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Demography-adjusted tests of neutrality based on genome-wide SNP data

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  • Rafajlović, M.
  • Klassmann, A.
  • Eriksson, A.
  • Wiehe, T.
  • Mehlig, B.

Abstract

Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and the population size remains constant over time. However, it is unclear how such tests are affected if the last assumption is dropped. Here, we extend the unifying framework for tests based on the site frequency spectrum, introduced by Achaz and Ferretti, to populations of varying size. Key ingredients are the first two moments of the site frequency spectrum. We show how these moments can be computed analytically if a population has experienced two instantaneous size changes in the past. We apply our method to data from ten human populations gathered in the 1000 genomes project, estimate their demographies and define demography-adjusted versions of Tajima’s D, Fay & Wu’s H, and Zeng’s E. Our results show that demography-adjusted test statistics facilitate the direct comparison between populations and that most of the differences among populations seen in the original unadjusted tests can be explained by their underlying demographies. Upon carrying out whole-genome screens for deviations from neutrality, we identify candidate regions of recent positive selection. We provide track files with values of the adjusted and unadjusted tests for upload to the UCSC genome browser.

Suggested Citation

  • Rafajlović, M. & Klassmann, A. & Eriksson, A. & Wiehe, T. & Mehlig, B., 2014. "Demography-adjusted tests of neutrality based on genome-wide SNP data," Theoretical Population Biology, Elsevier, vol. 95(C), pages 1-12.
  • Handle: RePEc:eee:thpobi:v:95:y:2014:i:c:p:1-12
    DOI: 10.1016/j.tpb.2014.05.002
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    References listed on IDEAS

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    1. Joshua M Akey & Michael A Eberle & Mark J Rieder & Christopher S Carlson & Mark D Shriver & Deborah A Nickerson & Leonid Kruglyak, 2004. "Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes," PLOS Biology, Public Library of Science, vol. 2(10), pages 1-1, September.
    2. Myers, Simon & Fefferman, Charles & Patterson, Nick, 2008. "Can one learn history from the allelic spectrum?," Theoretical Population Biology, Elsevier, vol. 73(3), pages 342-348.
    3. 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.
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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. Klassmann, A. & Ferretti, L., 2018. "The third moments of the site frequency spectrum," Theoretical Population Biology, Elsevier, vol. 120(C), pages 16-28.
    3. Ferretti, Luca & Klassmann, Alexander & Raineri, Emanuele & Ramos-Onsins, Sebastián E. & Wiehe, Thomas & Achaz, Guillaume, 2018. "The neutral frequency spectrum of linked sites," Theoretical Population Biology, Elsevier, vol. 123(C), pages 70-79.

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