Whole‐genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations

Dissecting the genetic basis of phenotypic variation in natural populations is a long‐standing goal in evolutionary biology. One open question is whether quantitative traits are determined only by large numbers of genes with small effects, or whether variation also exists in large‐effect loci. We conducted genomewide association analyses of forehead patch size (a sexually selected trait) on 81 whole‐genome‐resequenced male collared flycatchers with extreme phenotypes, and on 415 males sampled independent of patch size and genotyped with a 50K SNP chip. No SNPs were genomewide statistically significantly associated with patch size. Simulation‐based power analyses suggest that the power to detect large‐effect loci responsible for 10% of phenotypic variance was