo erectus and Homo heidelbergensis may soon be within the realm of possibility.
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Affiliation(s)
- Stephanie Marciniak
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada.
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Alison Devault
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; MYcroarray, Ann Arbor, MI, USA
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada; MYcroarray, Ann Arbor, MI, USA
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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28
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Devault AM, McLoughlin K, Jaing C, Gardner S, Porter TM, Enk JM, Thissen J, Allen J, Borucki M, DeWitte SN, Dhody AN, Poinar HN. Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array. Sci Rep 2014; 4:4245. [PMID: 24603850 PMCID: PMC3945050 DOI: 10.1038/srep04245] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/12/2014] [Indexed: 11/24/2022] Open
Abstract
Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis (“Black Death” plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.
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Affiliation(s)
- Alison M Devault
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada
| | - Kevin McLoughlin
- Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Crystal Jaing
- Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Shea Gardner
- Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Teresita M Porter
- Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada
| | - Jacob M Enk
- 1] McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada [2] Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada
| | - James Thissen
- Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Jonathan Allen
- Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Monica Borucki
- Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Sharon N DeWitte
- Departments of Anthropology and Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Anna N Dhody
- The College of Physicians of Philadelphia, Mütter Museum, 19 S 22nd St, Philadelphia, PA 19103, USA
| | - Hendrik N Poinar
- 1] McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L9, Canada [2] Department of Biology, McMaster University, 1280 Main St W, Hamilton, Ontario L8S 4K1, Canada [3] Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, Ontario L8S4L8, Canada
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Abstract
We report metrics from complete genome capture of nuclear DNA from extinct mammoths using biotinylated RNAs transcribed from an Asian elephant DNA extract. Enrichment of the nuclear genome ranged from 1.06- to 18.65-fold, to an apparent maximum threshold of ∼80% on-target. This projects an order of magnitude less costly complete genome sequencing from long-dead organisms, even when a reference genome is unavailable for bait design.
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Affiliation(s)
- Jacob M Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
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Devault AM, Golding GB, Waglechner N, Enk JM, Kuch M, Tien JH, Shi M, Fisman DN, Dhody AN, Forrest S, Bos KI, Earn DJD, Holmes EC, Poinar HN. Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849. N Engl J Med 2014; 370:334-40. [PMID: 24401020 DOI: 10.1056/nejmoa1308663] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the 19th century, there were several major cholera pandemics in the Indian subcontinent, Europe, and North America. The causes of these outbreaks and the genomic strain identities remain a mystery. We used targeted high-throughput sequencing to reconstruct the Vibrio cholerae genome from the preserved intestine of a victim of the 1849 cholera outbreak in Philadelphia, part of the second cholera pandemic. This O1 biotype strain has 95 to 97% similarity with the classical O395 genome, differing by 203 single-nucleotide polymorphisms (SNPs), lacking three genomic islands, and probably having one or more tandem cholera toxin prophage (CTX) arrays, which potentially affected its virulence. This result highlights archived medical remains as a potential resource for investigations into the genomic origins of past pandemics.
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Affiliation(s)
- Alison M Devault
- From the McMaster Ancient DNA Centre (A.M.D., J.M.E., M.K., S.F., K.I.B., H.N.P.), Departments of Anthropology (A.M.D., M.K., K.I.B., H.N.P.), Biology (J.M.E., G.B.G., H.N.P.), and Mathematics and Statistics (D.J.D.E.), and the Michael G. DeGroote Institute for Infectious Disease Research (N.W., D.J.D.E., H.N.P.), McMaster University, Hamilton, ON, and the Dalla Lana School of Public Health, Toronto (D.N.F.) - all in Canada; the Department of Mathematics, Ohio State University, Columbus (J.H.T.); Marie Bashir Institute for Infectious Diseases and Biosecurity Institute, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney (M.S., E.C.H.); and the College of Physicians of Philadelphia, Mütter Museum, Philadelphia (A.N.D.)
