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Brázda V, Dobrovolná M, Bohálová N, Mergny JL. G-quadruplexes in the evolution of hepatitis B virus. Nucleic Acids Res 2023; 51:7198-7204. [PMID: 37395407 PMCID: PMC10415126 DOI: 10.1093/nar/gkad556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/23/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023] Open
Abstract
Hepatitis B virus (HBV) is one of the most dangerous human pathogenic viruses found in all corners of the world. Recent sequencing of ancient HBV viruses revealed that these viruses have accompanied humanity for several millenia. As G-quadruplexes are considered to be potential therapeutic targets in virology, we examined G-quadruplex-forming sequences (PQS) in modern and ancient HBV genomes. Our analyses showed the presence of PQS in all 232 tested HBV genomes, with a total number of 1258 motifs and an average frequency of 1.69 PQS per kbp. Notably, the PQS with the highest G4Hunter score in the reference genome is the most highly conserved. Interestingly, the density of PQS motifs is lower in ancient HBV genomes than in their modern counterparts (1.5 and 1.9/kb, respectively). This modern frequency of 1.90 is very close to the PQS frequency of the human genome (1.93) using identical parameters. This indicates that the PQS content in HBV increased over time to become closer to the PQS frequency in the human genome. No statistically significant differences were found between PQS densities in HBV lineages found in different continents. These results, which constitute the first paleogenomics analysis of G4 propensity, are in agreement with our hypothesis that, for viruses causing chronic infections, their PQS frequencies tend to converge evolutionarily with those of their hosts, as a kind of 'genetic camouflage' to both hijack host cell transcriptional regulatory systems and to avoid recognition as foreign material.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
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2
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Hagen EH, Blackwell AD, Lightner AD, Sullivan RJ. Homo medicus: The transition to meat eating increased pathogen pressure and the use of pharmacological plants in Homo. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:589-617. [PMID: 36815505 DOI: 10.1002/ajpa.24718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/24/2023]
Abstract
The human lineage transitioned to a more carnivorous niche 2.6 mya and evolved a large body size and slower life history, which likely increased zoonotic pathogen pressure. Evidence for this increase includes increased zoonotic infections in modern hunter-gatherers and bushmeat hunters, exceptionally low stomach pH compared to other primates, and divergence in immune-related genes. These all point to change, and probably intensification, in the infectious disease environment of Homo compared to earlier hominins and other apes. At the same time, the brain, an organ in which immune responses are constrained, began to triple in size. We propose that the combination of increased zoonotic pathogen pressure and the challenges of defending a large brain and body from pathogens in a long-lived mammal, selected for intensification of the plant-based self-medication strategies already in place in apes and other primates. In support, there is evidence of medicinal plant use by hominins in the middle Paleolithic, and all cultures today have sophisticated, plant-based medical systems, add spices to food, and regularly consume psychoactive plant substances that are harmful to helminths and other pathogens. We propose that the computational challenges of discovering effective plant-based treatments, the consequent ability to consume more energy-rich animal foods, and the reduced reliance on energetically-costly immune responses helped select for increased cognitive abilities and unique exchange relationships in Homo. In the story of human evolution, which has long emphasized hunting skills, medical skills had an equal role to play.
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Affiliation(s)
- Edward H Hagen
- Department of Anthropology, Washington State University, Pullman, Washington, USA
| | - Aaron D Blackwell
- Department of Anthropology, Washington State University, Pullman, Washington, USA
| | - Aaron D Lightner
- Department of Anthropology, Washington State University, Pullman, Washington, USA
- Department of the Study of Religion, Aarhus University, Aarhus, Denmark
| | - Roger J Sullivan
- Department of Anthropology, California State University, Sacramento, California, USA
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3
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Frostegård J. Antibodies against phosphorylcholine and protection against atherosclerosis, cardiovascular disease and chronic inflammation. Expert Rev Clin Immunol 2022; 18:525-532. [PMID: 35471137 DOI: 10.1080/1744666x.2022.2070475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Chronic inflammatory diseases include cardiovascular disease (CVD) atherosclerosis, rheumatic and autoimmune diseases, and others, constitute a large part of the disease burden. It is therefore of major importance to improve understanding of underlying mechanisms, prediction and treatment. AREAS COVERED Broad fields including atherosclerosis, immunology and inflammation are covered, through searches on Pubmed and background knowledge. Phosphorylcholine (PC) is both a danger associated molecular pattern (DAMP), present on oxidized LDL (OxLDL) in atherosclerotic lesions and dead cells, and a pathogen associated molecular pattern (PAMP), present on microorganisms. IgM and IgG1 antibodies against PC (anti-PC) are associated with protection in several chronic inflammatory conditions, especially in CVD and atherosclerosis where most research has been done. PC-immunization ameliorates atherosclerosis in animal models and several potential underlying mechanisms have been proposed, including anti-inflammatory, decreased uptake of OxLDL in the artery wall, promotion of T regulatory cells. Anti-PC develops during the first years of life. Low levels of IgM and IgG1 anti-PC may be caused by lack of exposure to microorganisms, including nematodes and helminths among others. EXPERT OPINION anti-PC could improve prediction of clinical outcome and raising anti-PC could be developed into a novel therapy.
