Basic Reptile Genetics 101

A look at mutations and how they are reproduced

Over the last 15 years or so the practice of breeding snakes exhibiting various mutations of color or pattern has gained wide popularity.
With the influx of newcomers to the hobby, a lot of questions are generated about how these traits are inherited and a lot of misconceptions are prevalent among this group of new herpers.
I hope this page will serve as a basic primer of the most common genetic principles as they apply to herpetoculture and hopefully make clearer some issues that initially seem much more complicated than they are.

There are several terms you will see with great regularity when the subject of reptile genetics and morphs is discussed. Some of these are simple recessive, codominate (codom), "super", het and 66% het. I'll get to each of these as we go along and you'll see that it's not really difficult once you get the grasp of a few key concepts.
I'll use ball pythons as my primary example on this page due to the variety of morphs in existance, both co-dominant and recessive.

Genes

First let's briefly discuss genes and what they are. I'm not going to attempt to make this into a college level scientific discussion, I'm not preparing you for a career in the field of genetics. I'm not going to go into terms like alleles and loci and get all academic with you. I'm going to keep this simple, just to convey the concept to provide the foundation of understanding how we reproduce the various mutations in captivity.
For those of you who are more academically inclined, you will notice some technically inaccurate uses of terminology, or what you might consider an oversimplified explanation. This page is aimed at the newcomers to this area and I will be using terms as they are commonly applied by the laymen in our hobby, despite the fact that their definitions may not be strictly accurate or complete scientifically.
Everything you will read from here on will be solely for the purpose of describing, for the average snake keeper, genetic mutations of snakes and how they are reproduced.

Just as in humans, everything about a snake is determined by various genes and how they interact with each other. The genes with which we as snake keepers are concerned affect coloration and pattern.
The snakes receive one half of their genetic material from each parent. Each individual gene is one of a pair and each pair of genes is made up of one gene from each parent.

For the purposes of our discussion here, we will consider genes to fall into one of two catagories, either recessive or dominant. A dominant gene does just what the name suggests, it dominates over recessive genes. What this means is any time a dominant gene is present it will be expressed regardless of what type of gene it's paired with. In order for a recessive gene to be expressed it has to be paired with another recessive gene just like it. We'll go into this some more in the next section on simple recessive traits.

We consider a gene to be a mutation, or morph, based on a comparison with what the snake most often appears like in the wild. This wild type pattern and coloration is usually just referred to as "normal". I don't care for that terminology because it carries with it a negative stigma, but that is the term that is used.
Let's go ahead and get into the different ways genes are expressed and how they are inherited.

Simple Recessive Traits

A simple recessive trait is a mutation that requires two like genes to be paired in order for it to be expressed. When two like genes are paired, the snake is called homozygous. Some people just call it "visual", as in a visual albino.
If a recessive gene is paired with a normal gene, then it's effect will not be visible in the snake. This condition is called heterozygous, or het for short. The term, as used in herpetoculture, simply means that the snake is carrying the gene for a recessive trait, but it does not visually express the trait.
Some examples of recessive traits in ball pythons are Albino, Clown, and Genetic Stripe. In order for a snake to visually express a recessive trait, both parents must at least carry the gene and each must pass it on to the offspring.
In other words you can produce a visual albino by breeding either an albino to a het or by breeding two hets, but you cannot produce an albino from breeding one albino parent and one normal, non het, parent.
Once you understand how the genes are passed to the next generation you can predict statistically how many offspring will receive which genes. It's important to remember that any prediction made is only statistical, it is not necessarily what you will get from a single clutch.
To make these predictions we use something called a punnett square. This is just a diagram to demonstrate the possible combinations in which a specific set of genes from two parents can be passed on to the offspring.
Here is an example of a punnett square used to diagram the potential offspring produced from two snakes which are het for albino.

