Genome-wide association analysis
Admixture mapping revealed a number of genomic regions that were
strongly associated with plumage traits that differ between
yellow-fronted and red-fronted tinkerbirds (Table 1). After accounting
for the one expected false positive per trait based on our significance
threshold of -log10(α = 6), there were eight
significant associations of chromosomes with traits. We found that crown
colour was significantly associated with three chromosomes. Crown hue
was significantly associated with SNPs on chromosome 24 (on scaffolds
70213, 70285 and 70295), crown score with SNPs on chromosome 20 (on
scaffolds 67410, 67420, 67433 and 67445), and both were significantly
associated with SNPs on chromosome 8 (Fig. 2). Indeed, the same six SNPs
on adjacent scaffolds 50344, 50345, and 50346 on chromosome 8 were
significantly associated with both crown hue and crown score (as well as
50201 for crown score and 50321 for crown hue). The variant most
strongly associated with crown score was an indel on scaffold 50201 on
chromosome 8, which aligns to the region 13-21 kbp upstream ofCYP2J19A in zebra finch, and 16-28 kbp upstream of cytochrome
P450 gene XM_009910004 in downy woodpecker (manually annotated asCYP2J19 by Twyman et al. 2018a). The cluster of SNPs on adjacent
scaffolds 50344, 50345, and 50346 on chromosome 8 spans approx. 150 kbp
and is located 1.8 Mbp from CYP2J19A in zebra finch. It overlaps
with several other genes in zebra finch: Leucine-rich repeat-containing
protein 42 (LRRC42 ), Intraflagellar transport protein 25 homolog
(HSPB11 ), iodothyronine deiodinase 1 (DIO1 ), YIP1 domain
family member 1 (YIPF1 ), Nucleoporin NDC1 (NDC1 ),
and GLIS family zinc finger 1 (GLIS1 ). There was no
significant association with crown chroma. There was also a significant
association with regions of the genome and supercilium score, associated
with chromosome 4 (Table 1). There were no chromosomes with
>2 significant SNPs associated with wing bar percent of
yellow over black.