Skip to content

Research at St Andrews

Detection of selective sweeps in structured populations: a comparison of recent methods

Research output: Contribution to journalArticle

DOI

Open Access permissions

Open

Abstract

Identifying genomic regions targeted by positive selection has been a longstanding interest of evolutionary biologists. This objective was difficult to achieve until the recent emergence of Next Generation Sequencing, which is fostering the development of large-scale catalogs of genetic variation for increasing number of species. Several statistical methods have been recently developed to analyze these rich datasets but there is still a poor understanding of the conditions under which these methods produce reliable results. This study aims at filling this gap by assessing the performance of genome-scan methods that consider explicitly the physical linkage among SNPs surrounding a selected variant. Our study compares the performance of seven recent methods for the detection of selective sweeps (iHS, nSL, EHHST, xp-EHH, XP-EHHST, XPCLR and hapFLK). We use an individual-based simulation approach to investigate the power and accuracy of these methods under a wide range of population models under both hard and soft sweeps. Our results indicate that XPCLR and hapFLK perform best and can detect soft sweeps under simple population structure scenarios if migration rate is low. All methods perform poorly with moderate to high migration rates, or with weak selection and very poorly under a hierarchical population structure. Finally, no single method is able to detect both starting and nearly completed selective sweeps. However, combining several methods (XPCLR or hapFLK with iHS or nSL) can greatly increase the power to pinpoint the selected region.
Close

Details

Original languageEnglish
Pages (from-to)89-103
JournalMolecular Ecology
Volume25
Issue number1
Early online date12 Oct 2015
DOIs
StatePublished - Jan 2016

    Research areas

  • Positive selection, Haplotype structure, Genome scan

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Patterns of phenotypic plasticity and local adaptation in the wide elevation range of the alpine plant Arabis alpina

    de Villemereuil, P., Mouterde, M., Gaggiotti, O. E. & Till-Buttraud, I. Sep 2018 In : Journal of Ecology. 106, 5, p. 1952–1971 20 p.

    Research output: Contribution to journalArticle

  2. Diversity from genes to ecosystems: a unifying framework to study variation across biological metrics and scales

    Gaggiotti, O. E., Chao, A., Peres-Neto, P., Chiu, C-H., Edwards, C., Fortin, M-J., Jost, L., Richards, C. & Selkoe, K. 1 Aug 2018 In : Evolutionary Applications. 11, 7, p. 1176-1193 18 p.

    Research output: Contribution to journalArticle

  3. Differentiation measures for conservation genetics

    Jost, L., Archer, F., Flanagan, S., Gaggiotti, O., Hoban, S. & Latch, E. Aug 2018 In : Evolutionary Applications. 11, 7, p. 1139-1148 10 p.

    Research output: Contribution to journalArticle

  4. Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species

    Carroll, E. L., Alderman, R., Bannister, J. L., Bérube, M., Best, P. B., Boren, L., Baker, C. S., Constantine, R., Findlay, K., Harcourt, R., Lemaire, L., Palsbøll, P. J., Patenaude, N. J., Rowntree, V. J., Seger, J., Steel, D., Valenzuela, L. O., Watson, M. & Gaggiotti, O. E. 3 May 2018 In : Heredity. 16 p.

    Research output: Contribution to journalArticle

Related by journal

  1. Molecular Ecology (Journal)

    Abbott, R. J. (Editor)
    20032010

    Activity: Publication peer-review and editorial workEditor of research journal

  2. Molecular Ecology (Journal)

    Ritchie, M. G. (Editor)
    2001

    Activity: Publication peer-review and editorial workEditor of research journal

Related by journal

  1. Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum

    Wang, X-J., Hu, Q-J., Guo, X-Y., Wang, K., Ru, D-F., German, D. A., Weretilnyk, E. A., Abbott, R. J., Lascoux, M. & Liu, J-Q. Jul 2018 In : Molecular Ecology. 27, 14, p. 2943-2955

    Research output: Contribution to journalArticle

  2. Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes

    Moran, P., Pascoal, S., Cezard, T., Risse, J., Ritchie, M. G. & Bailey, N. W. 10 Jun 2018 In : Molecular Ecology. Early view

    Research output: Contribution to journalArticle

  3. Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

    Ru, D., Sun, Y., Wang, D., Chen, Y., Wang, T., Hu, Q., Abbott, R. J. & Liu, J. Dec 2018 In : Molecular Ecology. 27, 23, p. 4875-4887 13 p.

    Research output: Contribution to journalArticle

  4. These aren’t the loci you’re looking for: principles of effective SNP filtering for molecular ecologists

    O'Leary, S. J., Puritz, J. B., Willis, S. C., Hollenbeck, C. M. & Portnoy, D. S. Aug 2018 In : Molecular Ecology. 27, 16, p. 3193-3206 14 p.

    Research output: Contribution to journalArticle

  5. Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

    Balao, F., Trucchi, E., Wolfe, T., Hao, B-H., Lorenzo, M. T., Baar, J., Sedman, L., Kosiol, C., Amman, F., Chase, M. W., Hedrén, M. & Paun, O. 4 Jul 2017 In : Molecular Ecology. 26, 14, p. 3649-3662 14 p.

    Research output: Contribution to journalArticle

ID: 212922766