Het albino x Het albino (Aa X Aa)
	A	a
A	AA	Aa
a	Aa	aa

In the above diagram the pink boxes denote the two possible genes that control this trait which can be contributed by the female. The blue boxes denote the same for the male. The yellow boxes represent the offspring. Since we have four yellow boxes, each one represents a 25% statistical average of all the hatchlings. In this example both parents possess an Aa genotype. The capital "A" is used to represent the dominant gene for normal coloration, while the lowercase "a" represents the recessive gene for albinism.

We see the potential combinations that can be produced by these parents are "AA", "Aa", and "aa". AA is homozygous for normal coloration, meaning this animal cannot directly produce an albino. the Aa are het albino offspring, and the aa is an albino.
We also see the statistical percentages that will be produced. The diagram shows one AA, so 25% of the offspring will not get the albino gene. There is one aa so 25% of the offspring will be visually albino. There are two Aa boxes, so 50% of the offspring will be heterozygous for albino.
Now let's change the parents a little. This time we will breed a visual albino male (aa) with a het albino female (Aa). Here is the resulting diagram from this breeding.

Albino x Het albino (aa X Aa)
	A	a
a	Aa	aa
a	Aa	aa

Now we get much different results. First we see since the male had no normal gene to offer, he only passed on the albino gene so all the offspring automatically got one copy of that gene. This left us with only two possible combinations either Aa, het albinos, or aa, visual albinos.
We still have four boxes, so each one represents 25% of the offspring. Two of the boxes contain Aa and two contain aa, so that means that 50% of the offspring will be visual albino and 50% will be het albino.
Remember though, the Punnett square only provides the statistical possibilities. You have to have a large sample group for the statistics to play out properly. This means that when you're only producing a single clutch you could produce four albinos or four hets just as easily. In the second example, 50% of the offspring are shown to be albino. What this means basically is that each individual egg has a 50/50 chance of being an albino. If that was a four egg clutch and the first two hatched out with normal coloration it does not automatically mean that the other two will be albinos.

Double Recessive Traits

Ok then, that's pretty simple, but what if you have two recessive traits involved in a single breeding? This can be done with the Punnett square as well. We'll make one using two normal colored snakes which are heterozygous for both albino and clown. These snakes would be called "double hets" and their genes would be represented by AaCc for the sake of this example. the Aa would be het for albino and the Cc would be het for clown, so CC would result in a normal pattern while cc would be a visual clown.
Here is the diagram:

Double het x Double het (AaCc X AaCc)
	AC	Ac	aC	ac
AC	AACC	AACc	AaCC	AaCc
Ac	AACc	AAcc	AaCc	Aacc
aC	AaCC	AaCc	aaCC	aaCc
ac	AaCc	Aacc	aaCc	aacc

Ok, in this example each parent must contribute one gene concerning the albino trait and one gene concerning the clown trait. The resulting diagram shows 16 possible combinations which are 9 different genotypes.
Those genotypes are:

AACC (normal color and pattern, carrying no recessive genes for either trait)
AaCC (normal color and pattern, het for albino)
AACc (normal, het for clown)
AaCc (normal, double het for both traits)
aaCC (albino, not het for clown)
aaCc (albino het for clown)
Aacc (clown, het for albino)
AAcc (clown, not het for albino)
aacc (homozygous for both traits, an albino clown)

The diagram also tells us that out of every 16 eggs produced, statistically the visual mutations will be 3 albinos, 3 clowns, and one albino clown which of course would be the main goal of this particular breeding.
That pretty much describes the basics of how a recessive gene is inherited. However, it still leaves one very big subject that is always a part of breeding for recessive traits, the possible het. We'll look at that next.

Possible Hets

I think if any one topic about genetics in snake breeding causes the most confusion it's the subject of possible hets. You see ads for "50% possible het pied" or "66% possible het albino". So what do these percentages mean and where do they come from?
Possible het means that a snake has the possibility of being het for a given trait, but there's no guarantee it is. The degree of the potential is expressed in a percentage which is determined by the parents. The only way to get possible hets is in a breeding where neither parent is a visual morph, but at least one parent is known to be het.
Let's look back at the first Punnett square where we bred the two het albinos together.

