Skip to content

Research at St Andrews

Identifying consistent allele frequency differences in studies of stratified populations

Research output: Contribution to journalArticle

Abstract

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.
Close

Details

Original languageEnglish
Pages (from-to)1899-1909
JournalMethods in Ecology and Evolution
Volume8
Issue number12
Early online date15 Jun 2017
DOIs
Publication statusPublished - 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. Landscape, colonization and life history: their effects on genetic diversity in four sympatric species inhabiting a dendritic system

    Ruzzante, D., McCraken, G., Salisbury, S., Brewis, H., Keefe, D., Gaggiotti, O. E. & Perry, R., 2 Apr 2019, (Accepted/In press) In : Canadian Journal of Fisheries and Aquatic Sciences.

    Research output: Contribution to journalArticle

  2. Behavioural mechanisms of sexual isolation involving multiple modalities and their inheritance

    Moran, P., Hunt, J., Mitchell, C., Ritchie, M. G. & Bailey, N. W., Mar 2019, In : Journal of Evolutionary Biology. 32, 3, p. 243-258

    Research output: Contribution to journalArticle

  3. 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., 1 Jan 2019, In : Heredity. 122, 1, p. 53-68

    Research output: Contribution to journalArticle

  4. Social effects on fruit fly courtship song

    Marie-Orleach, L., Bailey, N. W. & Ritchie, M. G., Jan 2019, In : Ecology and Evolution. 9, 1, p. 410-416 7 p.

    Research output: Contribution to journalArticle

Related by journal

  1. A 2.6-gram sound and movement tag for studying the acoustic scene and kinematics of echolocating bats

    Stidsholt, L., Johnson, M., Beedholm, K., Jakobsen, L., Kugler, K., Brinkløv, S., Salles, A., Moss, C. F. & Madsen, P. T., Jan 2019, In : Methods in Ecology and Evolution. 10, 1, p. 48-58 11 p.

    Research output: Contribution to journalArticle

  2. Model selection with overdispersed distance sampling data

    Howe, E. J., Buckland, S. T., Després-Einspenner, M-L. & Kühl, H. S., Jan 2019, In : Methods in Ecology and Evolution. 10, 1, p. 38-47

    Research output: Contribution to journalArticle

  3. State-switching continuous-time correlated random walks

    Michelot, T. & Blackwell, P. G., 14 Feb 2019, In : Methods in Ecology and Evolution. Early View

    Research output: Contribution to journalArticle

  4. inlabru: an R package for Bayesian spatial modelling from ecological survey data

    Bachl, F. E., Lindgren, F., Borchers, D. L. & Illian, J. B., 21 Mar 2019, In : Methods in Ecology and Evolution. Early View, 7 p.

    Research output: Contribution to journalArticle

  5. Estimating effective detection area of static passive acoustic data loggers from playback experiments with cetacean vocalisations

    Nuuttila, H. K., Brundiers, K., Dähne, M., Koblitz, J. C., Thomas, L., Courtene-Jones, W., Evans, P. G. H., Turner, J. R., Bennell, J. D. & Hiddink, J. G., Dec 2018, In : Methods in Ecology and Evolution. 9, 12, p. 2362-2371

    Research output: Contribution to journalArticle

Related by journal

  1. Methods in Ecology and Evolution (Journal)

    Michael Blair Morrissey (Member of editorial board)
    1 Jan 20171 Jan 2020

    Activity: Publication peer-review and editorial work typesEditor of research journal

  2. Methods in Ecology and Evolution (Journal)

    Theoni Photopoulou (Editor)
    2017 → …

    Activity: Publication peer-review and editorial work typesEditor of research journal

  3. Methods in Ecology and Evolution (Journal)

    Oscar Eduardo Gaggiotti (Member of editorial board)
    1 Sep 2014 → …

    Activity: Publication peer-review and editorial work typesEditor of research journal

ID: 249951261