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Porter TM, Golding GB, King C, Froese D, Zazula G, Poinar HN. Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility. Mol Ecol Resour 2013; 13:798-810. [PMID: 23694692 DOI: 10.1111/1755-0998.12124] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 01/03/2023]
Abstract
DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1 and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, sequenced control reactions were used to produce a contaminant library that was used to filter similar sequences from sample libraries. Contaminant filtering resulted in the removal of 1% of reads or 0.3% of operational taxonomic units. We found similar richness, overlap, abundance and taxonomic diversity from the 12S, 16S and trnL markers from each soil core. Jaccard dissimilarity across the two soil cores was highest for metazoan taxa detected by the 12S and cox1 markers. Taxonomic community distances were similar for each marker across the two soil cores when the chi-squared metric was used; however, the 12S and cox1 markers did not cluster well when the Goodall similarity metric was used. A comparison of plant macrofossil vs. read abundance corroborates previous work that suggests eastern Beringia was dominated by grasses and forbs during cold stages of the Pleistocene, a habitat that is restricted to isolated sites in the present-day Yukon.
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Affiliation(s)
- Teresita M Porter
- Department of Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4K1.
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32
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Abstract
The successful reconstruction of an ancient bacterial genome from archaeological material presents an important methodological advancement for infectious disease research. The reliability of evolutionary histories inferred by the incorporation of ancient data, however, are highly contingent upon the level of genetic diversity represented in modern genomic sequences that are publicly accessible, and the paucity of available complete genomes restricts the level of phylogenetic resolution that can be obtained. Here we add to our original analysis of the Yersinia pestis strain implicated in the Black Death by consolidating our dataset for 18 modern genomes with single nucleotide polymorphism (SNP) data for an additional 289 strains at over 600 positions. The inclusion of this additional data reveals a cluster of Y. pestis strains that diverge at a time significantly in advance of the Black Death, with divergence dates roughly coincident with the Plague of Justinian (6th to 8th century AD). In addition, the analysis reveals further clues regarding potential radiation events that occurred immediately preceding the Black Death, and the legacy it may have left in modern Y. pestis populations. This work reiterates the need for more publicly available complete genomes, both modern and ancient, to achieve an accurate understanding of the history of this bacterium.
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Affiliation(s)
- Kirsten I. Bos
- Institute for Archeological Sciences, University of Tübingen, Tübingen, Germany
- Laboratoire de Paléoanthropologie, École Pratique des Hautes Études, Université de Bordeaux, Bordeaux, France
- * E-mail: (KB); (JK)
| | - Philip Stevens
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Sharon N. DeWitte
- University of South Carolina, Departments of Anthropology and Biological Sciences, Columbia, South Carolina, United States of America
| | - Johannes Krause
- Institute for Archeological Sciences, University of Tübingen, Tübingen, Germany
- * E-mail: (KB); (JK)
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Abstract
Owing to their constant low temperatures, glacial ice and permafrost might contain the oldest nucleic acids and microbial cells on Earth, which could prove key to reconstructing past ecosystems and for the planning of missions to other planets. However, recent claims concerning viable cells and microbial nucleic acids obtained from ice- and permafrost cores from hundreds of thousands to millions of years old are not properly authenticated and the findings could be the result of contamination. Here, we discuss the processes that restrict the long-term survival of DNA and/or RNA molecules in ice and permafrost, and highlight sources of contamination that could result in false claims. Additionally, we present a set of precautions, controls and criteria to help ensure that future cultures and sequences are authentic.
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Affiliation(s)
- Eske Willerslev
- Department of Evolutionary Biology, Zoological Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
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Abstract
Deaths from cholera in London, UK, were recorded weekly from 1824 to 1901. Three features of the time series stand out: (i) cholera deaths were strongly seasonal, with peak mortality almost always in the summer, (ii) the only non-summer outbreaks occurred in the spring of 1832, the autumn of 1848 and the winter of 1853, and (iii) extraordinarily severe summer outbreaks occurred in 1832, 1849, 1854 and 1866 (the four 'great' cholera years). The non-summer outbreaks of 1832, 1848 and 1853 appear to have been herald waves of newly invading cholera strains. In addition, a simple mathematical model confirms that a non-summer introduction of a new cholera strain can result in an initial herald wave, followed by a severe outbreak the following summer. Through the analysis of the genomes of nineteenth-century specimens, it may be possible to identify the strains that caused these herald waves and the well-known cholera epidemics that followed.
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Affiliation(s)
- Joseph H Tien
- Department of Mathematics, Ohio State University, Columbus, OH 43210, USA.
