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Genome-wide detection and characterization of positive selection in human populations

Author

Listed:
  • Pardis C. Sabeti

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA)

  • Patrick Varilly

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA)

  • Ben Fry

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA)

  • Jason Lohmueller

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA)

  • Elizabeth Hostetter

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA)

  • Chris Cotsapas

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA)

  • Xiaohui Xie

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA)

  • Elizabeth H. Byrne

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA)

  • Steven A. McCarroll

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA)

  • Rachelle Gaudet

    (Harvard University, Cambridge, Massachusetts 02138, USA)

  • Stephen F. Schaffner

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA)

  • Eric S. Lander

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    MIT, Cambridge, Massachusetts 02139, USA
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Harvard Medical School, Boston, Massachusetts 02115, USA)

Abstract

HapMap2 raises the bar The International HapMap Consortium has produced a second-generation version of its remarkable haplotype map of the human genome. The Phase II HapMap charts human genetic variation even more extensively than the original, tripling of the number of genetic markers included. The original HapMap was instrumental in making large-scale genome-wide association studies possible. An indication of how this type of work will be extended with 'HapMap2' is presented in this issue: Sabeti et al. build on previous work detecting signs of positive natural selection on human genes. With many more markers now available, they have discovered three examples of apparent population-specific selection based on geographic area — involving gene pairs linked to Lassa virus in West Africa, skin pigmentation in Europe and hair follicle development in Asia — and they speculate on how these may relate to human biology.

Suggested Citation

  • Pardis C. Sabeti & Patrick Varilly & Ben Fry & Jason Lohmueller & Elizabeth Hostetter & Chris Cotsapas & Xiaohui Xie & Elizabeth H. Byrne & Steven A. McCarroll & Rachelle Gaudet & Stephen F. Schaffner, 2007. "Genome-wide detection and characterization of positive selection in human populations," Nature, Nature, vol. 449(7164), pages 913-918, October.
    • Handle: RePEc:nat:nature:v:449:y:2007:i:7164:d:10.1038_nature06250
    DOI: 10.1038/nature06250
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    Cited by:

    1. Yichen Zheng & Thomas Wiehe, 2019. "Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps," PLOS Computational Biology, Public Library of Science, vol. 15(11), pages 1-32, November.
    2. 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.
    3. Mohammad Hossein Olyaee & Alireza Khanteymoori & Khosrow Khalifeh, 2020. "A chaotic viewpoint-based approach to solve haplotype assembly using hypergraph model," PLOS ONE, Public Library of Science, vol. 15(10), pages 1-19, October.
    4. Xiao Zhang & Mark Blaxter & Jonathan M. D. Wood & Alan Tracey & Shane McCarthy & Peter Thorpe & Jack G. Rayner & Shangzhe Zhang & Kirstin L. Sikkink & Susan L. Balenger & Nathan W. Bailey, 2024. "Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    5. Lauren A. Choate & Gilad Barshad & Pierce W. McMahon & Iskander Said & Edward J. Rice & Paul R. Munn & James J. Lewis & Charles G. Danko, 2021. "Multiple stages of evolutionary change in anthrax toxin receptor expression in humans," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    6. Michael DeGiorgio & Zachary A Szpiech, 2022. "A spatially aware likelihood test to detect sweeps from haplotype distributions," PLOS Genetics, Public Library of Science, vol. 18(4), pages 1-37, April.
    7. Hyeongmin Kim & Ki Duk Song & Hyeon Jeong Kim & WonCheoul Park & Jaemin Kim & Taeheon Lee & Dong-Hyun Shin & Woori Kwak & Young-jun Kwon & Samsun Sung & Sunjin Moon & Kyung-Tai Lee & Namshin Kim & Joo, 2015. "Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-16, April.
    8. Pol Solé-Navais & Julius Juodakis & Karin Ytterberg & Xiaoping Wu & Jonathan P. Bradfield & Marc Vaudel & Abigail L. LaBella & Øyvind Helgeland & Christopher Flatley & Frank Geller & Moshe Finel & Men, 2024. "Genome-wide analyses of neonatal jaundice reveal a marked departure from adult bilirubin metabolism," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    9. Liye Zhang & Neahga Leonard & Rick Passaro & Mai Sy Luan & Pham Tuyen & Le Thi Ngoc Han & Nguyen Huy Cam & Larry Vogelnest & Michael Lynch & Amanda E. Fine & Nguyen Thi Thanh Nga & Nguyen Long & Benja, 2024. "Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    10. Chen, Hua & Hey, Jody & Slatkin, Montgomery, 2015. "A hidden Markov model for investigating recent positive selection through haplotype structure," Theoretical Population Biology, Elsevier, vol. 99(C), pages 18-30.

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