Het albino x Het albino (Aa X Aa)
	A	a
A	AA	Aa
a	Aa	aa

Alright, in this example we produce one albino hatchling, two heterozygous hatchlings, and one normal hatchling. The problem is you can't tell which ones are het and which one is normal. You did produce one albino, but the other three look normal, those three are "possible" hets, since you have no idea which ones actually are until they are raised and bred themselves.
Here is where the percentages come from. In this example, we will statistically produce 25% albinos. That leaves 75% of the offspring which might be het albinos. Of this 75% 2 out of every 3 should be het. Two out of three is 66%, when you cut off the decimal anyway, so those three normal looking hatchlings are 66% het albinos.

The 50% hets come from breeding a het to a normal, or wild type mate. I'll let you draw out the square yourself, but the resulting offspring comes out to be 50% normal, not carrying the gene, and 50% that are het. Since once again you have no way to tell which is which, the entire clutch are considered 50% het for the trait.
Now if you purchase a 50% het albino, and it goes on to produce an albino then it is no longer a 50% het. Once it reproduces the trait, it is a proven het and there's no more percentage involved. That being said, if you buy a 50% het, raise it and breed it to a known het, or a visual, and no visuals are produced that doesn't necessarily mean that it isn't het after all. It may very well be normal, but it might also have just been bad odds. You need at least 2 or 3 clutches with no visuals before you can really consider it to definitely be a normal.
Occasionally you might see 33% hets or even 25% hets. In my opinion no snake should ever be sold with this label for a price any higher than a normal hatchling. A 33% het would be the normal colored offspring of an unproven 66% het. With the 66 or 50% hets, at least one parent is known to be carrying the gene. The problem is once you get below those percentages you don't even know if the gene is there at all in the parents. While mathmatically you can demonstrate the 33% possibility, in my opinion it borders on being unethical to charge more for a snake labeled as such, and you should never buy one based on anything less that a 50% chance of being het if your desire is to produce that morph.
That being said, it should still be mentioned that a snake has the potential to carry the gene, even if it is an extremely slim chance, just so that potential genetics are known. This is particularly important if the buyer is specifically not wanting to introduce a given gene into a project, as in the case of attempting to prove out an unknown trait. `

Co-dominant Traits

Another type of mutation we see in ball pythons as well as a few other pythons and boas is a co-dominant mutation. Some examples of co-dominant traits in ball pythons are pastel and Mojave. The tiger phase of reticulated pythons is another well known example.
These traits create another bit of confusion for those who are just learning about them but in reality they behave exactly like a recessive gene with one difference, the hets are visually different from a normal snake not carrying the gene.
When two copies of the gene are paired in a homozygous animal, you get a third phase we call a super. So a simple way to look at it is a pastel is just a het super pastel. The result is co-dominant traits show up in the first generation. Let's make a Punnett square to demonstrate.
In this square we will use NN to denote a normal wild type female and Np to denote a pastel male.

Pastel x Normal (Np X NN)
	N	N
N	NN	NN
p	Np	Np

We see that the results of this breeding produce half normal colored hatchlings (NN) and half pastel hatchlings (Np), so the pastel trait shows up in the first generation. This means that there cannot be a "het pastel". I have on occasion seen animals sold as such by people trying to take advantage of those who are less educated on the subject, but you rarely see such attempts anymore.
Now we know that it's a simple process to produce a pastel, but what about the super pastel, which would be denoted as "pp" in a Punnett square. For that you need two pastel parents.
Here's how the square would work for that breeding.

Pastel x Pastel (Np X Np)
	N	p
N	NN	Np
p	Np	pp

You'll notice that the outcome of this breeding is identical to the outcome of the breeding above of the Het albino x Het albino. We wind up with these statistical possibilities:

25% normal (NN)
50% pastel (Np)
and 25% super pastel (pp)

Now We have our super pastel, which is the dominant form of the pastel gene. A super pastel will pass the pastel gene on to all of it's offspring. This is what makes the super pastel so valuable in a breeding group, it can only produce pastels, so you can quickly insert the pastel gene into any other project.

