IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-31487-x.html
   My bibliography  Save this article

Population genomics of ancient and modern Trichuris trichiura

Author

Listed:
  • Stephen R. Doyle

    (Wellcome Sanger Institute)

  • Martin Jensen Søe

    (University of Copenhagen)

  • Peter Nejsum

    (Aarhus University)

  • Martha Betson

    (University of Surrey)

  • Philip J. Cooper

    (St George’s University of London
    Universidad Internacional del Ecuador)

  • Lifei Peng

    (School of Basic Medical Sciences, Guangdong Medical University)

  • Xing-Quan Zhu

    (Shanxi Agricultural University)

  • Ana Sanchez

    (Brock University, St. Catharines)

  • Gabriela Matamoros

    (Ciudad Universitaria, Universidad Nacional Autónoma de Honduras)

  • Gustavo Adolfo Fontecha Sandoval

    (Ciudad Universitaria, Universidad Nacional Autónoma de Honduras)

  • Cristina Cutillas

    (Universidad de Sevilla)

  • Louis-Albert Tchuem Tchuenté

    (University of Yaoundé I)

  • Zeleke Mekonnen

    (Jimma University)

  • Shaali M. Ame

    (Public Health Laboratory Ivo de Carneri)

  • Harriet Namwanje

    (Vector Control Division, Ministry of Health)

  • Bruno Levecke

    (Ghent University)

  • Matthew Berriman

    (Wellcome Sanger Institute)

  • Brian Lund Fredensborg

    (University of Copenhagen)

  • Christian Moliin Outzen Kapel

    (University of Copenhagen)

Abstract

The neglected tropical disease trichuriasis is caused by the whipworm Trichuris trichiura, a soil-transmitted helminth that has infected humans for millennia. Today, T. trichiura infects as many as 500 million people, predominantly in communities with poor sanitary infrastructure enabling sustained faecal-oral transmission. Using whole-genome sequencing of geographically distributed worms collected from human and other primate hosts, together with ancient samples preserved in archaeologically-defined latrines and deposits dated up to one thousand years old, we present the first population genomics study of T. trichiura. We describe the continent-scale genetic structure between whipworms infecting humans and baboons relative to those infecting other primates. Admixture and population demographic analyses support a stepwise distribution of genetic variation that is highest in Uganda, consistent with an African origin and subsequent translocation with human migration. Finally, genome-wide analyses between human samples and between human and non-human primate samples reveal local regions of genetic differentiation between geographically distinct populations. These data provide insight into zoonotic reservoirs of human-infective T. trichiura and will support future efforts toward the implementation of genomic epidemiology of this globally important helminth.

