Basic Genetics

One of the most fascinating aspects of herpetoculture today is the production and combination of many new genetic mutations. In the Leopard Gecko (Eublepharis macularus)) alone, there are a few hundred possible colour and pattern combinations - many of which are still waiting to be hatched for the first time. New morphs crop up relatively frequently, and some are poorly understood. If your goal as a herpetologist is to create a new pattern or morph in your desired species, then having a basic understanding of genetics is incredibly important. It will also help explain the high cost of some of the newer morphs available. Bringing a new morph to the market can take several years and require a lot of patience and forethought.

A simple way to think about genetics is to consider that any morphological trait, whether positive or negative, is controlled by one (or a number of) pair(s) of alleles. Each parent provides one allele upon fertilization.

Firstly, it’s important to get a few basic definitions out of the way:

Dominant – To put it simply, they are what you will see any time they are present, whether as a pair or in combination with a recessive allele. Typically, all 'normal' traits are dominant, while 'abnormal' traits are recessive.
Recessive - Recessive alleles will only be visible if paired with another recessive allele. Typically, any animal expressing an abnormal trait is in possession of a matched pair of recessive alleles, while any animal appearing normal may or may not be carrying one recessive allele. (There are a few exceptions to this - more on them later.)
Homozygous - Having two paired alleles of the same case (AA or aa). Whether the alleles are dominant traits or recessive traits, they are both the same and the trait will be expressed visually.
Heterozygous - Having two paired alleles of different case (Aa). Typically, these animals appear normal, being indistinguishable from normal homozygous animals (AA).
Punnett Square - A simple table used by geneticists to determine the outcome of various combinations of alleles. The letters representing each allele passed on by the parents are placed in the top row and left column. The resulting combinations are placed into the appropriate squares and the results can then be tallied up. Usually, the males' genetic traits are listed in the top row, while the females' are listed in the left column.
Genotype – The combination of alleles present at any given locus that code for a given trait.
Phenotype – The physical character associated with the genotype. For example, wild type, normal or albino.
Locus - Gene pairs in all life forms are always connected in a particular order. Each place in this order is referred to as a locus (as in location). It is very important to understand that while each locus accepts only two alleles, there may be several types of alleles, which may fit at that locus. Thus many combinations of alleles could possibly be present at any one locus.
Allele - The proper term for what most breeders refer to as a 'gene'. The most common allele at any given locus is, of course, the 'normal' or 'wild-type'. An abnormal allele at any locus is usually referred to as a mutation. Remember that in most cases, both alleles at that locus must be mutated for the appearance of the animal to be altered. The exception would be dominant or incomplete dominant alleles.

When recording these traits on paper, each mutation is abbreviated as the combination of a few letters. (Aa or aa or AA). One letter is provided by each parent. Capital letters represent dominant traits, while lower case represents recessive traits. Different letters are used to represent different traits.

Figure 1.
		Male
		a	a
Female	A	Aa	Aa
	A	Aa	Aa

This Punnett square (Figure 1) actually illustrates the basic first breeding used to propagate a new and desirable trait.

In this case, a male Albino Leopard Gecko (Amelanistic, represented as (aa) is crossed with a normal female (AA) in an effort to produce more albinos.

Each of the resulting offspring receives one allele from each parent. Thus they are all heterozygous for amelanism (Aa). The presence of the dominant allele will control the appearance, and all offspring appear normal. However, each is carrying a hidden recessive gene for amelanism.

Figure 2.
		Male
		A	a
Female	A	AA	Aa
	a	Aa	aa

When these offspring are bred together, the results are shown in the Punnett square above (Figure 2). These lead to more interesting results.

25% are AA (completely normal)
50% are Aa (heterozygous for amelanism)
25% are aa (homozygous for amelanism)

Remember that the appearance of the heterozygous offspring is controlled by the dominant allele.

Therefore 75% of the offspring appear normal. Of this normal looking group, any one individual has a 66% chance of carrying the recessive gene for amelanism. This is the source of animals sold as '66% hets'.

Often, buyers fail to understand this and believe that each specimen is 66% heterozygous. This is NOT the case - any given specimen either is or is not carrying the recessive gene, they simply have a 66% chance of possessing the hoped for gene.

