Genetic Basis and Evolution of Structural Color Polymorphism in an Australian Songbird

Abstract

Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaptation under differential selection. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could in principle produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genome resequencing to investigate the genetic basis of melanism by comparing the blue and black M. leucopterus subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene ASIP and four candidate genes that may contribute to feather nanostructure development. Contrary to the prediction of convergent evolution of island melanism, we detected signatures of a selective sweep in genomic regions containing ASIP and SCUBE2 not in the black subspecies but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This proposed re-evolution was likely driven by a preexisting female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.

Keywords: avian plumage color; color genetics; feather coloration; male ornamentation; structural color; white-winged fairywren.

Fig. 1.

Geographical distribution and sampling sites of M. leucopterus. Malurus leucopterus males from BI (M. l. edouardi, denoted by black circles on the map) and DHI (M. l. leucopterus, denoted by black triangles) have black nuptial plumage. Malurus leucopterus males distributed across the Australian continent (M. l. leuconotus, denoted by blue triangles) are with blue plumage. Light blue color indicates the range of M. leucopterus. Refer to supplementary table S1, Supplementary Material online for detailed information of sampled individuals. The map was generated using QGIS 3.24. Illustrations of birds were reproduced with the permission of Lynx Edicions.

Fig. 2.

Hypotheses of plumage color evolution in the white-winged fairywren (M. leucopterus). Left side of the figure shows the two hypotheses: hypothesis A (H_A)—independent evolution of black plumage on DHI and BI; hypothesis B (H_B)—evolution of blue plumage on the mainland from birds with black plumage. Right side shows the corresponding positions of the plumage color change on the phylogenetic tree predicted by the two hypotheses. In the M. leucopterus clade, the upper half of the branches leading to the subspecies indicates scenario under hypothesis A, and the lower half of the branches represents hypothesis B. Hypothesized color changes are indicated by boxes (H_A: with diagonal lines and “A” above, H_B: with vertical lines and “B” below, black: change from blue to black, blue: change from black to blue). The heart symbol denotes proposed female color preference based on male petal carrying behavior. Female preference for blue color likely maintained in all M. leucopterus subspecies, and female preference for red color might have evolved in the common ancestor of M. melanocephalus and M. alboscapulatus. Diagrams of feather barb cross-section are illustrated based on Driskell et al. (2010). c, cortex; s, spongy layer, m, melanosome. Illustrations of birds were reproduced with the permission of Lynx Edicions.

Fig. 3.

Phylogenetic positions of M. leucopterus subspecies. SNAPP tree based on 6,790 nuclear SNPs. Illustrations of birds were reproduced with the permission of Lynx Edicions.

Fig. 4.

Genome-wide differentiation between black and blue M. leucopterus. Points indicate overlapping sliding window F_ST values in 50 kb windows. Red points above red horizontal line are above 99.9th percentile. Five divergent regions with genes that are potentially relevant to plumage color development are highlighted in pink, with scaffold and gene identities labeled. Scaffolds are reordered as pseodochromosomes according to the T. guttata genome. Illustrations of birds were reproduced with the permission of Lynx Edicions.

Fig. 5.

The genomic landscape of the five divergent regions between black and blue M. leucopterus. The five regions are: a) scaffold 132 containing SCUBE2, b) scaffold 283 containing THBS2, c) scaffold 285 containing ASIP, d) scaffold 8 containing THBS4, and e) scaffold 18 containing NECTIN3. F_ST, SNP associations, genetic diversity (π), RND, Fay and Wu's H, and CLR are shown in different panels for each region. Blue, and black solid and dotted lines in the same panel of π, Fay and Wu's H, and CLR represent mainland, DHI, and BI populations, respectively. Annotated genes in those regions are depicted using blocks and lines to represent exons and introns, respectively, in the top panel.

Fig. 6.

Phylogeny and individual genotypes of the two regions of divergence. Phylogenetic tree reconstructed using SNAPP based on SNPs from the whole divergence peak region contains a) SCUBE2 or b) ASIP. c, d) Genotypes at SNPs between black and blue Malurus leucopterus populations in the (c) SCUBE2 and (d) ASIP regions. Each row represents one individual. Black triangles and circles denote M. leucopterus from DHI and BI, respectively. Light blue, black, and dark blue indicate positions homozygous for the allele that was the same as the reference genome (from a M. l. leuconotus sampled in Queensland, Australia), homozygous for the allele different from the reference, and heterozygous for both alleles, respectively. Missing values are represented by white. Number in parentheses indicates the polymorphic site number of each gene. Illustrations of birds were reproduced with the permission of Lynx Edicions.

Fig. 7.

a) Genotypes and b) allele frequencies at 54 SNPs in the five highly divergent genomic regions (see Fig. 5) that were strongly associated (−log[P] > 6) with plumage color differentiation between M. l. leucopterus from DHI and M. l. leuconotus from the mainland. a) Genotypes of M. l. edouardi from BI, other bi-colored wrens, and outgroups are also shown. Each row represents one individual. Light blue, black, and dark blue indicate positions homozygous for the allele that was the same as the reference genome (from a M. l. leuconotus sampled in Queensland, Australia), homozygous for the allele different from the reference, and heterozygous for both alleles, respectively. Each column represents one SNP position. The scaffolds where the SNPs originated from are indicated at the bottom. b) Each row represents the allele frequencies of one species or subspecies of M. leucopterus, ranging from 0 (all alleles were different from the reference) to 1 (all alleles were the same as the reference). Illustrations of birds were reproduced with the permission of Lynx Edicions.