Abstract
Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-β superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.
Highlights
Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood
Given that multiple phenotypes are associated with head colour, one hypothesis is that the Red locus is a supergene, defined as a tight cluster of genes acting as a mechanical unit in particular allelic combinations[14], which is often facilitated by a chromosomal inversion, as recently demonstrated in several avian species[15,16,17,18]
By using high-depth/low SNP density RADSeq[20] and low-depth/high SNP density wholegenome sequencing, we identified a region on the Z chromosome strongly associated with red–black head colouration (1000 permutations, P < 0.05, Fig. 1a, Supplementary Figs. 1 and 2) within the candidate interval identified in a previous linkage analysis[21]
Summary
Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. In a genome-wide association study (GWAS) in 32 RADsequenced samples, we used Fisher’s exact tests with one degree of freedom for a dominant model of penetrance in a 2 × 2 contingency table of phenotype (black or red) by genotype (a/a or not a/a) using PLINK v1.959 (Fig. 1a).
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