On the Origin of Pigeon Plumage Patterns: A Role for Hybridization

“Believing that it is always best to study some special group, I have, after deliberation, taken up domestic pigeons.”

– Charles Darwin (1859)

If you have difficulty sleeping at night, grab the Origin of Species by Charles Darwin and turn to the section “On the Breeds of Domestic Pigeons”. His seemingly endless description of various pigeon breeds is bound to make your eyes close. But all joking aside, as Darwin already knew, pigeons are an excellent study system to answer numerous biological questions. This is exemplified by a recent study in the journal eLife that explored the genetic basis of plumage patterns in domestic pigeons (Columba livia).


Four Phenotypes, One Locus

There are over 350 breeds of domestic pigeon, showing a variety of plumage pigmentation patterns. Classic experiments have shown that the pigmentation of the wing is determined by variation at a single locus that results in four phenotypes: T-check, checker, bar and barless (see pictures below). Darwin already deduced that bar is the ancestral state. However, checker and T-check are common in feral populations, suggesting an adaptive advantage for these plumage patterns in cities.


The four wing patterns in domestic pigeons (from: Vickrey et al. 2018 eLife)


A Candidate Gene: NDP

When you study the genetic basis of a particular trait, it is useful to have a target gene in mind. So, Anna Vickrey and her colleagues compared the genomes of bar and checker pigeons to see if there were any significant differences. One genomic region – on scaffold 68 – stood out prominently. This region contains, among others, the gene NDP, which is differentially expressed in crow subspecies (black and hooded crow) that differ in their plumage patterns. The same holds true for these pigeons, experiments showed that NDP is significantly more expressed in checker feathers.

fst peak

Comparing the genomes of checker and bar pigeons uncovered a differentiated region on scaffold 68 (the huge peak on the left) that contains the gene NDP (from: Vickrey et al. 2018 eLife).


Speckled Pigeon

Further analyses of the NDP-containing region indicated that it originates from another species: the speckled pigeon (C. guinea). It was probably introduced after the domestication of the rock pigeon, which started about 5000 years ago. Apparently, this result is not that surprising to pigeon breeders:

“Pigeon fanciers have long hypothesized that the checker pattern in the rock pigeon (Columba livia) resulted from a cross-species hybridization event with the speckled pigeon, a species with a checker-like wing pattern”

speckled pigeon.JPG

Pigeon breeders already suspected that the speckled pigeon had something to do with plumage patterns in domestic pigeons (from: http://www.wikipedia.com/)


Vision Defects

Finally, there is also a connection with humans here (apart from the domestication of pigeons). In humans, a defect NDP gene can result in Norrie disease, a genetic disorder that primarily affects the eye and almost always leads to blindness. Interestingly, the barless phenotype in pigeons is associated with a defect NDP-gene as well. Moreover, pigeon breeders have known for a long time that barless pigeons often have issues with vision. When the researchers compared the defect NDP genes in humans and barless pigeons, it turned out that in both species there was a nonsense mutation at the start of the protein. Who would have seen that coming!



Vickrey, A.I., Bruders, R., Kronenberg, Z., Mackey, E., Bohlender, R.J., Maclary, E.T., Maynez, R., Osborne, E.J., Johnson, K.P., Huff, C.D., Yandell, M. & Shapiro, M.D. (2018) Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 7, e34803.  DOI: 10.7554/eLife.34803


This paper has been added to the Columbiformes page.

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