Association analyses suggest two candidate loci involved in tawny
owl coloration patterns.
Mapping
RADseq reads against reference genome resulted in 95% (± 0.6 SD)
mapping rate, where an average of 9 million reads (± 5mio SD) were
utilized per individual. Catalogues construction resulted in the
discovery of 1165325 loci, with an average size of 185.7 sites and an
average coverage of 46.2x (± 20.9x SD). Filtering for minor allelic
frequency (0.05), presence in 80% of the dataset, and collecting one
random SNP per RAD-locus resulted in a panel of 19212 bi-allelic SNPs.
Average coverage per individual after variant calling was 59x (± 30x
SD). The distribution of RADseq reads across genomic regions of
candidate loci for coloration implied that our strategy indeed covered
not only flanking regions but also the coding sequence, despite not a
single locus in the coding sequence has passed the variant calling
pipeline (Table S5A and B). The search for structure at a
meta-population level identified two clusters, though neither were
associated with colour, family, or temporal stamp (Fig. S2-S3). Numbers
varied between clusters, with cluster 1 containing most of the samples.
Association studies jointly revealed a total of 2 markers concordantly
associated with the colour phenotype, which we will henceforth refer to
as 602-G/C (log(p) = 6.31) and 3657-C/T(log(p) = 4.54) (Table 2). Exploring the effect size of those
associations revealed a high predictive power for the colour “grey”
either when genotypes are analysed independently for each locus or
jointly. Specifically, independent genotype combinations showed that
heterozygotes and homozygotes for the least common allele to have
between 70% and 90% probability of being grey and between to 55% to
100% when genotypes of both loci are interpreted together (Fig. 2).
Notably, the probability increase is explained by the number of copies
of the less common allele in each genotype (Table S6-S11)