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Affiliation(s)
- Johan Frostegård
- Institute of Environmental Medicine, Karolinska Institutet, Nobels väg 15, 17165 Stockholm, Sweden,
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4
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Vågene ÅJ, Honap TP, Harkins KM, Rosenberg MS, Giffin K, Cárdenas-Arroyo F, Leguizamón LP, Arnett J, Buikstra JE, Herbig A, Krause J, Stone AC, Bos KI. Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. Nat Commun 2022; 13:1195. [PMID: 35256608 PMCID: PMC8901693 DOI: 10.1038/s41467-022-28562-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/25/2022] [Indexed: 12/30/2022] Open
Abstract
Previous ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal access to marine resources- a scenario incompatible with TB transmission directly from infected pinnipeds or their tissues. In this study, we investigate the causative agent of TB in ten pre-colonial, non-coastal individuals from South America. We reconstruct M. pinnipedii genomes (10- to 15-fold mean coverage) from three contemporaneous individuals from inland Peru and Colombia, demonstrating the widespread dissemination of M. pinnipedii beyond the coast, either through human-to-human and/or animal-mediated routes. Overall, our study suggests that TB transmission in the pre-colonial era Americas involved a more complex transmission pathway than simple pinniped-to-human transfer.
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Affiliation(s)
- Åshild J Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Tanvi P Honap
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
- Department of Anthropology, University of Oklahoma, Norman, OK, USA.
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA.
| | - Kelly M Harkins
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Michael S Rosenberg
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Judith Arnett
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
- University of the Andes, School of Medicine, Bogotá, Colombia
| | - Jane E Buikstra
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
- Institute of Human Origins, Arizona State University, Tempe, AZ, USA.
| | - Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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5
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Michail G, Karapetsi L, Madesis P, Reizopoulou A, Vagelas I. Metataxonomic Analysis of Bacteria Entrapped in a Stalactite's Core and Their Possible Environmental Origins. Microorganisms 2021; 9:microorganisms9122411. [PMID: 34946013 PMCID: PMC8705861 DOI: 10.3390/microorganisms9122411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 02/02/2023] Open
Abstract
Much is known about microbes originally identified in caves, but little is known about the entrapment of microbes (bacteria) in stalactites and their possible environmental origins. This study presents data regarding the significant environmental distribution of prokaryotic bacterial taxa of a Greek stalactite core. We investigated the involvement of those bacteria communities in stalactites using a metataxonomic analysis approach of partial 16S rRNA genes. The metataxonomic analysis of stalactite core material revealed an exceptionally broad ecological spectrum of bacteria classified as members of Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and other unclassified bacteria. We concluded that (i) the bacterial transport process is possible through water movement from the upper ground cave environment, forming cave speleothems such as stalactites, (ii) bacterial genera such as Polaromonas, Thioprofundum, and phylum Verrucomicrobia trapped inside the stalactite support the paleoecology, paleomicrobiology, and paleoclimate variations, (iii) the entrapment of certain bacteria taxa associated with water, soil, animals, and plants such as Micrococcales, Propionibacteriales, Acidimicrobiales, Pseudonocardiales, and α-, β-, and γ-Proteobacteria.
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Affiliation(s)
- George Michail
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
- Correspondence:
| | - Lefkothea Karapetsi
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (L.K.); (P.M.)
- Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), 57001 Thessaloniki, Greece
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (L.K.); (P.M.)
- Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), 57001 Thessaloniki, Greece
| | | | - Ioannis Vagelas
- Department of Agriculture Crop Production and Rural Environment, University of Thessaly, 38446 Volos, Greece;
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6
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Wu X, Ning C, Key FM, Andrades Valtueña A, Lankapalli AK, Gao S, Yang X, Zhang F, Liu L, Nie Z, Ma J, Krause J, Herbig A, Cui Y. A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road. PLoS Pathog 2021; 17:e1009886. [PMID: 34547027 PMCID: PMC8486138 DOI: 10.1371/journal.ppat.1009886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 10/01/2021] [Accepted: 08/11/2021] [Indexed: 01/03/2023] Open
Abstract
Salmonella enterica (S. enterica) has infected humans for a long time, but its evolutionary history and geographic spread across Eurasia is still poorly understood. Here, we screened for pathogen DNA in 14 ancient individuals from the Bronze Age Quanergou cemetery (XBQ), Xinjiang, China. In 6 individuals we detected S. enterica. We reconstructed S. enterica genomes from those individuals, which form a previously undetected phylogenetic branch basal to Paratyphi C, Typhisuis and Choleraesuis-the so-called Para C lineage. Based on pseudogene frequency, our analysis suggests that the ancient S. enterica strains were not host adapted. One genome, however, harbors the Salmonella pathogenicity island 7 (SPI-7), which is thought to be involved in (para)typhoid disease in humans. This offers first evidence that SPI-7 was acquired prior to the emergence of human-adapted Paratyphi C around 1,000 years ago. Altogether, our results show that Salmonella enterica infected humans in Eastern Eurasia at least 3,000 years ago, and provide the first ancient DNA evidence for the spread of a pathogen along the Proto-Silk Road.
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Affiliation(s)
- Xiyan Wu
- School of Life Sciences, Jilin University, Changchun, China
- School of History and Culture, Henan University, Kaifeng, China
| | - Chao Ning
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Felix M. Key
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Aida Andrades Valtueña
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Shizhu Gao
- College of Pharmacia Sciences, Jilin University, Changchun, China
| | - Xuan Yang
- School of Life Sciences, Jilin University, Changchun, China
| | - Fan Zhang
- School of Life Sciences, Jilin University, Changchun, China
| | - Linlin Liu
- Department of Radiation Oncology, The Second Hospital of Jilin University, Changchun, China
| | - Zhongzhi Nie
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
| | - Jian Ma
- School of Cultural Heritage, Northwest University, Xi’an, China
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, China
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
- Key Laboratory for Evolution of Past Life and Environment in Northeast Asia (Jilin University), Ministry of Education, Changchun, China
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7
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Zacho CM, Bager MA, Margaryan A, Gravlund P, Galatius A, Rasmussen AR, Allentoft ME. Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes. PLoS One 2021; 16:e0256353. [PMID: 34424926 PMCID: PMC8382189 DOI: 10.1371/journal.pone.0256353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/04/2021] [Indexed: 11/19/2022] Open
Abstract
Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.
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Affiliation(s)
- Claus M. Zacho
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martina A. Bager
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Anders Galatius
- Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Arne R. Rasmussen
- Institute of Conservation, Royal Danish Academy—Architecture, Design, Conservation, Copenhagen, Denmark
| | - Morten E. Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Australia
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8
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Arning N, Wilson DJ. The past, present and future of ancient bacterial DNA. Microb Genom 2020; 6:mgen000384. [PMID: 32598277 PMCID: PMC7478633 DOI: 10.1099/mgen.0.000384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.
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Affiliation(s)
- Nicolas Arning
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
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9
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Arriola LA, Cooper A, Weyrich LS. Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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10
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Nelson EA, Buikstra JE, Herbig A, Tung TA, Bos KI. Advances in the molecular detection of tuberculosis in pre-contact Andean South America. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2020; 29:128-140. [PMID: 31964606 DOI: 10.1016/j.ijpp.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 12/06/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Andean paleopathological research has significantly enhanced knowledge about the geographical distribution and evolution of tuberculosis (TB) in pre-Columbian South America. In this paper, we review the history and progress of research on ancient tuberculosis (TB) in the Andean region, focusing on the strengths and limitations of current approaches for the molecular detection of ancient pathogens, with special attention to TB. As a case study, we describe a molecular screening approach for the detection of ancient Mycobacterium tuberculosis in individuals from Late Intermediate Period (1000-1400 CE) contexts at the site of Huari, Peru. We evaluate 34 commingled human vertebrae and combine morphological assessments of pathology with high throughput sequencing and a non-selective approach to ancient pathogen DNA screening. Our method enabled the simultaneous detection of ancient M. tuberculosis DNA and an evaluation of the environmental microbial composition of each sample. Our results show that despite the dominance of environmental DNA, molecular signatures of M. tuberculosis were identified in eight vertebrae, six of which had no observable skeletal pathology classically associated tuberculosis infection. This screening approach will assist in the identification of candidate samples for downstream genomic analyses. The method permits higher resolution disease identification in cases where pathology may be absent, or where the archaeological context may necessitate a broad differential diagnosis based on morphology alone.
