Zoonoses and their traces in ancient genomes – a possible indicator for ancient life-style changes?

Dawid Leciej; Karl-Heinz Herzig; Olaf Thalmann

doi:10.20883/medical.e467

Authors

Dawid Leciej Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poland https://orcid.org/0000-0002-8893-6940
Karl-Heinz Herzig Department of Pediatric Gastroenterology and Metabolic Diseases, Poznań University of Medical Sciences, Poland; University of Oulu, Research Unit of Biomedicine, Medical Research Center, Faculty of Medicine, Oulu University Hospital, Oulu, Finland https://orcid.org/0000-0003-4460-2604
Olaf Thalmann Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poland https://orcid.org/0000-0003-1700-0130

DOI:

https://doi.org/10.20883/medical.e467

Keywords:

zoonoses, paleoepidemiology, paleogenomics, paleoepigenomics, neolithic, ancient DNA

Abstract

Humans are constantly exposed to health risks inherent to the environment in which they live, thereby including non-human fauna. Zoonoses are infectious diseases caused by agents such as bacteria, parasites, or viruses being transmitted to humans from wild animals and livestock. The close proximity of animals and humans facilitate the spread of zoonoses, so it is intriguing to hypothesize that populations accustomed to different lifestyles will also vary in the prevalence of zoonotic agents. The Neolithic era in human history is characterised by a dramatic transition in lifestyle, from hunting and gathering to farming. Thus, with the changes in the reservoir of animal species humans were exposed to zoonotic agents potentially penetrating human populations. Due to the rapid development of sequencing technologies and methodology in ancient DNA research, it is now possible to generate complete genomes of ancient specimens and pinpoint those genomic regions or epigenetic signatures that might be influenced by past zoonotic transmissions. Unravelling such traces, particularly on a population-scale, will help to overcome the lack of generalisation that hampered previous research focusing exclusively on the model fossils in human evolution, and facilitate a better understanding of the aetiology of diseases, including those caused by zoonotic agents.

Downloads

Download data is not yet available.

References

Chomel B. Zoonoses. In: Encyclopedia of Microbiology. Elsevier Inc.; 2009:820-90. https://doi.org/10.1016/B978-012373944-5.00213-3

Marí Saéz A, Weiss S, Nowak K, Lapeyre V, Zimmermann F, Düx A, Kühl HS, Kaba M, Regnaut S, Merkel K, Sachse A, Thiesen U, Villányi L, Boesch C, Dabrowski PW, Radonić A, Nitsche A, Leendertz SAJ, Petterson S, Becker S, Krähling V, Couacy‐Hymann E, Akoua‐Koffi C, Weber N, Schaade L, Fahr J, Borchert M, Gogarten JF, Calvignac‐Spencer S, Leendertz FH. Investigating the zoonotic origin of the West African Ebola epidemic. EMBO Molecular Medicine. 2014 Dec 30;7(1):17-23. https://doi.org/10.15252/emmm.201404792

Field HE. Bats and Emerging Zoonoses: Henipaviruses and SARS. Zoonoses and Public Health. 2009 Aug;56(6-7):278-284. https://doi.org/10.1111/j.1863-2378.2008.01218.x

Walsh PD, Biek R, Real LA. Wave-Like Spread of Ebola Zaire. Harvey P. PLoS Biology. 2005 Oct 25;3(11):e371. https://doi.org/10.1371/journal.pbio.0030371

Larson G, Burger J. A population genetics view of animal domestication. Trends in Genetics. 2013 Apr;29(4):197-205. https://doi.org/10.1016/j.tig.2013.01.003

Latham K. Human Health and the Neolithic Revolution: An Overview of Impacts of the Agricultural Transition on Oral Health, Epidemiology, and the Human Body. Nebraska Anthropologist. 2013;:187.

Fournié G, Pfeiffer DU, Bendrey R. Early animal farming and zoonotic disease dynamics: modelling brucellosis transmission in Neolithic goat populations. Royal Society Open Science. 2017 Feb;4(2):160943. https://doi.org/10.1098/rsos.160943

Spyrou MA, Bos KI, Herbig A, Krause J. Ancient pathogen genomics as an emerging tool for infectious disease research. Nature Reviews Genetics. 2019 Apr 5;20(6):323-340. https://doi.org/10.1038/s41576-019-0119-1

Kahila Bar-Gal G, Kim MJ, Klein A, Shin DH, Oh CS, Kim JW, Kim T, Kim SB, Grant PR, Pappo O, Spigelman M, Shouval D. Tracing hepatitis B virus to the 16th century in a Korean mummy. Hepatology. 2012 Oct 14;56(5):1671-1680. https://doi.org/10.1002/hep.25852

