Skip to content

Research at St Andrews

Identifying consistent allele frequency differences in studies of stratified populations

Research output: Research - peer-reviewArticle


Open Access permissions



1. With increasing application of pooled-sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply. However, there are potential problems with the way such tests are used,which means that underlying assumptions about the data are frequently violated.
2. These problems are highlighted by simulation of simple but realistic population genetic models of neutral evolution and the performance of different tests are assessed. We present alternative tests (including GLMs with quasibinomial error structure) with attractive properties for the analysis of allele frequency differences and re-analyse a published dataset.
3. The simulations show that common statistical tests for consistent allele frequency differences perform poorly, with high false positive rates. Applying tests that do not confound heterogeneity and main effects significantly improves inference. Variation in sequencing coverage likely produces many false positives and re-scaling allele frequencies to counts out of a common value or an effective sample size reduces this effect.
4. Many researchers are interested in identifying allele frequencies that vary consistently across replicates to identify loci underlying phenotypic responses to selection or natural variation in phenotypes. Popular methods that have been suggested for this task perform poorly in simulations. Overall, quasibinomial GLMs perform better and also have the attractive feature of allowing correction for multiple testing by standard procedures and are easily extended to other designs.


Original languageEnglish
Pages (from-to)1899-1909
JournalMethods in Ecology and Evolution
Issue number12
Early online date15 Jun 2017
StatePublished - Dec 2017

    Research areas

  • Allele frequency differences, Quaibinomial GLM, CMH-test, Pool-seq, Selection, Experimental evolution

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

View graph of relations

Related by author

  1. Increased socially mediated plasticity in gene expression accompanies rapid adaptive evolution

    Pascoal, S., Liu, X., Fang, Y., Paterson, S., Ritchie, M. G., Rockliffe, N., Zuk, M. & Bailey, N. W. 14 Feb 2018 In : Ecology Letters. 21, 4, p. 546-556

    Research output: Research - peer-reviewArticle

  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. 20 Feb 2018 In : Evolutionary Applications. Early View, 18 p.

    Research output: Research - peer-reviewArticle

  3. Fixed-effect variance and the estimation of repeatabilities and heritabilities: issues and solutions

    de Villemereuil, P., Morrissey, M. B., Nakagawa, S. & Schielzeth, H. 15 Feb 2018 In : Journal of Evolutionary Biology. Early View

    Research output: Research - peer-reviewArticle

  4. 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. 9 Feb 2018 (Accepted/In press) In : Journal of Ecology. In press

    Research output: Research - peer-reviewArticle

  5. Differential gene expression is not required for facultative sex allocation: a transcriptome analysis of brain tissue in the parasitoid wasp Nasonia vitripennis

    Cook, N., Boulton, R., Green, J., Trivedi, U., Tauber, E., Pannebakker, B. A., Ritchie, M. G. & Shuker, D. M. Feb 2018 In : Royal Society Open Science. 5, 8 p., 171718

    Research output: Research - peer-reviewArticle

Related by journal

  1. Attributing changes in the distribution of species abundance to weather variables using the example of British breeding birds

    Oedekoven, C. S., Elston, D. A., Harrison, P. J., Brewer, M. J., Buckland, S. T., Johnston, A., Foster, S. & Pearce-Higgins, J. W. Dec 2017 In : Methods in Ecology and Evolution. 8, 12, p. 1690-1702

    Research output: Research - peer-reviewArticle

  2. Distance sampling with camera traps

    Howe, E. J., Buckland, S. T., Després-Einspenner, M-L. & Kühl, H. Nov 2017 In : Methods in Ecology and Evolution. 8, 11, p. 1558-1565

    Research output: Research - peer-reviewArticle

  3. Inference of selection gradients using performance measures as fitness proxies

    Franklin, O. D. & Morrissey, M. B. Jun 2017 In : Methods in Ecology and Evolution. 8, 6, p. 663-677 15 p.

    Research output: Research - peer-reviewArticle

  4. Echolocation detections and digital video surveys provide reliable estimates of the relative density of harbour porpoises

    Williamson, L. D., Brookes, K. L., Scott, B. E., Graham, I. M., Bradbury, G., Hammond, P. S. & Thompson, P. M. 13 Jul 2016 In : Methods in Ecology and Evolution. 7, 7, p. 762-769 8 p.

    Research output: Research - peer-reviewArticle

Related by journal

  1. Methods in Ecology and Evolution (Journal)

    Gaggiotti, O. E. (Member of editorial board)
    1 Sep 2014 → …

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

ID: 249951261