Inferring selection and allelic frequency shifts
The impossibility to test for expression of candidate genes at this
point led us to indirectly explore whether neutral evolution could
explain genotype and allele frequency dynamics in the population.
Molecular signatures of selection often reflect allele frequency shifts
from one generation to another. This was possible to investigate with
our dataset because of the timestamps associated with breeding pairs and
respective offspring and annual monitoring of individual presence in
nesting boxes. We first inspected whether genotype frequencies deviated
from Hardy-Weinberg equilibrium across years, by calculating
year-to-year observed and expected frequencies following the
Hardy-Weinberg equation (Wittke-Thompson, Pluzhnikov, & Cox, 2005),
considering only offspring, adults and both. We then compared the
pairwise frequencies of both alleles and genotypes of candidate loci
with Wright’s F-statistics across years. To understand at what point
observed values significantly deviate from neutral expected
distributions, we randomly selected 100 pairs of loci for among the
RADseq dataset, calculated F-statistics, and estimated 97.5% confidence
intervals of the F-statistic distribution. F-statistics calculations
were performed in Arlequin v3.5.2.2 (Excoffier & Lischer, 2010).