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Affiliation(s)
- Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str 10, 07745 Jena, Germany; Eberhard Karls Universität Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany.
| | - Jane E Buikstra
- Center for Bioarchaeological Research, Arizona State University, 1151 S. Forest Ave., Tempe, AZ, 85281, USA.
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str 10, 07745 Jena, Germany.
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, VU Station B #356050, Nashville, TN 37235, USA.
| | - Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str 10, 07745 Jena, Germany.
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11
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Emery MV, Bolhofner K, Winingear S, Oldt R, Montes M, Kanthaswamy S, Buikstra JE, Fulginiti LC, Stone AC. Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques. Forensic Sci Int Genet 2020; 46:102272. [PMID: 32172220 DOI: 10.1016/j.fsigen.2020.102272] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/19/2022]
Abstract
Thermal degeneration of the DNA molecule presents a special challenge to medico-legal investigations since low DNA yields, fragmented DNA molecules, and damaged nucleotide bases hinder accurate STR genotyping. As a consequence, fragments of severely burned human remains are often not amenable to standard DNA recovery. However, current ancient DNA (aDNA) extraction methods have proven highly effective at obtaining ultrashort DNA fragments (∼50 bp) from degraded palaeontological and archaeological specimens. In this study, we compare DNA yields and STR results obtained from two established aDNA and forensic DNA extraction protocols by sampling multiple skeletal elements recovered from victims (n = 23) involved in fire-related incidents. DNA yields and STR results suggest an inverse correlation between DNA yield and STR quality and increasing temperature. Despite the rapid thermal destruction of DNA at high temperatures, we generated higher quality full and partial STR profiles using the aDNA extraction protocol across all burn categories than the forensic total bone demineralization extraction method. Our analysis suggests adopting aDNA extraction methods as an alternative to current forensic practices to improve DNA yields from challenging human remains.
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Affiliation(s)
- M V Emery
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States.
| | - K Bolhofner
- Center for Bioarchaeological Research, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States; School of Mathematical and Natural Sciences, Arizona State University, United States
| | - S Winingear
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States
| | - R Oldt
- School of Life Sciences, Arizona State University, United States
| | - M Montes
- School of Mathematical and Natural Sciences, Arizona State University, United States
| | - S Kanthaswamy
- School of Life Sciences, Arizona State University, United States; School of Mathematical and Natural Sciences, Arizona State University, United States
| | - J E Buikstra
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeological Research, Arizona State University, United States
| | - L C Fulginiti
- School of Human Evolution and Social Change, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States
| | - A C Stone
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeological Research, Arizona State University, United States.
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12
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Baker BJ, Crane-Kramer G, Dee MW, Gregoricka LA, Henneberg M, Lee C, Lukehart SA, Mabey DC, Roberts CA, Stodder ALW, Stone AC, Winingear S. Advancing the understanding of treponemal disease in the past and present. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:5-41. [PMID: 31956996 DOI: 10.1002/ajpa.23988] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022]
Abstract
Syphilis was perceived to be a new disease in Europe in the late 15th century, igniting a debate about its origin that continues today in anthropological, historical, and medical circles. We move beyond this age-old debate using an interdisciplinary approach that tackles broader questions to advance the understanding of treponemal infection (syphilis, yaws, bejel, and pinta). How did the causative organism(s) and humans co-evolve? How did the related diseases caused by Treponema pallidum emerge in different parts of the world and affect people across both time and space? How are T. pallidum subspecies related to the treponeme causing pinta? The current state of scholarship in specific areas is reviewed with recommendations made to stimulate future work. Understanding treponemal biology, genetic relationships, epidemiology, and clinical manifestations is crucial for vaccine development today and for investigating the distribution of infection in both modern and past populations. Paleopathologists must improve diagnostic criteria and use a standard approach for recording skeletal lesions on archaeological human remains. Adequate contextualization of cultural and environmental conditions is necessary, including site dating and justification for any corrections made for marine or freshwater reservoir effects. Biogeochemical analyses may assess aquatic contributions to diet, physiological changes arising from treponemal disease and its treatments (e.g., mercury), or residential mobility of those affected. Shifting the focus from point of origin to investigating who is affected (e.g., by age/sex or socioeconomic status) and disease distribution (e.g., coastal/ inland, rural/urban) will advance our understanding of the treponemal disease and its impact on people through time.