Some co-dominant genes, while inherited the same, behave a little differently in the dominant form. The super pastel is really a magnified version of a pastel. The effect to the coloration of the snake is the same just to a much greater degree. In some co-dominant traits however, the super form is radically different from the het form. Mojave is a good example of this. The Mojave gene is inherited the same way a pastel gene is, but the super Mojave is a patternless white snake with blue eyes, called a blue eyed leucistic.
With the introduction of co-dominant traits though, the fun is just beginning. Let's look at what happens when you combine two of these traits.

Combining Co-dominant Traits

Breeding two snakes with different co-dominant traits together gets even more interesting. Just as seen with the codom x normal breedings where the trait is expressed in the first generation, a codom x codom breeding can result in both traits showing up in a single animal in the first generation. For this example we'll use the Bumblebee ball python, which is a snake that has both the pastel and spider mutations.
Remember, a codom trait is just a visual het, it's still inherited like a recessive trait. Since this cross involves two different co-dominant traits, we will use the same Punnett square as we did for the double recessives above.
For this Punnett square we'll use NpZZ to denote a Pastel female, and NNZs to denote a Spider male. The lowercase "p" is the gene for the color mutation Pastel, and the lowercase "s" is the gene for the pattern mutation Spider. Since the presence of the gene even in the het form results in it being seen, that means the Pastel female would have to be "ZZ", or normal, at the location on the chromosome which controls the Spider pattern mutation. The same will be true for the Spider at the location which controls the Pastel color mutation.
Here's what it will look like:

Spider x Pastel (NpZZ X NNZs)
	NZ	NZ	pZ	pZ
NZ	NNZZ	NNZZ	NpZZ	NpZZ
Ns	NNZs	NNZs	NpZs	NpZs
NZ	NNZZ	NNZZ	NpZZ	NpZZ
Ns	NNZs	NNZs	NpZs	NpZs

The results of this square show us that statistically we can expect equal numbers of four different genotypes from this breeding. They are:

25% normal (NNZZ)
25% Pastel (NpZZ)
25% Spider (NNZs)
25% Bumblebee (NpZs)

Essentially, the Bumblebee is itself a double het. It is heterozygous for both super pastel and super spider, but since both of those traits are co-dominant, they are both expressed in their heterozygous state in the form of a Bumblebee.
I would note at this point that the Spider trait is a dominate trait itself, which means the homozygous or "super" form is visually the same as the heterozygous form. The only difference is that a homozygous spider, which would be NNss for the purposes of a Punnett square, will pass on the Spider gene to all of it's offspring, which means they will all be spiders and none will have a normal pattern. That's as far as I will take the co-dominate breedings here for the sake of not creating undue confusion.

Traits such as the Bumblebee and the albino clown that we have looked at here are what we refer to as "designer mutations". A designer morph is the combination of two or more mutations in a single snake. While theoretically it is possible that such a snake could be born in the wild it is extremely unlikely that the necessary genes would come together outside of captivity. For this reason the designer mutations are a product of our captive breeding, and they are one of the things that make working with the various morphs so interesting. The more mutations that are discovered the more potential ways there are for them to be combined. We are just seeing the beginning of the development in this area with the ball pythons. In the coming years we will start seeing triple recessives and beyond. Like combining the Albino, Axanthic, and Genetic Stripe traits to create a Striped Snow. We can't even guess what effect some of the traits will have on each other, and new morphs are still turning up from time to time to add even more possibilities. The next 10 years are going to reveal some unbelievable looking designer morphs, many of which will turn out to completely surprise us.
I hope this page has helped you gain a basic understanding of how these genes are inherited and I wish you luck on developing your own new and unique combinations.