Suggested Citation

  • Stephen R. Doyle & Martin Jensen Søe & Peter Nejsum & Martha Betson & Philip J. Cooper & Lifei Peng & Xing-Quan Zhu & Ana Sanchez & Gabriela Matamoros & Gustavo Adolfo Fontecha Sandoval & Cristina Cut, 2022. "Population genomics of ancient and modern Trichuris trichiura," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31487-x
    DOI: 10.1038/s41467-022-31487-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-31487-x
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-31487-x?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Joseph K Pickrell & Jonathan K Pritchard, 2012. "Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data," PLOS Genetics, Public Library of Science, vol. 8(11), pages 1-17, November.
    2. Ashot Margaryan & Daniel J. Lawson & Martin Sikora & Fernando Racimo & Simon Rasmussen & Ida Moltke & Lara M. Cassidy & Emil Jørsboe & Andrés Ingason & Mikkel W. Pedersen & Thorfinn Korneliussen & Hel, 2020. "Population genomics of the Viking world," Nature, Nature, vol. 585(7825), pages 390-396, September.
    3. Anders Bergström & Chris Stringer & Mateja Hajdinjak & Eleanor M. L. Scerri & Pontus Skoglund, 2021. "Origins of modern human ancestry," Nature, Nature, vol. 590(7845), pages 229-237, February.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Alexandros G. Sotiropoulos & Epifanía Arango-Isaza & Tomohiro Ban & Chiara Barbieri & Salim Bourras & Christina Cowger & Paweł C. Czembor & Roi Ben-David & Amos Dinoor & Simon R. Ellwood & Johannes Gr, 2022. "Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Romain Fournier & Zoi Tsangalidou & David Reich & Pier Francesco Palamara, 2023. "Haplotype-based inference of recent effective population size in modern and ancient DNA samples," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Alejandro Ochoa & John D Storey, 2021. "Estimating FST and kinship for arbitrary population structures," PLOS Genetics, Public Library of Science, vol. 17(1), pages 1-36, January.
    4. Mateus H. Gouveia & Amy R. Bentley & Thiago P. Leal & Eduardo Tarazona-Santos & Carlos D. Bustamante & Adebowale A. Adeyemo & Charles N. Rotimi & Daniel Shriner, 2023. "Unappreciated subcontinental admixture in Europeans and European Americans and implications for genetic epidemiology studies," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    5. Buzbas, Erkan Ozge & Verdu, Paul, 2018. "Inference on admixture fractions in a mechanistic model of recurrent admixture," Theoretical Population Biology, Elsevier, vol. 122(C), pages 149-157.
    6. Bárbara Sousa da Mota & Simone Rubinacci & Diana Ivette Cruz Dávalos & Carlos Eduardo G. Amorim & Martin Sikora & Niels N. Johannsen & Marzena H. Szmyt & Piotr Włodarczak & Anita Szczepanek & Marcin M, 2023. "Imputation of ancient human genomes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    7. Ningbo Chen & Xiaoting Xia & Quratulain Hanif & Fengwei Zhang & Ruihua Dang & Bizhi Huang & Yang Lyu & Xiaoyu Luo & Hucai Zhang & Huixuan Yan & Shikang Wang & Fuwen Wang & Jialei Chen & Xiwen Guan & Y, 2023. "Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Soraggi, Samuele & Wiuf, Carsten, 2019. "General theory for stochastic admixture graphs and F-statistics," Theoretical Population Biology, Elsevier, vol. 125(C), pages 56-66.
    9. Casey B. Mulligan, 2021. "Peltzman Revisited: Quantifying 21st Century Opportunity Costs of FDA Regulation," NBER Working Papers 29574, National Bureau of Economic Research, Inc.
    10. Crystal M. Tomlin & Sitaram Rajaraman & Jeanne Theresa Sebesta & Anne-Cathrine Scheen & Mika Bendiksby & Yee Wen Low & Jarkko Salojärvi & Todd P. Michael & Victor A. Albert & Charlotte Lindqvist, 2024. "Allopolyploid origin and diversification of the Hawaiian endemic mints," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    11. Humberto García-Ortiz & Francisco Barajas-Olmos & Cecilia Contreras-Cubas & Miguel Ángel Cid-Soto & Emilio J. Córdova & Federico Centeno-Cruz & Elvia Mendoza-Caamal & Isabel Cicerón-Arellano & Marlen , 2021. "The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    12. Cecilia Padilla-Iglesias & Javier Blanco-Portillo & Bogdan Pricop & Alexander G. Ioannidis & Balthasar Bickel & Andrea Manica & Lucio Vinicius & Andrea Bamberg Migliano, 2024. "Deep history of cultural and linguistic evolution among Central African hunter-gatherers," Nature Human Behaviour, Nature, vol. 8(7), pages 1263-1275, July.
    13. Philippe Gambette & Leo van Iersel & Mark Jones & Manuel Lafond & Fabio Pardi & Celine Scornavacca, 2017. "Rearrangement moves on rooted phylogenetic networks," PLOS Computational Biology, Public Library of Science, vol. 13(8), pages 1-21, August.
    14. Ran Tian & Yaolei Zhang & Hui Kang & Fan Zhang & Zhihong Jin & Jiahao Wang & Peijun Zhang & Xuming Zhou & Janet M. Lanyon & Helen L. Sneath & Lucy Woolford & Guangyi Fan & Songhai Li & Inge Seim, 2024. "Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    15. Elena Arciero & Sufyan A. Dogra & Daniel S. Malawsky & Massimo Mezzavilla & Theofanis Tsismentzoglou & Qin Qin Huang & Karen A. Hunt & Dan Mason & Saghira Malik Sharif & David A. Heel & Eamonn Sherida, 2021. "Fine-scale population structure and demographic history of British Pakistanis," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    16. Chris J. Brauer & Jonathan Sandoval-Castillo & Katie Gates & Michael P. Hammer & Peter J. Unmack & Louis Bernatchez & Luciano B. Beheregaray, 2023. "Natural hybridization reduces vulnerability to climate change," Nature Climate Change, Nature, vol. 13(3), pages 282-289, March.
    17. Feng Liu & Jiantao Zhao & Honghe Sun & Cheng Xiong & Xuepeng Sun & Xin Wang & Zhongyi Wang & Robert Jarret & Jin Wang & Bingqian Tang & Hao Xu & Bowen Hu & Huan Suo & Bozhi Yang & Lijun Ou & Xuefeng L, 2023. "Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    18. Marina Muzzio & Josefina M B Motti & Paula B Paz Sepulveda & Muh-ching Yee & Thomas Cooke & María R Santos & Virginia Ramallo & Emma L Alfaro & Jose E Dipierri & Graciela Bailliet & Claudio M Bravi & , 2018. "Population structure in Argentina," PLOS ONE, Public Library of Science, vol. 13(5), pages 1-13, May.
    19. Baharian, Soheil & Gravel, Simon, 2018. "On the decidability of population size histories from finite allele frequency spectra," Theoretical Population Biology, Elsevier, vol. 120(C), pages 42-51.
    20. Juraj Bergman & Rasmus Ø. Pedersen & Erick J. Lundgren & Rhys T. Lemoine & Sophie Monsarrat & Elena A. Pearce & Mikkel H. Schierup & Jens-Christian Svenning, 2023. "Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31487-x. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.