But wouldn't it have been more effective to breed one of our heterozygous offspring back to the original male? The results of such a cross are shown in the Punnett square below (Figure 3).

50% are Aa (heterozygous for amelanism)
50% are aa (homozygous for amelanism)

As you can see, this cross did produce more amelanistic offspring. Also, all of the normal appearing offspring are known heterozygous - not just suspected. Remember that the appearance of the heterozygous offspring is controlled by the dominant allele. Therefore 50% of the offspring appear normal, but are carrying the recessive gene for amelanism. The remaining 50% are completely amelanistic, just like the original male

Figure 3.
		Male
		a	a
Female	A	Aa	Aa
	a	aa	aa

As we have already learned, the underlying principle of genetics is the simple understanding that any trait, positive or negative, is controlled by a set of paired alleles. Each parent at fertilisation provides one allele.

But what happens when we cross specimens possessing different genetic traits?

Here we will cross one of our male Amelanistic (A) Geckos to a female patternless Gecko (B) (Formally reffered to as Leucistic, but this is not the case).

Since each genetic trait is controlled by a different allele pair, we will now be using two letters (A & B) to represent our two pairs of alleles, with lower case for the recessive state and upper case for the dominant state:

The result is shown in the Punnett square Below (Figure 4).

100% of our offspring are 'double heterozygous' for amelanism and patternless (AaBb) and appear normal. This is because each gecko is in possession of the dominant allele to offset the other gecko recessive one for both traits.

Figure 4.
		Male
		Ab	Ab
Female	aB	AaBb	AaBb
	aB	AaBb	AaBb

In order to produce offspring which visually express both traits, we must now breed these offspring back together.

The results are shown in the Punnett Square below (Figure 5):

9/16 Normal (3 are heterozygous for amelanism, 3 for patternless)
3/16 Amelanistic (2 are heterozygous for patternless)
3/16 Anerythristic (2 are heterozygous for patternless)
1/16 Amelanistic & Patternless

As you can see, only one in sixteen offspring exhibit both genetic traits, which in this case means it is lacking in black pigmentation (melanin) and the uniform banded pattern commonly associated with this species. It is commonly referred to as a ‘patternless albino'. Animals such as this one (exhibiting two recessive traits) are called double recessive.

With such limited numbers of these double recessives being produced, it is easy to see why these animals command higher prices.

Figure 5
		Male
		AB	Ab	aB	ab
	AB	AABB	AABb	AaBB	AaBb
Female	Ab	AABb	AAbb	AaBb	AaBb
	aB	AaBB	AaBb	aaBB	aaBb
	ab	AaBb	Aabb	aaBb	aabb

As interest in new, more desirable phenotypes increases, breeders seek even more uncommon traits. In search of these, a further level of genetics understanding is required, so more definitions are required:

Incomplete dominant – Ok, this is a special type of dominance in which the allele in question creates different phenotypes when present with either a dominant or a recessive allele. This can be represented as an intermediate state. In a number of cases, an incomplete dominant trait may not express itself visually when paired with a dominant allele. This is believed to be the case with one form of hypomelanism in the Leopard Gecko. The important thing to remember is that in cases of incomplete dominance, the phenotype is dependent on the interaction with the other allele.

This can be a difficult concept to understand, but this is believed to be an inbreeding avoidance mechanism, where novel genotypes and phenotypes can arise from closely related individuals. This becomes particularly important when considering traits such as colouration (camouflage), or even traits such as head size (prey specilisation).

In the Punnett Square, incomplete dominant traits are recorded using the same letter as the 'normal' dominant trait, but with the addition of an apostrophe. This is known as a 'prime'. In our examples here, a incomplete dominant form of hypomelanism is notated as H', pronounced 'H prime'.

Figure 6.
		Male
		H'	H
Female	H	H'H	HH
	H	H'H	HH

A well-known example of co-dominance is the trait of hypomelanism in the Colombian Boa Constrictor. In the Punnett Square above (Figure 6), we cross a male 'Hypo' to a normal female.

