IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0233808.html
   My bibliography  Save this article

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina

Author

Listed:
  • Pierre Luisi
  • Angelina García
  • Juan Manuel Berros
  • Josefina M B Motti
  • Darío A Demarchi
  • Emma Alfaro
  • Eliana Aquilano
  • Carina Argüelles
  • Sergio Avena
  • Graciela Bailliet
  • Julieta Beltramo
  • Claudio M Bravi
  • Mariela Cuello
  • Cristina Dejean
  • José Edgardo Dipierri
  • Laura S Jurado Medina
  • José Luis Lanata
  • Marina Muzzio
  • María Laura Parolin
  • Maia Pauro
  • Paula B Paz Sepúlveda
  • Daniela Rodríguez Golpe
  • María Rita Santos
  • Marisol Schwab
  • Natalia Silvero
  • Jeremias Zubrzycki
  • Virginia Ramallo
  • Hernán Dopazo

Abstract

Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.

Suggested Citation

  • Pierre Luisi & Angelina García & Juan Manuel Berros & Josefina M B Motti & Darío A Demarchi & Emma Alfaro & Eliana Aquilano & Carina Argüelles & Sergio Avena & Graciela Bailliet & Julieta Beltramo & C, 2020. "Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina," PLOS ONE, Public Library of Science, vol. 15(7), pages 1-30, July.
    • Handle: RePEc:plo:pone00:0233808
    DOI: 10.1371/journal.pone.0233808
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0233808
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0233808&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0233808?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. John Novembre & Toby Johnson & Katarzyna Bryc & Zoltán Kutalik & Adam R. Boyko & Adam Auton & Amit Indap & Karen S. King & Sven Bergmann & Matthew R. Nelson & Matthew Stephens & Carlos D. Bustamante, 2008. "Genes mirror geography within Europe," Nature, Nature, vol. 456(7219), pages 274-274, November.
    2. John Novembre & Toby Johnson & Katarzyna Bryc & Zoltán Kutalik & Adam R. Boyko & Adam Auton & Amit Indap & Karen S. King & Sven Bergmann & Matthew R. Nelson & Matthew Stephens & Carlos D. Bustamante, 2008. "Genes mirror geography within Europe," Nature, Nature, vol. 456(7218), pages 98-101, November.
    3. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    4. Julian R Homburger & Andrés Moreno-Estrada & Christopher R Gignoux & Dominic Nelson & Elena Sanchez & Patricia Ortiz-Tello & Bernardo A Pons-Estel & Eduardo Acevedo-Vasquez & Pedro Miranda & Carl D La, 2015. "Genomic Insights into the Ancestry and Demographic History of South America," PLOS Genetics, Public Library of Science, vol. 11(12), pages 1-26, December.
    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. Andrey V Khrunin & Denis V Khokhrin & Irina N Filippova & Tõnu Esko & Mari Nelis & Natalia A Bebyakova & Natalia L Bolotova & Janis Klovins & Liene Nikitina-Zake & Karola Rehnström & Samuli Ripatti & , 2013. "A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-9, March.
    2. Gad Abraham & Michael Inouye, 2014. "Fast Principal Component Analysis of Large-Scale Genome-Wide Data," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-5, April.
    3. Diana Chang & Alon Keinan, 2014. "Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies," PLOS Computational Biology, Public Library of Science, vol. 10(9), pages 1-14, September.
    4. Bryc, Katarzyna & Bryc, Wlodek & Silverstein, Jack W., 2013. "Separation of the largest eigenvalues in eigenanalysis of genotype data from discrete subpopulations," Theoretical Population Biology, Elsevier, vol. 89(C), pages 34-43.
    5. Gil McVean, 2009. "A Genealogical Interpretation of Principal Components Analysis," PLOS Genetics, Public Library of Science, vol. 5(10), pages 1-10, October.
    6. Guindon, Stéphane & Guo, Hongbin & Welch, David, 2016. "Demographic inference under the coalescent in a spatial continuum," Theoretical Population Biology, Elsevier, vol. 111(C), pages 43-50.