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Affiliation(s)
- Brenda J Baker
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
| | - Gillian Crane-Kramer
- Department of Anthropology, State University of New York at Plattsburgh, Plattsburgh, New York
| | - Michael W Dee
- Centre for Isotope Research, University of Groningen, Groningen, Netherlands
| | - Lesley A Gregoricka
- Department of Sociology, Anthropology, and Social Work, University of South Alabama, Mobile, Alabama
| | - Maciej Henneberg
- Biological Anthropology and Comparative Anatomy Unit, Adelaide Medical School, University of Adelaide, Adelaide, Australia.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Christine Lee
- Department of Anthropology, California State University Los Angeles, Los Angeles, California
| | - Sheila A Lukehart
- Department of Medicine/Infectious Diseases and Global Health, University of Washington, Seattle, Washington
| | - David C Mabey
- Communicable Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Ann L W Stodder
- Office of Archaeological Studies, The Museum of New Mexico, Santa Fe, New Mexico
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
| | - Stevie Winingear
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
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13
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Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals. Nat Commun 2019; 10:5003. [PMID: 31676766 PMCID: PMC6825168 DOI: 10.1038/s41467-019-12862-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/26/2019] [Indexed: 12/11/2022] Open
Abstract
Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated ‘pathogen packages’ could have generated feedback that allowed modern humans to overcome disease burden earlier than Neanderthals, giving them an advantage in their subsequent spread into Eurasia. Modern humans and Neanderthals coexisted in the Levant for tens of thousands of years before modern humans spread and replaced Neanderthals. Here, Greenbaum et al. develop a model showing that transmission of disease and genes can explain the maintenance and then collapse of this contact zone.
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14
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Ali A, Melcher U. Modeling of Mutational Events in the Evolution of Viruses. Viruses 2019; 11:v11050418. [PMID: 31060293 PMCID: PMC6563203 DOI: 10.3390/v11050418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/27/2019] [Accepted: 05/02/2019] [Indexed: 11/24/2022] Open
Abstract
Diverse studies of viral evolution have led to the recognition that the evolutionary rates of viral taxa observed are dependent on the time scale being investigated—with short-term studies giving fast substitution rates, and orders of magnitude lower rates for deep calibrations. Although each of these factors may contribute to this time dependent rate phenomenon, a more fundamental cause should be considered. We sought to test computationally whether the basic phenomena of virus evolution (mutation, replication, and selection) can explain the relationships between the evolutionary and phylogenetic distances. We tested, by computational inference, the hypothesis that the phylogenetic distances between the pairs of sequences are functions of the evolutionary path lengths between them. A Basic simulation revealed that the relationship between simulated genetic and mutational distances is non-linear, and can be consistent with different rates of nucleotide substitution at different depths of branches in phylogenetic trees.
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Affiliation(s)
- Akhtar Ali
- Department of Biological Sciences, University of Tulsa, Tulsa, OK 74104, USA.
| | - Ulrich Melcher
- Department of Biochemistry & Molecular Biology, Oklahoma State University, Stillwater, OK 74078-3035, USA.
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15
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Wood JR, Díaz FP, Latorre C, Wilmshurst JM, Burge OR, Gutiérrez RA. Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile. Sci Rep 2018; 8:17208. [PMID: 30464240 PMCID: PMC6249261 DOI: 10.1038/s41598-018-35299-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/01/2018] [Indexed: 01/17/2023] Open
Abstract
Future climate change has the potential to alter the distribution and prevalence of plant pathogens, which may have significant implications for both agricultural crops and natural plant communities. However, there are few long-term datasets against which modelled predictions of pathogen responses to climate change can be tested. Here, we use 18S metabarcoding of 28 rodent middens (solidified deposits of rodent coprolites and nesting material) from the Central Atacama, spanning the last ca. 49 ka, to provide the first long-term late Quaternary record of change in plant pathogen communities in response to changing climate. Plant pathogen richness was significantly greater in middens deposited during the Central Andean Pluvial Event (CAPE); a period of increased precipitation between 17.5–8.5 ka. Moreover, the occurrence frequency of Pucciniaceae (rust fungi) was significantly greater during the CAPE, and the highest relative abundances for five additional potentially pathogenic taxa also occurred during this period. The results demonstrate the promising potential for ancient DNA analysis of late Quaternary samples to reveal insights into how plant pathogens responded to past climatic and environmental change, which could help predict how pathogens may responded to future change.
