IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0161018.html
   My bibliography  Save this article

A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity

Author

Listed:
  • Keith Hunley
  • Kiela Gwin
  • Brendan Liberman

Abstract

Our current understanding of pre-Columbian history in the Americas rests in part on several trends identified in recent genetic studies. The goal of this study is to reexamine these trends in light of the impact of post-Columbian admixture and the methods used to study admixture. The previously-published data consist of 645 autosomal microsatellite genotypes from 1046 individuals in 63 populations. We used STRUCTURE to estimate ancestry proportions and tested the sensitivity of these estimates to the choice of the number of clusters, K. We used partial correlation analyses to examine the relationship between gene diversity and geographic distance from Beringia, controlling for non-Native American ancestry (from Africa, Europe and East Asia), and taking into account alternative paths of migration. Principal component analysis and multidimensional scaling were used to investigate the relationships between Andean and non-Andean populations and to explore gene-language correspondence. We found that 1) European and East Asian ancestry estimates decline as K increases, especially in Native Canadian populations, 2) a north-south decline in gene diversity is driven by low diversity in Amazonian and Paraguayan populations, not serial founder effects from Beringia, 3) controlling for non-Native American ancestry, populations in the Andes and Mesoamerica have higher gene diversity than populations in other regions, and 4) patterns of genetic and linguistic diversity are poorly correlated. We conclude that patterns of diversity previously attributed to pre-Columbian processes may in part reflect post-Columbian admixture and the choice of K in STRUCTURE analyses. Accounting for admixture, the pattern of diversity is inconsistent with a north-south founder effect process, though the genetic similarities between Mesoamerican and Andean populations are consistent with rapid dispersal along the western coast of the Americas. Further, even setting aside the disruptive effects of European contact, gene-language congruence is unlikely to have ever existed at the geographic scale analyzed here.