    7. Marie-Claude Babron & Marie de Tayrac & Douglas N Rutledge & Eleftheria Zeggini & Emmanuelle Génin, 2012. "Rare and Low Frequency Variant Stratification in the UK Population: Description and Impact on Association Tests," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-9, October.
    8. Priya Moorjani & Nick Patterson & Joel N Hirschhorn & Alon Keinan & Li Hao & Gil Atzmon & Edward Burns & Harry Ostrer & Alkes L Price & David Reich, 2011. "The History of African Gene Flow into Southern Europeans, Levantines, and Jews," PLOS Genetics, Public Library of Science, vol. 7(4), pages 1-13, April.
    9. Wang Chaolong & Szpiech Zachary A & Degnan James H & Jakobsson Mattias & Pemberton Trevor J & Hardy John A & Singleton Andrew B & Rosenberg Noah A, 2010. "Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-22, January.
    10. Thomas Charlon & Manuel Martínez-Bueno & Lara Bossini-Castillo & F David Carmona & Alessandro Di Cara & Jérôme Wojcik & Sviatoslav Voloshynovskiy & Javier Martín & Marta E Alarcón-Riquelme, 2016. "Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-10, August.
    11. Diana Chang & Feng Gao & Andrea Slavney & Li Ma & Yedael Y Waldman & Aaron J Sams & Paul Billing-Ross & Aviv Madar & Richard Spritz & Alon Keinan, 2014. "Accounting for eXentricities: Analysis of the X Chromosome in GWAS Reveals X-Linked Genes Implicated in Autoimmune Diseases," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-31, December.
    12. Duforet-Frebourg, Nicolas & Slatkin, Montgomery, 2016. "Isolation-by-distance-and-time in a stepping-stone model," Theoretical Population Biology, Elsevier, vol. 108(C), pages 24-35.
    13. Aman Agrawal & Alec M Chiu & Minh Le & Eran Halperin & Sriram Sankararaman, 2020. "Scalable probabilistic PCA for large-scale genetic variation data," PLOS Genetics, Public Library of Science, vol. 16(5), pages 1-19, May.
    14. Thalida E Arpawong & Neil Pendleton & Krisztina Mekli & John J McArdle & Margaret Gatz & Chris Armoskus & James A Knowles & Carol A Prescott, 2017. "Genetic variants specific to aging-related verbal memory: Insights from GWASs in a population-based cohort," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-27, August.
    15. Matthieu Marbac & Mohammed Sedki & Tienne Patin, 2020. "Variable Selection for Mixed Data Clustering: Application in Human Population Genomics," Journal of Classification, Springer;The Classification Society, vol. 37(1), pages 124-142, April.
    16. Zheng, Xiuwen & Weir, Bruce S., 2016. "Eigenanalysis of SNP data with an identity by descent interpretation," Theoretical Population Biology, Elsevier, vol. 107(C), pages 65-76.
    17. Jason Sawler & Bruce Reisch & Mallikarjuna K Aradhya & Bernard Prins & Gan-Yuan Zhong & Heidi Schwaninger & Charles Simon & Edward Buckler & Sean Myles, 2013. "Genomics Assisted Ancestry Deconvolution in Grape," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-1, November.
    18. Marco Lopez-Cruz & Fernando M. Aguate & Jacob D. Washburn & Natalia Leon & Shawn M. Kaeppler & Dayane Cristina Lima & Ruijuan Tan & Addie Thompson & Laurence Willard Bretonne & Gustavo los Campos, 2023. "Leveraging data from the Genomes-to-Fields Initiative to investigate genotype-by-environment interactions in maize in North America," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    19. Beatrix Eugster & Rafael Lalive & Andreas Steinhauer & Josef Zweimüller, 2011. "The Demand for Social Insurance: Does Culture Matter?," Economic Journal, Royal Economic Society, vol. 121(556), pages 413-448, November.
    20. Filippini, Massimo & Wekhof, Tobias, 2021. "The effect of culture on energy efficient vehicle ownership," Journal of Environmental Economics and Management, Elsevier, vol. 105(C).

    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:plo:pone00:0233808. 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.