Genetics

By Michael Johnson

Leopard geckos (Eublepharis Macularius) are robust geckos with relatively large heads and have numerous tiny wart-like tubercles on their skin. The normal or wild color/ pattern are covered with light yellowish blotches and dark reticulated leopard-like spots over a grey-buff colored body.  Juveniles have broad dark and light bands across the body and tail and thus look surprisingly different than the adults.

Most geckos are nocturnal (night dwelling) and unlike most lizards, are capable of clicking vocalizations. Only geckos in the subfamily Eublepharinae (one of which is the Leopard gecko) have movable eyelids and are sometimes called "eyelid geckos". Leopard geckos can actually clean their eyes by licking them! Geckos have relatively good hearing when compared with other lizards. Hearing must be important otherwise they would not be able to vocalize.

Leopard geckos (Eublepharis macularius) are members of the subfamily Eublepharinae (which derives from the Latin Eu meaning good/true, and blephar meaning eyelid). The possession of a "true eyelid" distinguishes members of this subfamily, from other geckos, as other geckos do not possess eyelids. The second part of the species name, macularius, derives from the Latin macula meaning spot or blemish, which is self-explanatory (although it might not be so obvious in the future given the current popularity of selectively bred color morphs, particularly the patternless and hypo-morphs; the best of which have no black spotting at all).

Classification

Kingdom - Animalia

Phylum - Chordata

Subphylum - Vertebrata

Class - Reptilia

Order -Squamata

Suborder -Sauria

Family - Gekkonidae

Subfamily - Eublepharinae

Genus - Eublepharis

Species - Macularius 

Distribution

The Leopard Gecko is native to south-eastern Afghanistan, most of Pakistan, and north-west India, and inhabits primarily the rocky, dry grassland regions of these countries. As nocturnal creatures, they spend the day hidden under rocks or in dry burrows to escape the daytime heat, emerging at dusk to hunt insects.

Genetics Explained

For thousands of years farmers and herders have been selectively breeding their plants and animals to produce more useful hybrids.   It was somewhat of a hit or miss process since the actual mechanisms governing inheritance were unknown.  Knowledge of these genetic mechanisms finally came as a result of careful laboratory breeding experiments carried out over the last century and a half.

By the 1890's, the invention of better microscopes allowed biologists to discover the basic facts of cell division and sexual reproduction.  The focus of genetics research then shifted to understanding what really happens in the transmission of hereditary traits from parents to children.  A number of hypotheses were suggested to explain heredity, but Gregor Mendel, a little known Central European monk, was the only one who got it more or less right.  His ideas were published in 1866 but largely went unrecognized until 1900, which was long after his death.

While Mendel's research was with plants, the basic underlying principles of heredity that he discovered also apply to people and other animals because the mechanisms of heredity are essentially the same for all complex life forms. Through the selective cross-breeding of common pea plants (Pisum sativum) over many generations, Mendel discovered that certain traits show up in offspring without any blending of parent characteristics.  For instance, the pea flowers are either purple or white--intermediate colors do not appear in the offspring of cross-pollinated pea plants.  Mendel observed seven traits that are easily recognized and apparently only occur in one of two forms:

1. Flower color is purple or white

2. Flower position is Axil or terminal

3. Stem length is long or short

4. Seed shape is round or wrinkled

5. Seed color is yellow or green

6. Pod shape is inflated or constricted

This observation that these traits do not show up in offspring plants with intermediate forms was critically important because the leading theory in biology at the time was that inherited traits blend from generation to generation.  Most of the leading scientists in the 19th century accepted this "blending theory."  Charles Darwin proposed another equally wrong theory known as "pangenesis".  This held that hereditary "particles" in our bodies are affected by the things we do during our life time.  These modified particles were thought to migrate via blood to the reproductive cells and subsequently could be inherited by the next generation.  This was essentially a variation of Lamarck's incorrect idea of the "inheritance of acquired characteristics."

Mendel picked common garden pea plants for the focus of his research because they can be grown easily in large numbers and their reproduction can be manipulated.  Pea plants have both male and female reproductive organs.  As a result, they can either self-pollinate themselves or cross-pollinate with another plant.  In his experiments, Mendel was able to selectively cross-pollinate purebred plants with particular traits and observe the outcome over many generations.  This was the basis for his conclusions about the nature of genetic inheritance.

In cross-pollinating plants that either produces yellow or green peas exclusively, Mendel found that the first offspring generation always has yellow peas.  However, the following generation consistently has a 3:1 ratio of yellow to green.

This 3:1 ratio occurs in later generations as well.   Mendel realized that this was the key to understanding the basic mechanisms of inheritance.

He came to three important conclusions from these experimental results:

1. that the inheritance of each trait is determined by "units" or "factors" that are passed on to descendents unchanged (these units are now called genes)

2. that an individual inherits one such unit from each parent for each trait

3. that a trait may not show up in an individual but can still be passed on to the next generation.

