Both Brains and Beauty » exon shuffling

Increasing Genetic Variation

TJ — Tue, 02 Feb 2010 07:38:02 +0000

Altering Existing Genetic Variation

Genetic Drift

Genetic drift is a change in in genetic variation due to chance changes in allele frequencies. For example, genetic drift may occur as a matter of luck; one phenotype may simply never meet a member of the opposite sex in order to mate and produce offspring. Genetic drift is not affected by the relative fitness of individuals to their respective environments. In most cases, genetic drift occurs in small populations to the smaller gene pool compared to large populations. After many generations, genetic drift may cause an allele to be lost or fixed- the allele will reach either 0% frequency or 100% frequency. Genetic drift may also be observed in large populations, but its effect (loss or fixation of an allele) happens much more slowly than it would in a small population.

Two examples of genetic drift are the founder effect and the bottleneck effect. The founder effect occurs when a subset of a population breaks off from the larger population and establishes its own colony. Because the subset is not likely a representative sample of the larger population, genetic drift will cause the smaller colony to have a much different gene pool than that observed in the larger colony. The bottleneck effect occurs when a random event decreases the size of the population dramatically. This can be caused by such events as natural disasters, such as hurricanes or earthquakes, or through the destruction of habitat by humans or other forces. Because the decrease in the gene pool is random, the allele frequencies in the surviving population may be different from that of the original population. Sometimes, alleles can be completely eliminated by these chance events.

Gene Flow / Migration

These bears lived in different populations with different allele frequencies. By meeting each other, mating, and producing offspring, they will have caused gene flow between their populations.

Gene flow refers to the movement of genes between two populations that may have different gene frequencies. For example, a deer population that lives on the east side of a river may have different allele frequencies than the deer population on the west side of the river. If one year there is a drought and some deer are able to move to the other side of the river, mate, and produce offspring, the allele frequencies of each population may change as a result of the new gene pool. Gene flow is also sometimes called migration because it is often caused by migration of one population into the territory of another population. Thus, the genes in each population also “migrate” to the other population.

Gene flow has two important consequences. First, allele frequencies in each population experiencing migration is reduced. Scientists can evaluate the relative similarities and differences in allele frequencies in order to determine how isolated the populations are. The more similar the allele frequencies between two populations are, the less isolated the populations are in turn. Second, gene flow can introduce new alleles into a population. Since mutations are so rare, and beneficial mutations even rarer, populations that do have a rare beneficial mutation introduced into their population are most likely to share the allele via gene flow.

Non-Random Mating

Would you rather mate and produce offspring with the man above

or with this man? If you expressed a preference for either, you are practicing nonrandom mating based on phenotypic characteristics.

Non-random mating occurs when individuals choose mates based on phenotypic characteristics or genetic lineage. In non-random mating situations, the allele frequencies do not change, but the proportions of heterozygotes to homozygotes may change. Inbreeding is one example of non-random mating that increases the frequency of homozygotes in a population. Conservation biologists keep track of non-random mating in a population in order to make sure increased homozygosity does not lead to inbreeding depression. If evidence of inbreeding depression is seen, biologists may introduce animals from another population to increase the gene pool.

Natural Selection

Natural selection is a phenomenon in which the environment selects for individuals with beneficial traits and against individuals with unfavorable traits. Because natural selection is discussed in greater depth in other articles, it will only be mentioned as a factor here.

Sources of New Genetic Variation

Random Mutations

The different tail types for manx cats were brought about by random mutations.

Random mutations are changes in existing genes that can introduce new alleles into a population. However, mutations are very rare, and beneficial mutations are even rarer. In most cases, mutations are detrimental to an individual and those that do not result in death, disfigurement, or other forms of severe disadvantage are, at best, neutral. When a beneficial mutation does arise, other mechanisms such as genetic drift or natural selection must act upon them in order for the allele to rise in frequency in a population.

Gene Duplication

Abnormal events during crossover (meiosis) may increase the number of copies of a gene. Through several generations, the new gene family may have new presence in a gene pool and may have different gene products.

Exon Shuffling

Sometimes, instead of full gene duplications during crossover, exons may be inserted into another gene. The new gene may have new functions and will be acted upon by mechanisms such as genetic drift or natural selection before increasing in frequency in a population.

