A small genomic region explains the plumage differences between Townsend’s and Hermit Warbler

Three pigmentation genes might contribute to reproductive isolation.

If I had a dollar (or euro) for every time I read “hybrid zones are natural laboratories” in a paper, I could probably sequence a fair number of bird genomes. This popular phrase can be traced back to a classic paper by Godfrey Hewitt: “Hybrid zones-natural laboratories for evolutionary studies“. And it is certainly true. Hybrid zones are extremely useful settings to learn more about the evolutionary process. Moreover, because of the recombination of different genomic regions in hybrids, it is sometimes possible to uncover the genes underlying certain traits. This approach has been successful in finding “migration genes” in the Willow Warbler (Phylloscopus trochilus) and “plumage genes” in Vermivora warblers. A recent study in the journal Evolution Letters relied on a hybrid zone between Townsend’s Warbler (Setophaga townsendi) and Hermit Warbler (S. occidentalis) to identify the genetic underpinnings of several plumage traits.

Three Genes

Silu Wang and her colleagues quantified plumage patterns in 265 individuals. They focused on seven traits: (1) cheek coloration, (2) crown coloration, (3) throat bib darkening, (4) throat bib intensity, (5) extent of breast yellow, (6) presence of black streaks on the flank, and (7) intensity of green chroma on the back. Next, the researchers performed a genome-wide association study (GWAS) to determine which genetic variants correspond to particular traits. The analyses revealed that a single variant was significantly associated with the colors of the cheek, crown and flank. This variant is located in an intron of the RALY-gene, which is known to be involved in the yellow versus black pigmentation of mice and quail. In addition, two other pigmentation genes can be found in the same region: ASIP (influences skin pigmentation in vertebrates) and EIF2S2 (associated with human skin pigmentation). How these three genes work together is still unclear, but they might function as a “super-gene” (see this blog post for more on this topic).

Location of the hybrid zone (yellow) between Townsend’s Warbler (blue) and Hermit Warbler (purple), and an overview of the different plumage traits investigated in this study. From: Wang et al. (2020) Evolution Letters.

Reproductive Isolation

Next, the researchers used the genomic data to pinpoint differentiated sections in the genome that might be involved in reproductive isolation between these warblers. This search indicated four highly differentiated genomic regions, located on chromosomes 1A, 5, 20 and the Z-chromosome. Interestingly, the region on chromosome 20 corresponds to the location of the three pigmentation genes from the GWAS. This finding suggests that the ASIP-RALY region is involved in maintaining species-specific differences and preventing these warblers from merging into one species.

The exact mechanism of reproductive isolation remains to be determined. It could be that the ASIP-RALY region facilitates assortative mating (i.e. choosing a partner that looks like you). However, a recent simulation study suggested that assortative mating alone is insufficient to stabilize hybrid zones, some degree of postzygotic selection is needed. Another possibility is that the ASIP-RALY region contributes to lower fitness in hybrids. The patchy plumage patterns of hybrids might be a disadvantage in territorial disputes, complicating a hybrids’ attempt to secure a good territory. Exciting avenues for further research, showing how genomic analyses can generate hypotheses to be tested in the field.

Exploring genomic landscape of differentiation with different genomic datasets revealed several highly differentiated regions (highlighted with red dots), including the section with the three pigmentation genes. From: Wang et al. (2020) Evolution Letters.


Wang, S., Rohwer, S., de Zwaan, D. R., Toews, D. P., Lovette, I. J., Mackenzie, J., & Irwin, D. (2020). Selection on a small genomic region underpins differentiation in multiple color traits between two warbler species. Evolution Letters4(6), 502-515.

Featured image: Townsend’s Warbler (Setophaga townsendi) © Alan Vernon | Wikimedia Commons

This paper has been added to the Parulidae page.

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