Statistically, this cross will produce 50% hypomelanistic specimens. As always, each of the resulting offspring received one allele from each parent. Thus half are heterozygous for hypomelanism (Hypomelanistic, H'H), and half of the offspring are normal (HH).

When two hypomelanistic specimens are bred together, the results below (Figure 7) are the same genetically as any other pairing of two heterozygous specimens.

25% are HH (completely normal)
50% are H'H (heterozygous for hypomelanism)
25% are H'H' (homozygous for hypomelanism)

Figure 7.
		Male
		H'	H
Female	H'	H'H'	H'H
	H	H'H	HH

Remember that the appearance of these animals will be quite different, as the incomplete dominant trait expresses itself visually even in the heterozygous state. The normal (HH) animals will appear completely normal, while the heterozygous specimens (H'H) will appear hypomelanistic. In the case of the Colombian Boa Constrictor, homozygous for hypomelanism animals (H'H') will exhibit a much greater influence on appearance and are trade-named 'Super-Hypo'.

Another classic example is the 'Tiger' and 'Super-Tiger' morphs of Reticulated Python (Python reticulatus) developed by Al & Cindy Baldogo.

When the original Tiger Retic was bred to a normal snake, half the offspring were Tigers! Knowing full-well that the odds of the normal snake being heterozygous for 'Tiger' were astronomical, the Baldogos believed (correctly) that this trait was a incomplete dominant recessive. This was later proven when two of them were bred together. This breeding yielded yet another surprise when one-fourth of the offspring exhibited a new appearance - that of the 'Super-Tiger'. These animals are now known to be homozygous for the 'Tiger' trait, while 'Tigers' are heterozygous for the same trait.

In other species involving co-dominance, there may be no difference in appearance between heterozygous and homozygous individuals, although much work is needed in this area. This has severe consequences for the breeder, as it is possible that his or her cherished animal may in fact be heterozygous (H'H), rather than homozygous (H'H'). When this is the case, the only way to distinguish the two is through several breedings and tabulating the outcomes. Many of these genotypes have been inadequately explored, and there is still much room for new discoveries.

This is most likely the case with the two related traits in Leopard Geckos known as Hypomelanism and Hyperxanthism. These two traits have been demonstrated by breeding experiments to be incomplete dominant recessive traits when expressed against 'normal' genotypes.

Breeding two hypomelanistic or two hyperxanthic leopard geckos together does not always result in similar offspring. However, the resultant ratios of offspring are fairly consistent with expected results if these traits were incomplete dominant against normal traits. Confusingly, they also appear to be to incomplete dominant with each other. In other words all three traits have an equal chance of expressing themselves visually when combined. Additionally, it appears that Hypomelanism and Hyperxanthism can be expressed visually in the same animal, at the same time, yielding astonishing results. Much more study is needed on this subject - that is part of the appeal of working with these types of animals.

Another term applicable here (and simpler to understand) is termed Dominant. A dominant gene will alter the appearance of an individual when only one copy of the gene is present. it will equally alter the appearance if two copies are present. There is no 'Super' form of appearance. Needless to say, this makes determining whether such a specimen has one copy (heterozygous state) or two copies (homozygous state) a real challenge. Breeding trials to normal specimens are the only way to be certain.

What does all this mean? Simply put, it means that you better know your breeder when buying these animals! Moreover, you better make sure the breeder understands all of this - many don't.

While the previous pages have covered what most reptile keepers consider to be everything there is to know about genetics, in reality we have only covered the various modes of inheritance. Such a simplified understanding of genetics can lead to some serious errors. As our understanding of reptile mutations continues to evolve, we begin to see various outcomes of breeding trials which yield unexpected results. In reality, these results are perfectly understandable with an increased knowledge of the complexity of genetics.

