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.