Horizontal Gene Transfer

Typically, horizontal gene transfer is seen in bacteria. Through events such as endocytosis, genes from one species may be introduced into the genes of another species.

Population Genetics

TJ — Tue, 02 Feb 2010 04:36:52 +0000

Population geneticists primarily study allele and genotype frequencies. They use quantitative methods to analyze the frequency of alleles. For example, a population geneticist may study the frequency of certain patterns on the fur of wild cats, then will revisit the same population several generations later to find how the frequency of patterns has changed from the initial measurement. This type of study would give scientists a good idea of what genetic changes are happening in a population.

Darwin’s theory of natural selection posits that only a certain percentage of offspring in any given generation will survive to reproduce. Whether an individual survives or not depends on the inheritance of alleles that will increase its ability to survive in its environment. Alleles that do not benefit an individual and increase its chances at survival will not be passed down to future generations, thus decreasing the frequency of that particular allele in a population. Population geneticists can study changes in allele frequencies from generation to generation in order to determine what mechanisms underlie the natural selection in a given population.

New genetic variations can arise through mutation, gene duplication, exon shuffling, and horizontal gene transfer. Alterations to existing genetic variation can occur by natural selection, random genetic drift, migration, and nonrandom mating.

Nonrandom mating does not change the allele frequencies in populations, unless other evolutionary forces are also present. The other ways of increasing genetic variation will affect the allele frequencies in populations because they tend to increase heterozygosity.

Inbreeding is one form of nonrandom mating. Inbreeding occurs when two genetically related individuals mate and produce offspring. Homozygotes are more likely to be found in populations that have a high degree of inbreeding, due to the decreased genetic variation between breeding pairs. Sometimes, populations that have too much inbreeding will experience what is called an inbreeding depression. An inbreeding depression occurs when homozygotes are less fit to survive in their environment, resulting in decreased reproductive success in the population. Biologists will often intervene to introduce new genetic variation into a population by introducing new individuals, and thus new genes, into the population.

To calculate allele frequencies in a population, divide the number of copies of a particular allele in a population by the the total number of all alleles for that gene in a population.

To calculate genotype frequencies in a population, divide the number of individuals with a particular genotype in a population by the total number of individuals in a population.

For example, consider the following population:

49 dark green frogs with the genotype DD
42 brown frogs with the genotype Dd
9 yellow frogs with the genotype dd

Our population of frogs is diploid, meaning that each frog inherits one allele for a gene from each parent, so each individual has two total alleles for a particular gene. Homozygotes have two copies of the same allele; heterozygotes have one copy of two different alleles. This means that when we calculate our allele frequencies, we have to account for the fact that each individual frog has TWO copies of an allele for each gene.

To calculate the frequency of the r allele, we need to add up how many total d’s we have in our population. Each frog with the Dd genotype has one d, each frog with the rr genotype has two d’s, and each frog with the DD genotype has zero d’s. Once we get the figure for the total number of d’s in a population, we need to divide that by total number of ALL the alleles. We have:

(Dd) + 2(dd) / 2(DD) + 2(Dd) + 2(dd)

Keep in mind that we are multiplying the genotypes by two because we are counting alleles, and each individual has two alleles for each gene. Plugging in our population numbers to the above formula gives us:

42 + (2) (9) / 2 (49) + 2 (42) + 2 (9) = 60 / 200 = 0.3 = 30%

The allele frequency for d is 30%. Since we have only two alleles and each frequency must add up to 100%, we know that our other frequency, D, is 70%.

We can also calculate genotype frequencies. For this exercise, we are counting the genotypes, NOT individual alleles, so we do not need to multiply by two as we did in the above example. If we want to calculate the frequency of dd, we need to find the number of dd individuals in the population, and divide by the total number of individuals in the population. So we have:

dd / DD + Dd + dd

9 / 49 + 42 + 9 = 9 / 100 = 0.09 = 9%

So we know that 9% of the individuals in our population have the dd genotype. If we calculate the frequency of one of the other genotypes, we can add them together and subtract from 100% to find the frequency of the third genotype.

Understanding how to calculate allele and genotype frequencies is vital to understanding the Hardy-Weinberg Equilibrium and being able to use the Hardy-Weinberg equation. Be sure you understand how to do these calculations before you move onto Hardy-Weinberg problems.