Think of it like this: All humans look pretty much alike because each locus stays in order, yet each human has recognizable variations as a result of the different alleles present at each locus. For example, there are several alleles available for the eye colour locus. Thus we have friends with blue eyes, green eyes, brown eyes and so on - but they all have eyes because regardless of changes in the allele, the locus is still there. If we were to reduce the number of possible alleles at every locus to only one, all of us would be identical! (this is exactly what happens when a clone is created, every allele at every locus is identical to the original - not very realistic, but makes for some great sci-fi movies)

How does all this change anything? Well, let me give an example:

Recently a number of Cornsnake breeders attempted to sort out the confusion of what appeared to be several types of hypomelanism and a strange looking new albino form derived from one of the types of hypomelanism. What was discovered could not be explained by conventional knowledge of genetics as understood by most reptile breeders.

It seems that one type of hypomelanism (trade-named Ultra Hypo) when bred to another of the same would produce more Ultra Hypo specimens. No surprise there. The surprise comes in when one of these snakes is bred to an amelanistic (Albino) specimen. Conventional wisdom would lead the breeder to expect all of the offspring from this crossing to appear normal, and each to be heterozygous for both Ultra Hypo and Albino. Instead, all of the babies appeared to be a strange new type of Albino (trade-named Ultramel). And when an Ultramel was bred back to either an Albino or or an Ultra, half the the resulting offspring looked like each parent! Using conventional 'reptile breeder knowledge' of genetics, this should be impossible!

Ok, so clearly something interesting was going on and it seems that the new form of hypomelanism (Ultra) shared the same locus as amelanism. They were different alleles residing at the same locus. Thus Ultra specimens have two copies of the Ultra allele at that locus, while the albino specimens have two copies of the amelanism allele at that same locus. Ultramel specimens have one copy of each type at that same locus. Many readers would ask "If these Ultramels have only one copy of each trait, they must be heterozygous for these traits, and why don't they appear as wild-type Cornsnakes?" The answer is simple: Since there is one copy of each allele present at the locus, there can be no copy of the wild-type allele at that locus to control the appearance!

While it's great to have figured this out, it's also forced another problem upon us. Reptile breeders have grown accustomed to using a very simplified method of representing the genes involved in these mutations with a single letter. This system of notation for genes (as used in our example Punnett Squares) does not take into account the concept of different alleles being able to reside at the same loci. It assumes that each loci can have one of two alleles, the normal or wild-type and the mutation involved with that loci. But as we've just seen, more than one type of mutated allele can reside at the same loci.

So a more proper form of notation is being offered to the reptile community. Initially set forth in the 2005 Cornsnake Morph Guide, this is NOT something recently made up. It's the way it SHOULD have been presented to the reptile community from day one. Many mysteries could have been avoided if this system had been in place.

It works like this: Large letters represent each loci, with smaller superscripted letters representing the alleles for that loci. Normal or wild-type alleles are represented with a +. An example for an amelanistic specimen: aaaa. using the previously accepted method of notation, it would simply be: aa.

A specimen heterozygous for amelanism would be represented as: A+aa.

While this may appear only to be twice the letters and nothing more, the real value can be seen when used to describe the various Ultra, Ultramel, and Albinos from the example above: aaaa= Albino; auau= Ultra; aaau=Ultramel. Notice that we can now see that all involve the same loci (a) but the different alleles can now be seen at that loci (a or u). Better still, we can now see the various allele combinations present and easily predict what offspring we will produce from any given pairing! This would be impossible using the older system of notation.

Another concept which can 'mysteriously' affect the outcomes of breeding trials is that of linkage. Two types of linkage exist:

Trait Linkage - The physically connected pairs of genes don't exist on one long continuous strand. Rather, they exists in large groups of strands called Chromosomes. Oddly, strands have a tendency to break apart and sort in sections rather than in individual pairs of genes as most breeders assume. In other words the alleles of many adjacent loci (plural for locus) may be passed to an offspring as a set, rather than as individual genes.

I have heard this described in very simplified terms as being similar to flipping coins (bare with me, it makes things slightly easier to understand): When flipped loose, all sorts of heads and tails combinations are easily produced. But when some of them are taped together and flipped, some combinations are impossible to produce. But a persistent breeder knows that eventually the tape will come loose and he'll get the desired combination.

