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That we find no significant correlation between the location of mutations and predicted CTL epitopes might be due to differences between CTL epitopes in the strength of the immune selection pressure imposed on them, which would reduce the detection power of our method of testing for selection pressure.
In addition to testing for selection on individual traits, we also tested for directional selection on entire groups of traits.
It has been suggested that SNP-environment associations are more sensitive to detect subtle clines in allele frequencies than FST outlier tests and that both approaches might be complementary but not concordant when testing for selection [ 38].
Because recombination might yield false-positive results when testing for selection (Anisimova et al. 2003), we first screened the alignments for evidence of recombination using GARD (Kosakovsky Pond et al. 2006); this analysis underscored no recombination breakpoint in any alignment.
Before testing for selection, all codons containing gaps in any species in the alignment were removed (this applied to only six codons in TLR5; throughout the text, codon positions are numbered according to the chicken GaGaTLR5 sequence (see Additional file 1: Table S1).
It is appealing that testing for selection should be based on a strong biological working hypothesis [23].
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In an examination of end-of-course evaluations from over 3000 courses, Goos and Salomons (2017) disaggregate overall participation rates to test for selection bias in students' participation.
We also tested for selection using summary statistic-based methods.
Cells were tested for selection efficiency by immunoblotting.
In contrast, many population genetic hypotheses explicitly test for selection.
McDonald Kreitman tests (MK, [ 55]) were also performed to test for selection.
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