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Affiliation(s)
- Jamie R Wood
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, 7640, New Zealand.
| | - Francisca P Díaz
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile. .,FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Claudio Latorre
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Alameda, 340, Santiago, Chile.,Institute of Ecology and Biodiversity (IEB), Las Palmeras, 3425, Ñuñoa, Santiago, Chile
| | - Janet M Wilmshurst
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, 7640, New Zealand.,School of Environment, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Olivia R Burge
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, 7640, New Zealand
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,FONDAP Center for Genome Regulation & Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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16
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Abstract
Beginning some 10,000 years ago, humans began a dramatic alteration in living conditions relating especially to the shift in lifeway from foraging to farming. In addition to the initiation of and increasing focus on the production and consumption of domesticated plant carbohydrates, this revolutionary transformation in diet occasioned a decline in mobility and an increased size and agglomeration of populations in semipermanent or permanent settlements. These changes in life conditions presented an opportunity for increased transmission of pathogenic microbes from host to host, such as those that cause major health threats affecting most of the 7.5 billion members of our species today. This article discusses the bioarchaeology of infectious disease, focusing on tuberculosis, treponematosis, dental caries, and periodontitis, all of which continue to contribute to high levels of morbidity and mortality among the world's populations today.
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Affiliation(s)
- Clark Spencer Larsen
- Department of Anthropology, Ohio State University, Columbus, Ohio 43210-1106, USA
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17
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The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections. Genes (Basel) 2018; 9:genes9070317. [PMID: 29941858 PMCID: PMC6070984 DOI: 10.3390/genes9070317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/18/2022] Open
Abstract
Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, distribution, and coevolutionary host relationships of these pathogens, providing insights into pathogen emergence and disease prevention. Deep-sequenced pathogen genomes from clinical studies and ancient samples yield estimates of within-host and between-host evolutionary rates and provide data on changes in pathogen genomic stability and evolutionary responses. Here we examine three groups of pathogens transmitted mainly through sexual contact between modern humans to provide insight into ancient human behavior and history with their pathogens. Exploring ancient pathogen genomic divergence and the ancient viral-host parallel evolutionary histories will help us to reconstruct the origin of present-day geographical distribution and diversity of clinical pathogen infections, and will hopefully allow us to foresee possible environmentally induced pathogen evolutionary responses. Lastly, we emphasize that ancient pathogen DNA research should be combined with modern clinical pathogen data, and be equitable and provide advantages for all researchers worldwide, e.g., through shared data.
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18
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Larsen BB, Cole KL, Worobey M. Ancient DNA provides evidence of 27,000-year-old papillomavirus infection and long-term codivergence with rodents. Virus Evol 2018; 4:vey014. [PMID: 29977605 PMCID: PMC6007503 DOI: 10.1093/ve/vey014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The long-term evolutionary history of many viral lineages is poorly understood. Novel sources of ancient DNA combined with phylogenetic analyses can provide insight into the time scale of virus evolution. Here we report viral sequences from ancient North American packrat middens. We screened samples up to 27,000-years old and found evidence of papillomavirus (PV) infection in Neotoma cinerea (Bushy-tailed packrat). Phylogenetic analysis placed the PV sequences in a clade with other previously published PV sequences isolated from rodents. Concordance between the host and virus tree topologies along with a correlation in branch lengths suggests a shared evolutionary history between rodents and PVs. Based on host divergence times, PVs have likely been circulating in rodents for at least 17 million years. These results have implications for our understanding of PV evolution and for further research with ancient DNA from Neotoma middens.