It is important to realize that, in this experiment, the starting parent plants were homozygous for pea color.  That is to say, they each had two identical forms (or alleles) of the gene for this trait--2 yellows or 2 greens.  The plants in the generation were all heterozygous.   In other words, they each had inherited two different alleles--one from each parent plant.  It becomes clearer when we look at the actual genetic makeup, or genotype, of the pea plants instead.

Note that each generation plants inherited a Y allele from one parent and a G allele from the other.  When the plants breed, each has an equal chance of passing on either Y or G alleles to each offspring.

With all of the seven pea plant traits that Mendel examined, one form appeared dominant over the other.  Which is to say, it masked the presence of the other allele.  For example, when the genotype for pea color is YG (heterozygous), the phenotype is yellow.  However, the dominant yellow allele does not alter the recessive green one in any way.   Both alleles can be passed on to thenext generation unchanged.

Mendel's observations from these experiments can be summarized in two principles:

1. The principle of segregation

2. The principle of independent assortment

Mendel's observations from these experiments can be summarized in two principles:

1. the principle of segregation

2. the principle of independent assortment

According to the principle of segregation, for any particular trait, the pair of alleles of each parent separate and only one allele passes from each parent on to an offspring.  Which allele in a parent'spair of alleles is inherited is a matter of chance.  We now know that this segregation of alleles occurs during the process of sex cell formation (i.e. meiosis).

According to the principle of independent assortment, different pairs of alleles are passed to offspring independently of each other.  The result is that new combinations of genes present in neither parent are possible.  For example, a pea plant's inheritance of the ability to produce purple flowers instead of white ones does not make it more likely that it will also inherit the ability to produce yellow peas in contrast to green ones.  Likewise, the principle of independent assortment explains why the human inheritance of a particular eye color does not increase or decrease the likelihood of having 6 fingers on each hand.  Today, we know this is due to the fact that the genes for independently assorted traits are located on different chromosomes.  These two principles of inheritance, along with the understanding of unit inheritance and dominance, were the beginnings of our modern science of genetics.

How do Genes Combine?

The standard way of working out what the possible offspring of two parents will be is the Punnett Square.  Consider a single gene. Since each individual has one pair of each chromosome, they have two copies of each gene (one on each chromosome). Some genes also come in multiple copies, some even have thousands of copies, but that is another story - each of those repeated genes is still paired with a copy on the other chromosome of the pair. A Punnett square is a simple graphical way of figuring out how the genes from each parent might combine to produce an offspring. The Punnett square duplicates the observation that the reproductive cells (eggs and sperm) get only half the normal number of chromosomes. When an egg is produced, it will receive one pair of each of chromosome, not both. This is also true with sperm.

Since eggs and sperm each carry only one of each chromosome instead of a pair of each, they carry only one copy of each gene instead of two. Thus a female who carries two different flavors (alleles) for a particular gene, will produce some eggs with reproductive cells that carry one flavor, and some eggs that carry the other. Similarly, a male with two different alleles for the same gene will produce some sperm carrying one allele and some sperm carrying the other. This is the basis of the Punnett square - line up the possible reproductive cells for one parent along the top of the square, and the possible reproductive cells for the other along the left side of the square, then combine them in the middle to show all possible combinations of alleles of the genes from the two parents that may occur in their offspring. This simple diagram is a Punnett Square.

For example, contemplate a gene with dominant B and recessive b flavors (alleles). What happens if two parents each carrying one of each allele (Bb) (heterozygous) mate? Put the possible eggs for the mother along the top of the square, and the possible sperm for the father along the side. The square has four boxes in it, fill each box with the allele above it from the mother, and the allele beside it from the father. This is a possible combination of alleles of that gene in a child. The four boxes in the Punnett square represent the four possible combinations of the alleles.

This cross yields three possible genotypes in the offspring - BB, Bb, and bb. In addition to showing the possible genotypes of the offspring; the Punnett square also indicates how likely a particular child of this mating is to have a given genotype. In this case, there is a one in four (25%) chance that the child would be BB, two in four (50%) that it would be Bb and one in four (25%) that it would be bb. This is like throwing a four sided die, with BB written on one side, Bb written on two, and bb on the other. This die gets thrown once for each child. If the cross produces several children, each gets one toss of the die (except identical twins). Thus on average, about 25% of the children of this cross should have a genotype of bb. However, remember that this is a separate combination of egg and sperm, a separate toss of the dice for each individual. It is possible to throw the dice four times and get bb each time; likewise it is possible to get four out of four bb children from this cross. It is likely that one out of four will have a genotype of bb as well.

We have one gene with two alleles: B-dominant, b-recessive. Since an individual has a pair of each chromosome, they have two copies of the gene. An individual can have a genotype of BB (Homozygous dominant), Bb (Heterozygous), or bb (Homozygous Recessive). Any of these individuals could mate with any other, thus there are several possible crosses as shown in the Punnett Square.