Suggested Citation

  • Keith Hunley & Kiela Gwin & Brendan Liberman, 2016. "A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-17, August.
  • Handle: RePEc:plo:pone00:0161018
    DOI: 10.1371/journal.pone.0161018
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161018
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0161018&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0161018?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. Dray, Stéphane & Dufour, Anne-Béatrice, 2007. "The ade4 Package: Implementing the Duality Diagram for Ecologists," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i04).
    2. Pontus Skoglund & Swapan Mallick & Maria Cátira Bortolini & Niru Chennagiri & Tábita Hünemeier & Maria Luiza Petzl-Erler & Francisco Mauro Salzano & Nick Patterson & David Reich, 2015. "Genetic evidence for two founding populations of the Americas," Nature, Nature, vol. 525(7567), pages 104-108, September.
    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. Wenzel Kröber & Martin Böhnke & Erik Welk & Christian Wirth & Helge Bruelheide, 2012. "Leaf Trait-Environment Relationships in a Subtropical Broadleaved Forest in South-East China," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-11, April.
    2. Pengfei Song & Wen Qin & YanGan Huang & Lei Wang & Zhenyuan Cai & Tongzuo Zhang, 2020. "Grazing Management Influences Gut Microbial Diversity of Livestock in the Same Area," Sustainability, MDPI, vol. 12(10), pages 1-12, May.
    3. la Grange, Anthony & le Roux, Niël & Gardner-Lubbe, Sugnet, 2009. "BiplotGUI: Interactive Biplots in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 30(i12).
    4. Jonas Eberle & Renier Myburgh & Dirk Ahrens, 2014. "The Evolution of Morphospace in Phytophagous Scarab Chafers: No Competition - No Divergence?," PLOS ONE, Public Library of Science, vol. 9(5), pages 1-16, May.
    5. Liesbeth François & Katrien Wijnrocx & Frédéric G Colinet & Nicolas Gengler & Bettine Hulsegge & Jack J Windig & Nadine Buys & Steven Janssens, 2017. "Genomics of a revived breed: Case study of the Belgian campine cattle," PLOS ONE, Public Library of Science, vol. 12(4), pages 1-14, April.
    6. Leonardo Vallini & Carlo Zampieri & Mohamed Javad Shoaee & Eugenio Bortolini & Giulia Marciani & Serena Aneli & Telmo Pievani & Stefano Benazzi & Alberto Barausse & Massimo Mezzavilla & Michael D. Pet, 2024. "The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Hammond, Jim & Rosenblum, Nathaniel & Breseman, Dana & Gorman, Léo & Manners, Rhys & van Wijk, Mark T. & Sibomana, Milindi & Remans, Roseline & Vanlauwe, Bernard & Schut, Marc, 2020. "Towards actionable farm typologies: Scaling adoption of agricultural inputs in Rwanda," Agricultural Systems, Elsevier, vol. 183(C).
    8. Calenge, Clément, 2007. "Exploring Habitat Selection by Wildlife with adehabitat," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i06).
    9. Sara Rachik & Urania Christaki & Luen Luen Li & Savvas Genitsaris & Elsa Breton & Sébastien Monchy, 2018. "Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel)," PLOS ONE, Public Library of Science, vol. 13(5), pages 1-26, May.
    10. Serra W. Buchanan & Megan Baskerville & Maren Oelbermann & Andrew M. Gordon & Naresh V. Thevathasan & Marney E. Isaac, 2020. "Plant Diversity and Agroecosystem Function in Riparian Agroforests: Providing Ecosystem Services and Land-Use Transition," Sustainability, MDPI, vol. 12(2), pages 1-12, January.
    11. Catharine Prussing & Kevin J Emerson & Sara A Bickersmith & Maria Anice Mureb Sallum & Jan E Conn, 2019. "Minimal genetic differentiation of the malaria vector Nyssorhynchus darlingi associated with forest cover level in Amazonian Brazil," PLOS ONE, Public Library of Science, vol. 14(11), pages 1-16, November.
    12. Javier G. Serrano & Alejandra C. Ordóñez & Jonathan Santana & Elías Sánchez-Cañadillas & Matilde Arnay & Amelia Rodríguez-Rodríguez & Jacob Morales & Javier Velasco-Vázquez & Verónica Alberto-Barroso , 2023. "The genomic history of the indigenous people of the Canary Islands," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    13. Anna Favati & Josefina Zidar & Hanne Thorpe & Per Jensen & Hanne Løvlie, 2016. "The ontogeny of personality traits in the red junglefowl, Gallus gallus," Behavioral Ecology, International Society for Behavioral Ecology, vol. 27(2), pages 484-493.
    14. repec:jss:jstsof:22:i01 is not listed on IDEAS
    15. Luca Freschi & Roger Vargas & Ashaque Husain & S. M. Mostofa Kamal & Alena Skrahina & Sabira Tahseen & Nazir Ismail & Anna Barbova & Stefan Niemann & Daniela Maria Cirillo & Anna S. Dean & Matteo Zign, 2021. "Population structure, biogeography and transmissibility of Mycobacterium tuberculosis," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    16. Sólymos, Péter, 2009. "Processing Ecological Data in R with the mefa Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 29(i08).
    17. Alessandro Bellino & Daniela Baldantoni & Vittoria Milano & Lucia Santorufo & Jérôme Cortet & Giulia Maisto, 2021. "Spatial Patterns and Scales of Collembola Taxonomic and Functional Diversity in Urban Parks," Sustainability, MDPI, vol. 13(23), pages 1-11, November.
    18. Vasilios Liordos & Jukka Jokimäki & Marja-Liisa Kaisanlahti-Jokimäki & Evangelos Valsamidis & Vasileios J. Kontsiotis, 2021. "Niche Analysis and Conservation of Bird Species Using Urban Core Areas," Sustainability, MDPI, vol. 13(11), pages 1-15, June.
    19. María Concepción Vega-Hernández & Carmen Patino-Alonso, 2021. "Comparing COSTATIS and Generalized Procrustes Analysis with Multi-Way Public Education Expenditure Data," Mathematics, MDPI, vol. 9(15), pages 1-13, July.
    20. Jean-Pierre Rossi & Maxime Nardin & Martin Godefroid & Manuela Ruiz-Diaz & Anne-Sophie Sergent & Alejandro Martinez-Meier & Luc Pâques & Philippe Rozenberg, 2014. "Dissecting the Space-Time Structure of Tree-Ring Datasets Using the Partial Triadic Analysis," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-13, September.
    21. 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.

    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:pone00:0161018. 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.