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Anderson-Carpenter LL, McLachlan JS, Jackson ST, Kuch M, Lumibao CY, Poinar HN. Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics. BMC Evol Biol 2011; 11:30. [PMID: 21272315 PMCID: PMC3041685 DOI: 10.1186/1471-2148-11-30] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 01/27/2011] [Indexed: 11/10/2022] Open
Abstract
Background Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes. Results We successfully sequenced DNA from 64 samples (out of 126) comprised of bulk sediment and seeds, leaf fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10 copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments < 2000 years old, but we were able to successfully amplify DNA from samples up to 4600 years old. DNA sequences matched the taxonomic identity of the macrofossil from which they were extracted 79% of the time. Exceptions suggest that DNA molecules from surrounding nearby sediments may permeate or adhere to macrofossils in sediments. Conclusions An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights into the genetic consequences of long-term environmental change. The low DNA copy numbers we found in fossil material and the discovery of multiple sequence variants from single macrofossil extractions highlight the need for careful experimental and laboratory protocols. Further application of these protocols should lead to better understanding of the ecological and evolutionary consequences of environmental change.
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Okello JBA, Zurek J, Devault AM, Kuch M, Okwi AL, Sewankambo NK, Bimenya GS, Poinar D, Poinar HN. Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues. Anal Biochem 2010; 400:110-7. [PMID: 20079706 DOI: 10.1016/j.ab.2010.01.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/11/2010] [Accepted: 01/11/2010] [Indexed: 11/24/2022]
Abstract
Archival formalin-fixed paraffin-embedded (FFPE) human tissue collections are typically in poor states of storage across the developing world. With advances in biomolecular techniques, these extraordinary and virtually untapped resources have become an essential part of retrospective epidemiological studies. To successfully use such tissues in genomic studies, scientists require high nucleic acid yields and purity. In spite of the increasing number of FFPE tissue kits available, few studies have analyzed their applicability in recovering high-quality nucleic acids from archived human autopsy samples. Here we provide a study involving 10 major extraction methods used to isolate total nucleic acid from FFPE tissues ranging in age from 3 to 13years. Although all 10 methods recovered quantifiable amounts of DNA, only 6 recovered quantifiable RNA, varying considerably and generally yielding lower DNA concentrations. Overall, we show quantitatively that TrimGen's WaxFree method and our in-house phenol-chloroform extraction method recovered the highest yields of amplifiable DNA, with considerable polymerase chain reaction (PCR) inhibition, whereas Ambion's RecoverAll method recovered the most amplifiable RNA.
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Affiliation(s)
- John B A Okello
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario L8S4L9, Canada.
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Affiliation(s)
| | - Hendrik N. Poinar
- Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada
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Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Gröcke DR, Matheus P, Zazula G, Guthrie D, Froese D, Buigues B, de Marliave C, Flemming C, Poinar D, Fisher D, Southon J, Tikhonov AN, MacPhee RDE, Poinar HN. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol 2008; 18:1320-6. [PMID: 18771918 DOI: 10.1016/j.cub.2008.07.061] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2008] [Revised: 07/16/2008] [Accepted: 07/17/2008] [Indexed: 11/28/2022]
Abstract
Although the iconic mammoth of the Late Pleistocene, the woolly mammoth (Mammuthus primigenius), has traditionally been regarded as the end point of a single anagenetically evolving lineage, recent paleontological and molecular studies have shown that successive allopatric speciation events must have occurred within Pleistocene Mammuthus in Asia, with subsequent expansion and hybridization between nominal taxa [1, 2]. However, the role of North American mammoth populations in these events has not been adequately explored from an ancient-DNA standpoint. To undertake this task, we analyzed mtDNA from a large data set consisting of mammoth samples from across Holarctica (n = 160) and representing most of radiocarbon time. Our evidence shows that, during the terminal Pleistocene, haplotypes originating in and characteristic of New World populations replaced or succeeded those endemic to Asia and western Beringia. Also, during the Last Glacial Maximum, mammoth populations do not appear to have suffered an overall decline in diversity, despite differing responses on either side of the Bering land bridge. In summary, the "Out-of-America" hypothesis holds that the dispersal of North American woolly mammoths into other parts of Holarctica created major phylogeographic structuring within Mammuthus primigenius populations, shaping the last phase of their evolutionary history before their demise.
