Abstract

Most approaches that capture signatures of selective sweeps in population genomics data do not identify the specific mutation favored by selection. We present iSAFE (for “integrated selection of allele favored by evolution”), a method that enables researchers to accurately pinpoint the favored mutation in a large region (5 Mbp) by using a statistic derived solely from population genetics signals. iSAFE does not require knowledge of demography, the phenotype under selection, or functional annotations of mutations.

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Acknowledgements

This research was supported in part by the NSF (grant DBI-1458557 to A.A. and V.B.) and the NIH (grant R01GM114362 to V.B.).

Author information

Affiliations

  1. Department of Electrical & Computer Engineering, University of California San Diego, La Jolla, California, USA.

    • Ali Akbari
    • , Arya Iranmehr
    •  & Siavash Mirarab
  2. Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.

    • Joseph J Vitti
    •  & Pardis C Sabeti
  3. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

    • Joseph J Vitti
    •  & Pardis C Sabeti
  4. Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, USA.

    • Mehrdad Bakhtiari
    •  & Vineet Bafna

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Contributions

A.A., S.M., and V.B. conceived and designed the experiments and wrote the manuscript with input from all other authors; A.A., J.J.V., and A.I. performed the experiments; A.A. analyzed the data; A.A. and M.B. developed software tools; and P.C.S., S.M., and V.B. provided guidance throughout the study.

Competing interests

V.B. is a cofounder, has an equity interest in, and receives income from Digital Proteomics, LLC. The terms of this arrangement have been reviewed and approved by the University of California, San Diego, in accordance with its conflict-of-interest policies. Digital Proteomics was not involved in the research presented here.

Corresponding authors

Correspondence to Ali Akbari or Vineet Bafna.

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    iSAFE (v 0.1): integrated Selection of Allele Favored by Evolution

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DOI

https://doi.org/10.1038/nmeth.4606

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