Regarding the F-word: the effects of data Filtering on inferred genotype-environment associations

Collin Ahrens, Rebecca Jordan, Jason Bragg, Peter Harrison, Tara Hopley, Helen Bothwell, Kevin Murray, Dorothy Steane, John Whale, Margaret Byrne, Rose Andrew & Paul Rymer
Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results. These effects could be amplified in downstream predictions, including management strategies. Here, we investigate the effects of filtering on...
1 citation reported since publication in 2021.
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