This explains why certain double homozygous forms of reptiles can be incredibly difficult to produce. A well-known example is that of the famous 'Blazing Blizzard' Leopard Gecko. These are nothing more than the two traits of 'Blizzard' and 'Tremper Albino' existing in the homozygous state in one specimen. Learning of the value of these specimens, many breeders quickly bred albino and blizzard specimens together to create the needed double heterozygous specimens. These double hets were then bred together the next year, with breeders expecting the usual one in sixteen offspring to be the 'Blazing Blizzard'. Very few were produced, with many breeders producing as few as one in two thousand which turned out to be 'Blazing Blizzard'!

While all these breeders understood that something had gone wrong, few understood it was a simple case of trait linkage.
Sex Linkage - All of us are familiar with the famous 'X' and 'Y' chromosomes responsible for sex determination in humans (XX=Female & XY=Male). In snakes, it's the 'W' and 'Z' chromosomes (ZZ=Male & WZ=female) that are responsible for sex determination. Regardless of the name, these chromosomes each contain a very large number of loci containing many, many alleles.

Many of the loci which exist on the 'Z' chromosome do not exist on the 'W' chromosome. This can have unusual effects. In males, two copies of the 'Z' chromosome are present and the usual genetic rules apply to all loci contained within. However in females, those loci in the 'Z' chromosome corresponding to the missing loci from the 'W' chromosome will necessarily contain only one allele. Therefore, any allele present at these loci will have total control over the function of that locus. Thus even a recessive allele at these unpaired loci will be expressed! This state is properly termed Hemizygous.

While all of the previous information on genetics we've presented in these pages may have seemed complicated, they are as nothing compared to the next concept we'll introduce.

So far, everything we've discussed has been based on the assumption that a mutated allele at a single loci has been responsible for the changes in appearance reptile breeders covet. This is termed autosomal.

But what happens when multiple loci are responsible for altering a single change in appearance? Such results are termed polygenic, and they areunquestionably the most difficult to predict. In fact, for most polygenic traits there simply is no way to fully understand what is happening behind the scenes. Others, such as Bloodred Cornsnakes involve combinations of recessive alleles, incomplete dominant alleles, and groups of alleles best thought of as polygenic. It's like predicting the weather, there are just too many variables to ever be 100% accurate.

In truth, most appearances in animals (well, all life actually, including humans) are controlled by polygenic factors. Often these types of traits are termed 'selective traits' or are achieved through 'selective breeding'. But there's plenty of margin for error in such projects, and even the best laid plans will oft times go awry.

Sadly many coveted morphs of reptiles are no exception to these rules. Popular morphs of Leopard Gecko such as Jungle, Tangerine and Carrot-Tail are all good examples. Many breeders have bred two fine examples of these together and gotten junk, and many have bred two less than spectacular examples together and gotten some really impressive specimens. More often than not, the results are about what you would expect - a mixed bag of babies containing some nicer, some poorer and most about the same as the parents used. In general, it's wisest to simply acquire the best examples of a type that you can locate and hope for the best.

Why all the variation in offspring? Well, remember that these polygenic types are created by achieving the proper combination of several alleles at several loci. Some of these may be recessive alleles, some incomplete dominant, and some may even be dominant. Many may be trait-linked as well, and some may even be sex-linked. Most will not be discernible to the eye individually. Consider that the parents used in breeding trials are likely heterozygous for some or all of the alleles involved and you get quite the potential for variation. Trying to get all of these to turn out correctly gets progressively harder as the number of alleles involved increases.

Ok, so I guess there is one final type of genetic trait that proves somewhat of a complication for many breeders and this is Over-dominance. Over-dominance is one of the theories proposed to account for the lack of evidence of inbreeding depression in wild populations. Basically put, over-dominant characteristics represent increased Heterozygote fitness when compared to both homozygote genotypes.

Figure 8.
		Male
		A	a
Female	A	AA	Aa
	a	Aa	Aa

A question I’m often asked therefore is “why do I only get 50% of my offspring with the over-dominant characteristic, if I breed two parents with the correct phenotype?” And as you can see from the punnett square above (Figure 8), the answer is pretty clear. If it is a Heterozygote characteristic, then breeding two heterozygotes will lead to 50% homozygote production. Again this can be complicated by being polygenic

Good Luck!