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Affiliation(s)
- Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, 85721 AZ, USA
| | - Kenneth L Cole
- Northern Arizona University, School of Earth Sciences and Environmental Sustainability, 525 S. Beaver St., Flagstaff, 86011 AZ, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, 85721 AZ, USA
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19
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Rifkin RF, Potgieter M, Ramond J, Cowan DA. Ancient oncogenesis, infection and human evolution. Evol Appl 2017; 10:949-964. [PMID: 29151852 PMCID: PMC5680625 DOI: 10.1111/eva.12497] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/22/2017] [Indexed: 12/27/2022] Open
Abstract
The recent discovery that malignant neoplastic lesions date back nearly 2 million years ago not only highlights the antiquity of cancer in the human lineage, but also provides remarkable insight into ancestral hominin disease pathology. Using these Early Pleistocene examples as a point of departure, we emphasize the prominent role of viral and bacterial pathogens in oncogenesis and evaluate the impact of pathogens on human evolutionary processes in Africa. In the Shakespearean vernacular "what's past is prologue," we highlight the significance of novel information derived from ancient pathogenic DNA. In particular, and given the temporal depth of human occupation in sub-Saharan Africa, it is emphasized that the region is ideally positioned to play a strategic role in the discovery of ancient pathogenic drivers of not only human mortality, but also human evolution. Ancient African pathogen genome data can provide novel revelations concerning human-pathogen coevolutionary processes, and such knowledge is essential for forecasting the ways in which emerging zoonotic and increasingly transmissible diseases might influence human demography and longevity in the future.
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Affiliation(s)
- Riaan F. Rifkin
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
| | - Marnie Potgieter
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
| | - Jean‐Baptiste Ramond
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
| | - Don A. Cowan
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
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20
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Marciniak S, Perry GH. Harnessing ancient genomes to study the history of human adaptation. Nat Rev Genet 2017; 18:659-674. [PMID: 28890534 DOI: 10.1038/nrg.2017.65] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.
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Affiliation(s)
- Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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21
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Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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22
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Milner GR, Boldsen JL. Life not death: Epidemiology from skeletons. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2017; 17:26-39. [PMID: 28521910 DOI: 10.1016/j.ijpp.2017.03.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 03/07/2017] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
Analytically sophisticated paleoepidemiology is a relatively new development in the characterization of past life experiences. It is based on sound paleopathological observations, accurate age-at-death estimates, an explicit engagement with the nature of mortality samples, and analytical procedures that owe much to epidemiology. Of foremost importance is an emphasis on people, not skeletons. Transforming information gleaned from the dead, a biased sample of individuals who were once alive at each age, into a form that is informative about past life experiences has been a major challenge for bioarchaeologists, but recent work shows it can be done. The further development of paleoepidemiology includes essential contributions from paleopathology, archaeology or history (as appropriate), and epidemiology.
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Affiliation(s)
- George R Milner
- Department of Anthropology, 409 Carpenter Building, Pennsylvania State University, University Park, PA 16802, USA.
| | - Jesper L Boldsen
- Unit of Anthropology [ADBOU], Department of Forensic Medicine, University of Southern Denmark, Lucernemarken 20, DK 5260 Odense S, Denmark.
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23
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Houldcroft CJ, Ramond JB, Rifkin RF, Underdown SJ. Migrating microbes: what pathogens can tell us about population movements and human evolution. Ann Hum Biol 2017; 44:397-407. [PMID: 28511559 DOI: 10.1080/03014460.2017.1325515] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases. METHODS This study explores which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts. RESULTS Three stories are then presented of germs on a journey. The first is the story of HIV's spread on the back of colonialism and the railway networks over the last 150 years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2. CONCLUSIONS Evidence from modern African pathogen genomes can provide data on human behaviour and migration in deep time and contribute to the improvement of human quality-of-life and longevity.
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Affiliation(s)
- Charlotte J Houldcroft
- a Department of Archaeology and Anthropology, Division of Biological Anthropology , University of Cambridge , Cambridge , UK.,b McDonald Institute of Archaeological Research, University of Cambridge , Cambridge , UK
| | - Jean-Baptiste Ramond
- c Department of Genetics , Centre for Microbial Ecology and Genomics, Genomic Research Institute, University of Pretoria , Hatfield , South Africa
| | - Riaan F Rifkin
- c Department of Genetics , Centre for Microbial Ecology and Genomics, Genomic Research Institute, University of Pretoria , Hatfield , South Africa
| | - Simon J Underdown
- d Department of Anthropology & Geography, Human Origins and Palaeoenvironmental Research Group (HOPE) , Oxford Brookes University , Oxford , UK.,e Leverhulme Centre for Human Evolutionary Studies , Henry Wellcome Building , Cambridge , UK
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24
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Abstract
The recent Ebola epidemic provides a dramatic example of the devastation and fear generated by epidemics, particularly those caused by new emerging or reemerging diseases. A focus on the control and prevention of diseases in living populations dominates most epidemic disease research. However, research on epidemics in the past provides a temporal depth to our understanding of the context and consequences of diseases and is crucial for predicting how diseases might shape human biology and demography in the future. This article reviews recent research on historic epidemics of plague and tuberculosis, both of which have affected human populations for millennia. Research on these diseases demonstrates the range (and differential availability) of various lines of evidence (e.g., burial context, diagnostic skeletal lesions, molecular data) that inform about past disease in general. I highlight how research on past epidemics may be informative in ways that benefit living populations.