Günther T, Valdiosera C, Malmström H, Ureña I, Rodriguez-Varela R, Sverrisdóttir ÓO, Daskalaki EA, Skoglund P, Naidoo T, Svensson EM, Bermúdez de Castro JM, Carbonell E, Dunn M, Storå J, Iriarte E, Arsuaga JL, Carretero J, Götherström A, Jakobsson M. Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. Proceedings of the National Academy of Sciences. 2015 Sep 8;112(38):11917-11922. https://doi.org/10.1073/pnas.1509851112

Cooper A. Ancient DNA: Do It Right or Not at All. Science. 2000 Aug 18;289(5482):1139b-1139. https://doi.org/10.1126/science.289.5482.1139b

Orlando L, Gilbert MTP, Willerslev E. Reconstructing ancient genomes and epigenomes. Nature Reviews Genetics. 2015 Jun 9;16(7):395-408. https://doi.org/10.1038/nrg3935

Llamas B, Valverde G, Fehren-Schmitz L, Weyrich LS, Cooper A, Haak W. From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era. STAR: Science & Technology of Archaeological Research. 2016 Nov 30;3(1):1-14. https://doi.org/10.1080/20548923.2016.1258824

Sawyer S, Krause J, Guschanski K, Savolainen V, Pääbo S. Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA. Lalueza-Fox C. PLoS ONE. 2012 Mar 30;7(3):e34131. https://doi.org/10.1371/journal.pone.0034131

Keller M, Spyrou MA, Scheib CL, Neumann GU, Kröpelin A, Haas-Gebhard B, Päffgen B, Haberstroh J, Ribera i Lacomba A, Raynaud C, Cessford C, Durand R, Stadler P, Nägele K, Bates JS, Trautmann B, Inskip SA, Peters J, Robb JE, Kivisild T, Castex D, McCormick M, Bos KI, Harbeck M, Herbig A, Krause J. Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750). Proceedings of the National Academy of Sciences. 2019 Jun 4;116(25):12363-12372. https://doi.org/10.1073/pnas.1820447116

Zink AR, Molnár E, Motamedi N, Pálfy G, Marcsik A, Nerlich AG. Molecular history of tuberculosis from ancient mummies and skeletons. International Journal of Osteoarchaeology. 2007;17(4):380-391. https://doi.org/10.1002/oa.909

Enard D, Petrov DA. Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans. Cell. 2018 Oct;175(2):360-371.e13. https://doi.org/10.1016/j.cell.2018.08.034

Syvanen M. Cross-species gene transfer; implications for a new theory of evolution. Journal of Theoretical Biology. 1985 Jan;112(2):333-343. https://doi.org/10.1016/s0022-5193(85)80291-5

Jain R, Rivera MC, Lake JA. Horizontal gene transfer among genomes: The complexity hypothesis. Proceedings of the National Academy of Sciences. 1999 Mar 30;96(7):3801-3806. https://doi.org/10.1073/pnas.96.7.3801

Crisp A, Boschetti C, Perry M, Tunnacliffe A, Micklem G. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biology. 2015 Mar 13;16(1). https://doi.org/10.1186/s13059-015-0607-3

Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J, Morris AG, Alt KW, Caramelli D, Dresely V, Farrell M, Farrer AG, Francken M, Gully N, Haak W, Hardy K, Harvati K, Held P, Holmes EC, Kaidonis J, Lalueza-Fox C, de la Rasilla M, Rosas A, Semal P, Soltysiak A, Townsend G, Usai D, Wahl J, Huson DH, Dobney K, Cooper A. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature. 2017 Mar 8;544(7650):357-361. https://doi.org/10.1038/nature21674

Gokhman D, Lavi E, Prufer K, Fraga MF, Riancho JA, Kelso J, Paabo S, Meshorer E, Carmel L. Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan. Science. 2014 Apr 17;344(6183):523-527. https://doi.org/10.1126/science.1250368

Smith TA, Martin MD, Nguyen M, Mendelson TC. Epigenetic divergence as a potential first step in darter speciation. Molecular Ecology. 2016 Mar 14;25(8):1883-1894. https://doi.org/10.1111/mec.13561

Chown SL, Hodgins KA, Griffin PC, Oakeshott JG, Byrne M, Hoffmann AA. Biological invasions, climate change and genomics. Evolutionary Applications. 2014 Dec 9;8(1):23-46. https://doi.org/10.1111/eva.12234

Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005 Jul 31;437(7057):376-380. https://doi.org/10.1038/nature03959

Gokhman D, Mishol N, de Manuel M, de Juan D, Shuqrun J, Meshorer E, Marques-Bonet T, Rak Y, Carmel L. Reconstructing Denisovan Anatomy Using DNA Methylation Maps. Cell. 2019 Sep;179(1):180-192.e10. https://doi.org/10.1016/j.cell.2019.08.035