A simple case is a single gene is called a monohybrid cross simply meaning that there is one gene and two possible alleles for that gene. It is quite rare for an aspect of an organism's appearance to be controlled by genes as simple as this. Consider that each gene is a length of DNA with many base pairs - many possible sites where a mutation could produce a change. All genes have the potential to come in lots of mutant, "flavors" - lots of alleles. Adding a third or fourth allele for a gene doesn't make the Punnett square any more complex, as each parent can only have two copies (two alleles) of each gene. It is simply a matter of figuring out the alleles in each parent, lining them up on the top and side of the square and filling in the boxes with one allele from each parent.

Another step up in complexity is to consider two genes:  A dihybrid cross. (In a dihybrid cross we consider two independent genes. Think of these as being on two different chromosomes (most genes seem to assort independently but there aren't that many chromosomes that tells us about recombination, but that's another story...) If we have two genes that are independent, either copy of each could end up in a reproductive cell with either copy of the other. Thus our Punnett Square needs to have four rows along the top, and four rows along the side - to consider all four possible combinations of the two copies of the two genes.

Commonly Used Terms to Remember

Dominant - a genetic feature that hides the recessive trait. A dominant trait causes a phenotype that is seen in a heterozygous genotype. Many traits are determined by pairs of complementary genes, each inherited from a single parent. Often when these are paired and compared, one gene (the dominant) will be found to effectively shut out the instructions from the other, recessive gene. For example, if a person has one gene for blue eyes and one for brown, that person will always have brown eyes because they are the dominant trait.

Co-dominant - The result of 2 types of alleles that are equally dominant. When an organism is heterozygous for such traits, the resulting phenotype or expression of these two traits is a blending, because both traits are expressed equally.

Recessive - refers to an allele that causes a phenotype (visible or detectable characteristic) that is only seen in a homozygous genotype (an organism that has two copies of the same allele) and never in a heterozygous genotype. Every person has two copies of every gene on autosomal chromosomes, one from mother and one from father. If a genetic trait is recessive, a person needs to inherit two copies of the gene for the trait to be expressed. Thus, both parents have to be carriers of a recessive trait in order for a child to express that trait. If both parents are carriers, there is a 25% chance with each child to show the recessive trait.

Homozygous - carries two identical copies of the gene affecting a given trait on the two corresponding homologous chromosomes) same case (AA or aa).  Pure-bred or true breeding organisms are homozygous.

Heterozygous - has different alleles occupying the gene's position in each of the homologous chromosomes. In diploid organisms, the two different alleles were inherited from the organism's two parents. Having two paired alleles of a different case (Aa). Commonly referred to as, “Het”.

Line Bred Traits - refers to traits that were produced through selective breeding. Breeders selected the best examples of these traits in their collections and bred them together. Traits such as Tangerine, Hypo and Carrot Tail are all line-bred traits. These traits are not controlled by a pair of genes, but a selection of increase / decrease alleles. For example if you had a great specimen of a Leopard Gecko who had a 90% carrot tail and you bred it to a normal morph of Leopard Gecko, you would get a diverse range of hatchlings showing varying amounts of Carrot Tail; while some may show no Carrot color at all.

Wild Type - The typical form of an organism, strain, gene, or characteristic as it occurs in nature, as distinguished from mutant forms that may result from selective breeding.

Phenotype - an individual organism is either it’s total physical appearance and constitution or a specific manifestation of a trait, such as size, eye color, or behavior that varies between individuals. Phenotype is determined to a large extent by genotype, or by the identity of the alleles that an individual carries at one or more positions on the chromosomes. Many phenotypes are determined by multiple genes and influenced by environmental factors. Thus, the identity of one or a few known alleles does not always enable prediction of the phenotype.

Nevertheless, because phenotypes are much easier to observe than genotypes (it doesn't take chemistry or sequencing to determine a person's eye color), classical genetics uses phenotypes to deduce the functions of genes. Breeding experiments can then check these inferences. In this way, early geneticists were able to trace inheritance patterns without any knowledge of molecular biology.

Phenotypic Variation - (due to underlying heritable genetic variation) is a fundamental prerequisite for evolution by natural selection. The fitness of an organism is a high-level phenotype determined by the contributions of thousands of more specific phenotypes. Without phenotypic variation, individual organisms would all have the same fitness, and changes in phenotypic frequency would proceed without any selection (randomly).

Genotype - the composition of part of an individual's genome which contributes to determining a specific trait. It is a generally accepted theory that inherited genotype, transmitted epigenetic factors, and non-hereditary environmental variation contribute to the phenotype of an individual. Non-hereditary DNA mutations are not classically understood as representing the individuals' genotype. Therefore, scientists and doctors sometimes talk for example about the (geno) type of a particular cancer, thus separating the disease from the diseased. While codons for different amino acids may change in a random mutation (changing the sequence coding a gene), this doesn't necessarily alter the phenotype.