Lessons from the Urban Pigeon

Urban pigeon
Speckled, striped, barred: the genes of pigeon wing coloration demonstrate how basic questions can have implications for human health. Photo Credit: Christian Jansky, Wikimedia Commons

There is an entire community of pigeon collectors living amongst us. They marvel at the diversity of plumage, color, and patterning that this single species displays. In fact, none other than Charles Darwin himself fancied the pigeon species. These pigeon enthusiasts understand that we can learn a lot from pigeon diversity. In a recent publication, Vickrey and team found how pigeons pattern their wings. This exciting new research uncovered new information about human blindness and inter-species gene transfer.

Domestic rock pigeons, the same type of pigeons wandering the streets of New York City, have several different wing patterns: dark and speckled (termed T-check and Checker), light with black stripes (termed bar), and completely light (termed barless) (Figure 1). Each pattern comes with different traits. Dark colored male birds are more attractive to females allowing them to mate more successfully.  However, lighter winged companions stay warmer in harsher rural environments due to better fat storage. Interestingly, the rare completely light birds have poor vision. But how does the single pigeon species make all of these different wing patterns? And how does this patterning relate to different traits? Lead investigator Mike Shaprio at the University of Utah and first author Anna Vickery set out to understand these questions.

Figure 1: The different wing patterns of the Domestic rock pigeon. Adapted from Vickrey et al. Fig 1A.

They investigated what genetic information was different between speckled and light winged pigeons. Genetic information is stored in a biomolecule called DNA. There are four letters in the DNA alphabet – A, T, C, and G. In combination, these letters come together to spell thousands of different ‘molecular words’, termed genes. Each gene spells out a single molecular machine, termed protein, with a specific and unique function. By understanding which region of the DNA is different between dark winged birds and light winged birds, the authors hoped to identify the specific gene that determines wing pattern.

Vickrey and her team collected DNA from dozens of pigeons and looked for differences between all birds with dark and speckled wings compared to birds with light and striped wings. Normally, these types of analyses can result in multiple DNA differences. However, the authors found only a single DNA region! Looking more closely at this region, they noticed it contained an interesting gene: NPD. The NPD gene has already been seen by other scientists to control for wing color in crows and pigmentation in mice. Now, for the first time, the authors also showed that the NPD gene controls wing color in pigeons.

But how does one gene, NPD, make so many different patterns? The answer lies in how much of the gene the pigeon makes. In birds with dark wings, there is a lot of NPD. In birds with light wings and a stripe, there is a small amount of NPD. The level of NPD is controlled by the DNA directly surrounding the NPD gene. This neighboring DNA (known as the promoter and enhancer) acts as a landing pad for factors that turn genes on. When there is a longer sequence, more factors land on the gene, and they generate a strong ON signal to make a lot of the gene. When there is a short sequence, fewer factors land on the gene, and they generate a weak ON signal to make only a small amount of the gene. This was the difference between dark and light winged birds. Dark winged birds had an expansion of the neighboring DNA sequence, creating a long landing pad and generating a loud ON signal. In contrast, the light winged birds had a small neighboring DNA sequence, creating a small landing pad and only a whisper of an ON signal.

But the story doesn’t stop there. The authors had not yet found what made completely light winged birds with no stripe. Looking more closely at the NPD gene, they noticed that all completely light winged birds had the same error in DNA. This error caused the final protein made to be shorter than the normal protein. It is possible this shortened protein has a broken function that causes loss of black stripe pigmentation.

The same error in the human NPD gene is the underlying cause of Norrie disease. Patients with this disease suffer blindness and some have additional neurological deficiencies. Pigeons with the same NPD error also suffer from vision problems. This interesting connection could allow scientists to use completely light winged pigeons as a model system to better understand Norrie disease. Future work to understand how NPD in pigeons causes vision problems will hopefully shine light on the human disorder.

In addition to using their DNA data to identify the role of NPD in wing patterning, the authors used it to answer a long-standing question in the pigeon community: where did the speckling wing pattern come from? The wing patterns of the domestic rock pigeon look a lot like the specked wings on the African speckled pigeon, a completely different pigeon species. Many pigeon fanciers have long thought that there was some inter-species mixing that gave the rock pigeon their looks. By comparing the DNA sequence of the NPD gene both within each individual species and across several different species, the authors confirmed the pigeon community’s hunch. The NPD gene in rock pigeons did in fact come from the African speckled pigeon.

This inter-species mixing, known as introgression, is an exciting example of how new genetic information can be introduced into a species. This new genetic material has likely remained in the urban pigeon because it allows the individuals with it some fitness advantages. For example, female birds are more attracted to speckled wing males. It is as if the urban pigeon borrowed its cousin’s cool new coat to attract mates. It has been so successful that the new coat gene (aka NPD) is now a part of the urban pigeon closet (aka DNA). There are other possible reasons why this gene was able to transfer between species, and future work by the Shapiro lab will continue to explore other fitness advantages the NPD gene might confers.

The Shapiro team used DNA sequence analysis to identify and characterize a gene involved in pigeon wing pattern. In doing so, they highlighted the power of the pigeon as a model system to better understand human blindness and evolutionary history.
1. Vickrey et al. Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife (2018).


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