Swapping pigmentation genes across the Parulidae phylogeny

Genomic analyses reveal repeated exchange of pigmentation genes among these warblers.

The bird family Parulidae is known for its diversity in plumage patterns, primarily related to the pigments melanin (brown and black colors) and carotenoids (yellow, red and orange colors). Several studies have unraveled the genetic basis of these color differences, usually taking advantage of natural hybrids. Because genetic material gets shuffled around in hybrids, it can be easier to pinpoint particular genomic regions and identify candidate genes for further research. Most of these studies focused on hybridization between two species, such as the hybrid zone between Townsend’s Warbler (Setophaga townsendi) and Hermit Warbler (S. occidentalis). In a recent Current Biology study, Marcella Baiz and her colleagues took a broader perspective and compared the genomes of all 34 species in the genus Setophaga.

Gene Trees

Probing the genomes of these warblers revealed several divergent genomic regions that were shared by multiple species pairs. Some smaller regions contained the pigmentation genes ASIP (agouti signaling protein) and BCO2 (beta-carotene oxygenase 2). These genes also popped up in other studies on plumage coloration (see for example here and here) and are thus excellent candidates for more detailed analyses. Because different species have independently evolved similar plumage patterns, it is possible that these genes have been exchanged across the phylogeny of the Parulidae. To unravel the evolution of these genes, the researchers constructed gene trees for ASIP and BCO2, and compared these with the species tree.

The gene tree of ASIP was largely concordant with the expected phylogenetic relationships, suggesting that it has not been exchanged between species. The convergent evolution of black plumage patterns (in which ASIP is involved) might thus be due to repeated mutations. The situation for BCO2 is drastically different. Its gene tree deviated from the species tree, revealing several instances of introgression between distantly related species. These patterns were confirmed with the D-statistic, a commonly used test to detect introgression. The BCO2-gene has been exchanged between the Magnolia Warbler (S. magnolia) and the Yellow Warbler (S. petechia), and there was probably an introgression event involving the ancestor of the Prairie Warbler (S. discolor) and the Vitelline Warbler (S. vitellina).

The discordance between the species tree (left) and the BCO2 gene tree (right) point to repeated introgression of this gene. From: Baiz et al. (2021) Current Biology.

Tip of the Iceberg

These patterns show how the plumage patterns in the Parulidae evolved through the interplay of repeated mutations in some genes and extensive introgression of other genes. This study focused on just two genes (ASIP and BCO2), but many more genomic regions and candidate genes are waiting to be studied in more detail. The authors wrote that the parulid warblers have a “rich legacy of study, including cornerstones of community ecology and phylogenetic diversification”. I am confident that this bird family will continue to be a focal point of much more scientific research.


Baiz, M. D., Wood, A. W., Brelsford, A., Lovette, I. J., & Toews, D. P. (2021). Pigmentation genes show evidence of repeated divergence and multiple bouts of introgression in Setophaga warblers. Current Biology31(3), 643-649.

Featured image: Magnolia Warbler (Setophaga magnolia) © Cephas | Wikimedia Commons

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