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The WZA: A window-based method for characterizing genotype-environment association
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  • Tom Booker,
  • Sam Yeaman,
  • James Whiting,
  • Michael Whitlock
Tom Booker
The University of British Columbia

Corresponding Author:[email protected]

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Sam Yeaman
University of Calgary
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James Whiting
University of Calgary
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Michael Whitlock
The University of British Columbia
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Genotype environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the weighted-Z analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST. We analyze simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single-SNP based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes was sampled. We apply the WZA to previously published data from lodgepole pine and identified candidate loci that were not found in the original study.
16 Nov 2022Review(s) Completed, Editorial Evaluation Pending
16 Nov 2022Submitted to Molecular Ecology Resources
17 Nov 2022Reviewer(s) Assigned
20 Dec 2022Editorial Decision: Revise Minor
17 Jan 2023Review(s) Completed, Editorial Evaluation Pending
17 Jan 20231st Revision Received
23 Jan 2023Editorial Decision: Accept