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Affiliation(s)
- Sharon N. DeWitte
- Department of Anthropology and Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208
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25
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Frostegård J, Tao W, Råstam L, Lindblad U, Lindeberg S. Antibodies against Phosphorylcholine among New Guineans Compared to Swedes: An Aspect of the Hygiene/Missing Old Friends Hypothesis. Immunol Invest 2016; 46:59-69. [PMID: 27611006 DOI: 10.1080/08820139.2016.1213279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND We here study antibodies against phosphorylcholine (anti-PC) which we reported to be inversely associated with atherosclerosis, cardiovascular disease (CVD), and autoimmune conditions. In previous studies, we determined that this inverse association is more pronounced at low levels with high risk and at high levels, with decreased risk. We compare individuals from Kitava, New Guinea (with low risk of these conditions), with Swedish controls. METHODS We studied a group of 178 individuals from Kitava (age 20-86), and compared those above age 40 (n = 108) with a group of age- and sex-matched individuals from a population based cohort in Sweden (n = 108). Traditional risk factors for CVD and fatty acids were determined. IgM, IgG, and IgA anti-PC were tested by enzyme-linked immunosorbent assay (ELISA). RESULTS All anti-PC measures were significantly lower among Swedish controls as compared to Kitavans (p < 0.001), independent of traditional risk factors. Having low levels of anti-PC, defined as below 25th percentile of values among Swedish controls, was associated with this cohort after adjustment for other risk factors (OR 5.7, 95% CI 2.2-14.7 for IgM; OR 31.7, 95% CI 3.9-252 for IgA; and OR 11.1, 95% CI 2.4-51 for IgG). CONCLUSIONS PC is highly exposed on microorganisms and helminths (common on Kitava) exposing much PC which humans and hominids may have been exposed to for millions of years. We propose that low anti-PC levels in the developed world could be a new aspect of the hygiene hypothesis, generating a pro-inflammatory and pro-atherosclerotic state.
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Affiliation(s)
- Johan Frostegård
- a Department of IMM , Karolinska Institutet , Stockholm , Sweden
| | - WenJing Tao
- b Upper Gastrointestinal Surgery, Department of Molecular Medicine and Surgery , Karolinska Institutet , Stockholm , Sweden
| | - Lennart Råstam
- c Department of Clinical Sciences , Lund University , Lund , Sweden
| | - Ulf Lindblad
- d Department of Medicine , University of Gothenburg , Gothenburg , Sweden
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26
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Sholts SB, Bell JA, Rick TC. Ecce Homo: Science and Society Need Anthropological Collections. Trends Ecol Evol 2016; 31:580-583. [PMID: 27220779 DOI: 10.1016/j.tree.2016.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/03/2016] [Accepted: 05/05/2016] [Indexed: 11/28/2022]
Abstract
Scientific collections are crucial to understanding the biological and cultural diversity of the Earth. Anthropological collections document the human experience and the interactions between people, ecosystems, and organisms. Unfortunately, anthropological collections are often poorly known by the public and face a variety of threats to their permanent care and conservation.
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Affiliation(s)
- Sabrina B Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | - Joshua A Bell
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Torben C Rick
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
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27
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Willermet C. Biological Anthropology in 2015: Open Access, Biocultural Interactions, and Social Change. AMERICAN ANTHROPOLOGIST 2016. [DOI: 10.1111/aman.12529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Cathy Willermet
- Department of Sociology, Anthropology, and Social Work; Central Michigan University; Mount Pleasant MI 48859
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28
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Perry GH, Orlando L. Ancient DNA and human evolution. J Hum Evol 2015; 79:1-3. [DOI: 10.1016/j.jhevol.2014.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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