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Affiliation(s)
- Regis Debruyne
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada
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Willerslev E, Cappellini E, Boomsma W, Nielsen R, Hebsgaard MB, Brand TB, Hofreiter M, Bunce M, Poinar HN, Dahl-Jensen D, Johnsen S, Steffensen JP, Bennike O, Schwenninger JL, Nathan R, Armitage S, de Hoog CJ, Alfimov V, Christl M, Beer J, Muscheler R, Barker J, Sharp M, Penkman KEH, Haile J, Taberlet P, Gilbert MTP, Casoli A, Campani E, Collins MJ. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 2007; 317:111-4. [PMID: 17615355 PMCID: PMC2694912 DOI: 10.1126/science.1141758] [Citation(s) in RCA: 333] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
It is difficult to obtain fossil data from the 10% of Earth's terrestrial surface that is covered by thick glaciers and ice sheets, and hence, knowledge of the paleoenvironments of these regions has remained limited. We show that DNA and amino acids from buried organisms can be recovered from the basal sections of deep ice cores, enabling reconstructions of past flora and fauna. We show that high-altitude southern Greenland, currently lying below more than 2 kilometers of ice, was inhabited by a diverse array of conifer trees and insects within the past million years. The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections.
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Affiliation(s)
- Eske Willerslev
- Centre for Ancient Genetics, University of Copenhagen, Denmark.
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Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RDE, Buigues B, Tikhonov A, Huson DH, Tomsho LP, Auch A, Rampp M, Miller W, Schuster SC. Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA. Science 2005; 311:392-4. [PMID: 16368896 DOI: 10.1126/science.1123360] [Citation(s) in RCA: 439] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.
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Affiliation(s)
- Hendrik N Poinar
- McMaster Ancient DNA Center, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.
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Thalmann O, Hebler J, Poinar HN, Pääbo S, Vigilant L. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol Ecol 2004; 13:321-35. [PMID: 14717890 DOI: 10.1046/j.1365-294x.2003.02070.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Analysis of mitochondrial DNA sequence variation has been used extensively to study the evolutionary relationships of individuals and populations, both within and across species. So ubiquitous and easily acquired are mtDNA data that it has been suggested that such data could serve as a taxonomic 'barcode' for an objective species classification scheme. However, there are technical pitfalls associated with the acquisition of mtDNA data. One problem is the presence of translocated pieces of mtDNA in the nuclear genome of many taxa that may be mistaken for authentic organellar mtDNA. We assessed the extent to which such 'numt' sequences may pose an overlooked problem in analyses of mtDNA from humans and apes. Using long-range polymerase chain reaction (PCR), we generated necessarily authentic mtDNA sequences for comparison with sequences obtained using typical methods for a segment of the mtDNA control region in humans, chimpanzees, bonobos, gorillas and orangutans. Results revealed that gorillas are notable for having such a variety of numt sequences bearing high similarity to authentic mtDNA that any analysis of mtDNA using standard approaches is rendered impossible. Studies on humans, chimpanzees, bonobos or orangutans are apparently less problematic. One implication is that explicit measures need to be taken to authenticate mtDNA sequences in newly studied taxa or when any irregularities arise. Furthermore, some taxa may not be amenable to analysis of mtDNA variation at all.
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Affiliation(s)
- O Thalmann
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
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Abstract
Most animals that once lived have gone extinct. The remains of a few of these can be found in museum collections worldwide. As modern evolutionary biology is limited to the use of extant taxa, retrieving DNA from extinct or subfossil organisms can add significant insight into past population history and resolve phylogenies that can be tentative by morphology alone. DNA is a relatively weak molecule, comparatively speaking, yet under certain conditions it persists in the fossil record, despite what in vitro chemistry predicts. While most fossil remains do not contain DNA, museum specimens can be screened for the presence of conditions that would be conducive for nucleic acid preservation by measuring the extent of amino acid racemization and by looking at the extent of protein hydrolysis by pyrolysis gas chromatography/mass spectrometry. Results from these types of analyses suggest that the preservation of DNA is linked to the temperature and its constancy at a site rather than its age. Chemical analyses of coprolites from extinct herbivores from the late Pleistocene, as well as Archaic Native Americans, show the presence of compounds from the Maillard reaction. Upon the cleaving of these products, the defecator can be identified and his diet analyzed.
