IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v99y2015icp18-30.html
   My bibliography  Save this article

A hidden Markov model for investigating recent positive selection through haplotype structure

Author

Listed:
  • Chen, Hua
  • Hey, Jody
  • Slatkin, Montgomery

Abstract

Recent positive selection can increase the frequency of an advantageous mutant rapidly enough that a relatively long ancestral haplotype will be remained intact around it. We present a hidden Markov model (HMM) to identify such haplotype structures. With HMM identified haplotype structures, a population genetic model for the extent of ancestral haplotypes is then adopted for parameter inference of the selection intensity and the allele age. Simulations show that this method can detect selection under a wide range of conditions and has higher power than the existing frequency spectrum-based method. In addition, it provides good estimate of the selection coefficients and allele ages for strong selection. The method analyzes large data sets in a reasonable amount of running time. This method is applied to HapMap III data for a genome scan, and identifies a list of candidate regions putatively under recent positive selection. It is also applied to several genes known to be under recent positive selection, including the LCT, KITLG and TYRP1 genes in Northern Europeans, and OCA2 in East Asians, to estimate their allele ages and selection coefficients.

Suggested Citation

  • 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.
    • Handle: RePEc:eee:thpobi:v:99:y:2015:i:c:p:18-30
    DOI: 10.1016/j.tpb.2014.11.001
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580914000914
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.tpb.2014.11.001?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Pardis C. Sabeti & David E. Reich & John M. Higgins & Haninah Z. P. Levine & Daniel J. Richter & Stephen F. Schaffner & Stacey B. Gabriel & Jill V. Platko & Nick J. Patterson & Gavin J. McDonald & Han, 2002. "Detecting recent positive selection in the human genome from haplotype structure," Nature, Nature, vol. 419(6909), pages 832-837, October.
    2. 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.
    3. Chen, Hua, 2012. "The joint allele frequency spectrum of multiple populations: A coalescent theory approach," Theoretical Population Biology, Elsevier, vol. 81(2), pages 179-195.
    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. Costa, Rui J. & Wilkinson-Herbots, Hilde M., 2021. "Inference of gene flow in the process of speciation: Efficient maximum-likelihood implementation of a generalised isolation-with-migration model," Theoretical Population Biology, Elsevier, vol. 140(C), pages 1-15.
    2. Nicholas A Johnson & Marc A Coram & Mark D Shriver & Isabelle Romieu & Gregory S Barsh & Stephanie J London & Hua Tang, 2011. "Ancestral Components of Admixed Genomes in a Mexican Cohort," PLOS Genetics, Public Library of Science, vol. 7(12), pages 1-12, December.
    3. Champagnat, Nicolas & Lambert, Amaury, 2013. "Splitting trees with neutral Poissonian mutations II: Largest and oldest families," Stochastic Processes and their Applications, Elsevier, vol. 123(4), pages 1368-1414.
    4. Kirk E Lohmueller & Anders Albrechtsen & Yingrui Li & Su Yeon Kim & Thorfinn Korneliussen & Nicolas Vinckenbosch & Geng Tian & Emilia Huerta-Sanchez & Alison F Feder & Niels Grarup & Torben Jørgensen , 2011. "Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome," PLOS Genetics, Public Library of Science, vol. 7(10), pages 1-15, October.
    5. Sol Katzman & Andrew D Kern & Katherine S Pollard & Sofie R Salama & David Haussler, 2010. "GC-Biased Evolution Near Human Accelerated Regions," PLOS Genetics, Public Library of Science, vol. 6(5), pages 1-13, May.
    6. Devansh Pandey & Mariana Harris & Nandita R. Garud & Vagheesh M. Narasimhan, 2024. "Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Benjamin F Voight & Sridhar Kudaravalli & Xiaoquan Wen & Jonathan K Pritchard, 2006. "A Map of Recent Positive Selection in the Human Genome," PLOS Biology, Public Library of Science, vol. 4(3), pages 1-1, March.
    8. 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.
    9. 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.
    10. Clara C Elbers & Carolien G F de Kovel & Yvonne T van der Schouw & Juliaan R Meijboom & Florianne Bauer & Diederick E Grobbee & Gosia Trynka & Jana V van Vliet-Ostaptchouk & Cisca Wijmenga & N Charlot, 2009. "Variants in Neuropeptide Y Receptor 1 and 5 Are Associated with Nutrient-Specific Food Intake and Are Under Recent Selection in Europeans," PLOS ONE, Public Library of Science, vol. 4(9), pages 1-13, September.
    11. Bing Guo & Victor Borda & Roland Laboulaye & Michele D. Spring & Mariusz Wojnarski & Brian A. Vesely & Joana C. Silva & Norman C. Waters & Timothy D. O’Connor & Shannon Takala-Harrison, 2024. "Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    12. 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.
    13. 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.
    14. Yupeng Sang & Zhiqin Long & Xuming Dan & Jiajun Feng & Tingting Shi & Changfu Jia & Xinxin Zhang & Qiang Lai & Guanglei Yang & Hongying Zhang & Xiaoting Xu & Huanhuan Liu & Yuanzhong Jiang & Pär K. In, 2022. "Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    15. 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.
    16. Natsuhiko Kumasaka & Yusuke Nakamura & Naoyuki Kamatani, 2010. "The Textile Plot: A New Linkage Disequilibrium Display of Multiple-Single Nucleotide Polymorphism Genotype Data," PLOS ONE, Public Library of Science, vol. 5(4), pages 1-12, April.
    17. Gabrielle C. Ngwana-Joseph & Jody E. Phelan & Emilia Manko & Jamille G. Dombrowski & Simone Silva Santos & Martha Suarez-Mutis & Gabriel Vélez-Tobón & Alberto Tobón Castaño & Ricardo Luiz Dantas Macha, 2024. "Genomic analysis of global Plasmodium vivax populations reveals insights into the evolution of drug resistance," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    18. 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.
    19. 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.
    20. Xinkai Tong & Dong Chen & Jianchao Hu & Shiyao Lin & Ziqi Ling & Huashui Ai & Zhiyan Zhang & Lusheng Huang, 2023. "Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

    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:eee:thpobi:v:99:y:2015:i:c:p:18-30. 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: Catherine Liu (email available below). General contact details of provider: https://www.sciencedirect.com/journal/theoretical-population-biology .

    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.