The search for loci under selection: trends, biases and progress

Collin W. Ahrens, Paul D. Rymer, Adam Stow, Jason Bragg, Shannon Dillon, Kate D. L. Umbers, Rachael Y. Dudaniec*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    138 Citations (Scopus)


    Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP-based selection studies and help to progress landscape and evolutionary genomics.

    Original languageEnglish
    Pages (from-to)1342-1356
    Number of pages15
    JournalMolecular Ecology
    Issue number6
    Publication statusPublished - Mar 2018
    EventDetecting signatures of selection using genomics - Sydney
    Duration: 1 Sept 20162 Sept 2016


    • adaptive genetic variation
    • environmental association analysis
    • FST outlier analysis
    • genotype by environment
    • landscape genomics
    • single nucleotide polymorphism


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