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A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

Author

Listed:
  • Rasika Ann Mathias

    (Johns Hopkins University
    Bloomberg School of Public Health, JHU)

  • Margaret A. Taub

    (Bloomberg School of Public Health, JHU)

  • Christopher R. Gignoux

    (Stanford University School of Medicine)

  • Wenqing Fu

    (University of Washington)

  • Shaila Musharoff

    (Stanford University School of Medicine)

  • Timothy D. O'Connor

    (Institute for Genome Sciences, University of Maryland School of Medicine
    Program in Personalized and Genomic Medicine, University of Maryland School of Medicine
    University of Maryland School of Medicine)

  • Candelaria Vergara

    (Johns Hopkins University)

  • Dara G. Torgerson

    (University of California, San Francisco)

  • Maria Pino-Yanes

    (University of California, San Francisco
    CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III)

  • Suyash S. Shringarpure

    (Stanford University School of Medicine)

  • Lili Huang

    (Johns Hopkins University)

  • Nicholas Rafaels

    (Johns Hopkins University)

  • Meher Preethi Boorgula

    (Johns Hopkins University)

  • Henry Richard Johnston

    (Emory University)

  • Victor E. Ortega

    (Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine)

  • Albert M. Levin

    (Henry Ford Health System)

  • Wei Song

    (Institute for Genome Sciences, University of Maryland School of Medicine
    Program in Personalized and Genomic Medicine, University of Maryland School of Medicine
    University of Maryland School of Medicine)

  • Raul Torres

    (Biomedical Sciences Graduate Program, University of California, San Francisco)

  • Badri Padhukasahasram

    (Center for Health Policy and Health Services Research, Henry Ford Health System)

  • Celeste Eng

    (University of California, San Francisco)

  • Delmy-Aracely Mejia-Mejia

    (Centro de Neumologia y Alergias
    Faculty of Medicine, Centro Medico de la Familia)

  • Trevor Ferguson

    (Tropical Medicine Research Institute, The University of the West Indies)

  • Zhaohui S. Qin

    (Emory University)

  • Alan F. Scott

    (Johns Hopkins University)

  • Maria Yazdanbakhsh

    (Leiden University Medical Center)

  • James G. Wilson

    (University of Mississippi Medical Center)

  • Javier Marrugo

    (Instituto de Investigaciones Immunologicas, Universidad de Cartagena)

  • Leslie A. Lange

    (University of North Carolina)

  • Rajesh Kumar

    (Northwestern University
    The Ann & Robert H. Lurie Children’s Hospital of Chicago)

  • Pedro C. Avila

    (Northwestern University)

  • L. Keoki Williams

    (Center for Health Policy and Health Services Research, Henry Ford Health System
    Henry Ford Health System)

  • Harold Watson

    (Faculty of Medical Sciences Cave Hill Campus, The University of the West Indies
    Queen Elizabeth Hospital, The University of the West Indies)

  • Lorraine B. Ware

    (Vanderbilt University
    Microbiology and Immunology, Vanderbilt University)

  • Christopher Olopade

    (University of Chicago)

  • Olufunmilayo Olopade

    (University of Chicago)

  • Ricardo Oliveira

    (Laboratório de Patologia Experimental, Centro de Pesquisas Gonçalo Moniz)

  • Carole Ober

    (University of Chicago)

  • Dan L. Nicolae

    (University of Chicago
    University of Chicago)

  • Deborah Meyers

    (Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine)

  • Alvaro Mayorga

    (Centro de Neumologia y Alergias)

  • Jennifer Knight-Madden

    (Tropical Medicine Research Institute, The University of the West Indies)

  • Tina Hartert

    (Vanderbilt University)

  • Nadia N. Hansel

    (Johns Hopkins University)

  • Marilyn G. Foreman

    (Pulmonary and Critical Care Medicine, Morehouse School of Medicine)

  • Jean G. Ford

    (Bloomberg School of Public Health, JHU
    The Brooklyn Hospital Center)

  • Mezbah U. Faruque

    (National Human Genome Center, Howard University College of Medicine)

  • Georgia M. Dunston

    (National Human Genome Center, Howard University College of Medicine
    Howard University College of Medicine)

  • Luis Caraballo

    (Institute for Immunological Research, Universidad de Cartagena)

  • Esteban G. Burchard

    (University of California, San Francisco
    University of California, San Francisco)

  • Eugene Bleecker

    (Center for Human Genomics and Personalized Medicine, Wake Forest School of Medicine)

  • Maria Ilma Araujo

    (Immunology Service, Universidade Federal da Bahia)

  • Edwin Francisco Herrera-Paz

    (Centro de Neumologia y Alergias
    Faculty of Medicine, Centro Medico de la Familia
    Facultad de Medicina, Universidad Catolica de Honduras)

  • Kimberly Gietzen

    (Illumina, Inc.)

  • Wendy E. Grus

    (Knome Inc.)

  • Michael Bamshad

    (University of Washington)

  • Carlos D. Bustamante

    (Stanford University School of Medicine)

  • Eimear E. Kenny

    (Stanford University School of Medicine
    Icahn School of Medicine at Mount Sinai)

  • Ryan D. Hernandez

    (University of California, San Francisco
    Institute for Human Genetics, University of California, San Francisco
    California Institute for Quantitative Biosciences, University of California)

  • Terri H. Beaty

    (Bloomberg School of Public Health, JHU)

  • Ingo Ruczinski

    (Bloomberg School of Public Health, JHU)

  • Joshua Akey

    (University of Washington)

  • Kathleen C. Barnes

    (Johns Hopkins University
    Bloomberg School of Public Health, JHU)

Abstract

The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry.

Suggested Citation

  • Rasika Ann Mathias & Margaret A. Taub & Christopher R. Gignoux & Wenqing Fu & Shaila Musharoff & Timothy D. O'Connor & Candelaria Vergara & Dara G. Torgerson & Maria Pino-Yanes & Suyash S. Shringarpur, 2016. "A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome," Nature Communications, Nature, vol. 7(1), pages 1-10, November.
  • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12522
    DOI: 10.1038/ncomms12522
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    Cited by:

    1. Ashton Wiens & Henry B. Lovejoy & Zachary Mullen & Eric A. Vance, 2022. "A modelling strategy to estimate conditional probabilities of African origins: The collapse of the Oyo Empire and the transatlantic slave trade, 1817–1836," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 185(3), pages 1247-1270, July.
    2. 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.
    3. Brooke Szczesny & Meher Preethi Boorgula & Sameer Chavan & Monica Campbell & Randi K. Johnson & Kai Kammers & Emma E. Thompson & Madison S. Cox & Gautam Shankar & Corey Cox & Andréanne Morin & Wendy L, 2024. "Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. Rozaimi Mohamad Razali & Juan Rodriguez-Flores & Mohammadmersad Ghorbani & Haroon Naeem & Waleed Aamer & Elbay Aliyev & Ali Jubran & Andrew G. Clark & Khalid A. Fakhro & Younes Mokrab, 2021. "Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes," Nature Communications, Nature, vol. 12(1), pages 1-16, December.

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