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Affiliation(s)
- Hendrik N Poinar
- Max Planck Institute, Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany.
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Abstract
DNA was extracted from an 11,700-year-old rodent midden from the Atacama Desert, Chile and the chloroplast and animal mitochondrial DNA (mtDNA) gene sequences were analysed to investigate the floral environment surrounding the midden, and the identity of the midden agent. The plant sequences, together with the macroscopic identifications, suggest the presence of 13 plant families and three orders that no longer exist today at the midden locality, and thus point to a much more diverse and humid climate 11,700 years ago. The mtDNA sequences suggest the presence of at least four different vertebrates, which have been putatively identified as a camelid (vicuna), two rodents (Phyllotis and Abrocoma), and a cardinal bird (Passeriformes). To identify the midden agent, DNA was extracted from pooled faecal pellets, three small overlapping fragments of the mitochondrial cytochrome b gene were amplified and multiple clones were sequenced. These results were analysed along with complete cytochrome b sequences for several modern Phyllotis species to place the midden sequence phylogenetically. The results identified the midden agent as belonging to an ancestral P. limatus. Today, P. limatus is not found at the midden locality but it can be found 100 km to the north, indicating at least a small range shift. The more extensive sampling of modern Phyllotis reinforces the suggestion that P. limatus is recently derived from a peripheral isolate.
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MESH Headings
- Animals
- Base Sequence
- Chile
- Cytochrome b Group/chemistry
- Cytochrome b Group/genetics
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- Feces/chemistry
- Fossils
- Molecular Sequence Data
- Phylogeny
- Plants/classification
- Plants/genetics
- Polymerase Chain Reaction
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Rodentia/classification
- Rodentia/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Melanie Kuch
- Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22 04103 Leipzig, Germany
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Abstract
DNA that has been recovered from archaeological and palaeontological remains makes it possible to go back in time and study the genetic relationships of extinct organisms to their contemporary relatives. This provides a new perspective on the evolution of organisms and DNA sequences. However, the field is fraught with technical pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human remains are studied.
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Affiliation(s)
- M Hofreiter
- Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany
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Poinar HN, Kuch M, Sobolik KD, Barnes I, Stankiewicz AB, Kuder T, Spaulding WG, Bryant VM, Cooper A, Pääbo S. A molecular analysis of dietary diversity for three archaic Native Americans. Proc Natl Acad Sci U S A 2001; 98:4317-22. [PMID: 11296282 PMCID: PMC31832 DOI: 10.1073/pnas.061014798] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2-4 different animal species and 4-8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.
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Affiliation(s)
- H N Poinar
- Max-Planck-Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany.
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Abstract
DNA was extracted from five coprolites, excavated in Gypsum Cave, Nevada and radiocarbon dated to approximately 11 000, 20 000 and 28 500 years BP. All coprolites contained mitochondrial DNA sequences identical to a DNA sequence determined from a bone of the extinct ground sloth Nothrotheriops shastensis. A 157-bp fragment of the chloroplast gene for the large subunit of the ribulosebisphosphate carboxylase (rbcL) was amplified from the boluses and several hundred clones were sequenced. In addition, the same DNA fragment was sequenced from 99 plant species that occur in the vicinity of Gypsum Cave today. When these were compared to the DNA sequences in GenBank, 69 were correctly (two incorrectly) assigned to taxonomic orders. The plant sequences from the five coprolites as well as from one previously studied coprolite were compared to rbcL sequences in GenBank and the contemporary plant species. Thirteen families or orders of plants that formed part of the diet of the Shasta ground sloth could be identified, showing that the ground sloth was feeding on trees as well as herbs and grasses. The plants in the boluses further indicate that the climate 11 000 years BP was dryer than 20 000 and 28 500 years BP. However, the sloths seem to have visited water sources more frequently at 11 000 BP than at earlier times.
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Affiliation(s)
- M Hofreiter
- Max Planck Institute for Evolutionary Anthropology, Inselstr. 22, D-04103 Leipzig, Germany
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Poinar HN, Eglinton G. Preservation of DNA from endangered species. Science 2000; 289:726; author reply 726-7. [PMID: 10950715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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