Jumping gene turns snake white(r)

By Suzanne Saenko.

Snakes can be dangerous, but they are also quite beautiful. Especially astonishing is the variation in colour patterns in snakes.  Despite their incredibly diverse colour patterns, very little is known about how this diversity evolved and which genes and mutations are responsible for such variation. Luckily, snake enthusiasts have been breeding one particular harmless snake for decades, the corn snake (Pantherophis guttatus). This captive breeding led to many different colour patterns, for example the four you can see in the picture below. There are however many more. We kept both wild type and amelanistic (the oldest variation known) snakes in the lab and discovered that one gene jumped to a different place in the genome leading to the absence of black pigment. With this research we not only show how this colour pattern difference is caused, but also put the corn snake forward as a great model for evolutionary genetics in reptiles.

Adaptive variation in snake coloration

Almost every animal species on Earth can be distinguished by its characteristic colour pattern. These patterns are usually adaptive, i.e. they are involved in camouflage or scaring off predators. Snakes, in particular, show an incredible diversity in coloration. Many snake species have cryptic brown, grey, or green colours which make them impossible to spot against the background of sand, dirt, or grass. Venomous snakes, on the other side, often have conspicuous patterns of contrasting red, yellow, and black bands which serve to warn the potential predators. Skin patterns in snakes also reflect animal behaviour. For example, patches on the back are generally found in ambush hunting, slow-moving species such as pythons, while longitudinal stripes are often associated with rapid escape in slender, fast-moving, snakes.

Corn snake as a model for evolutionary genetics analysis of colour variation

The diversity of colours and patterns in snakes is striking, but how did it evolve? To explain the evolution of such variation, we need to identify the genes and mutations responsible for different colour variants. Therefore, we have to breed snakes in the laboratory, but not every species is suited for this purpose. Luckily, the North American corn snake Pantherophis guttatus is an ideal species to serve as a model for evolutionary genetic analysis of colour variation in reptiles. These harmless, non-venomous snakes are easy to keep in the lab and lay plenty of eggs. Their medium size and calm temperament also make them very popular pets in Europe and in the US. In fact, many generations of breeding by motivated corn snake owners have already resulted in a wide variety of different colours and patterns (so-called “morphs”), and more and more new variants become available every year.

Normal, or wild type corn snakes, have a light orange background colour covered with a pattern of dark orange  patches that are outlined with black. However, morphs that lack either black (amelanistic) or orange (anerythristic) pigment also exist, as well as morphs with an aberrant pattern (e.g. stripe) such as longitudinal lines (see the picture above). All these and many other variants appeared due to spontaneous mutations in the genome of corn snake. This offers the scientists an unique opportunity to identify genes involved in colour patterning of snakes and compare it to other animals.

The loss of black pigment (Amelanism) is caused by insertion of a “jumping gene” in the OCA2 gene

The first mutation in this snakes colour pattern appeared  almost half a century ago and caused the absence of black pigment (amelanistic). However, to identify where this mutation can be found in the genome, researchers at the University of Geneva and Uppsala University first had to sequence the complete genome of the corn snake. Next, we sequenced DNA (determined the order of building blocks in the DNA) from wild type snakes (with black pigment) and amelanistic snakes (without black pigment). By comparing the DNA of both types of snakes with the sequenced genome we were able to locate differences between wild type snakes and amelanist snakes

Surprisingly, we found one striking difference: all amelanistic snakes had a fragment of 5832 nucleotides (building blocks of DNA) in their OCA2 gene, but none of the wild type snakes did. This additional piece of DNA is inserted in the middle of the gene and makes it completely dysfunctional. OCA2 (Oculocutaneous locus 2) is responsible for making a receptor that is active in those cells that produce the black pigment called melanin. The receptor controls the proper level of activity allowing for the synthesis of melanin. If the receptor cannot function properly, the production of the black pigment is blocked, and the snake turns white(r).

We were even more surprised when we found that this 5832 nucleotide insertion is not unique, but exists in multiple copies in corn snake genome. It is also very similar to the so-called “transposons”, or “jumping genes” of other vertebrates. Transposons are DNA sequence that can change their position within a genome. Sometimes they “jump” into existing genes and create new mutations. In some cases, as with OCA2 in the corn snake, these mutations disturb a normal process, like melanin synthesis. But in others they can create new genetic functions and therefore lead to novel variants. For example, the evolution of egg-spots in some cichlid fish is also due to the insertion of such transposon near an important pigmentation gene (see http://www.nature.com/articles/ncomms6149).

Our research shows that corn snakes are a great model to identify variation in colour patterns. As colour patterns occur throughout all animal groups and have such diverse functions (camouflage, scaring off predators etc.), research to find the genetic basis of this variation provides important insights into how animals evolve. With all the morphs produced by snake breeders, we have our work set out for us!


Suzanne V. Saenko, Sangeet Lamichhaney, Alvaro Martinez Barrio, Nima Rafati, Leif Andersson and Michel C. Milinkovitch (2015) Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene. Scientific Reports 5:17118 | DOI: 101038/srep17118

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