User:Maloryross/sandbox

= Fixed Allele = ''A fixed allele is an allele that is the only variant that exists for that gene in a population. The term allele normally refers to one variant gene out of several possible for a particular locus in the DNA. When all but one allele go extinct, the remaining allele is said to be fixed and is homozygous for all members of the population. ''

Alleles can be dominant (complete or incomplete) or recessive, and any type of allele can become fixed in a population. Alleles exhibiting complete dominance will entirely mask the phenotype of the other allele when present in a heterozygote. Alleles exhibiting incomplete dominance will produce a phenotype that is different and often a mix of the dominant and recessive phenotypes. In diploid organisms (containing two copies of every chromosome), two copies of a recessive allele need to be present in the genotype of the organism in order for the recessive phenotype to be expressed.

Alleles that are dominant or recessive can also be beneficial, deleterious, or neutral. Beneficial alleles increase the fitness (i.e. the reproductive success of an organism in a particular environment) of an organism, whereas deleterious alleles decrease the organism’s fitness. Neutral alleles are neither beneficial or deleterious and have no effect on the fitness of the organism. Depending on the benefits or disadvantages that a fixed allele provides, the mean fitness of the overall population will change.

Fixation Rates
"Main article: Fixation (population genetics)"In general, an allele has a greater chance of becoming fixed if there are multiple copies present in the gene pool compared to only one copy that has arisen through mutation. Alleles that are already present in a population often have a greater frequency than new alleles that are created through mutation, and therefore they generally have a greater probability of becoming fixed than new alleles.

Natural Selection
Natural selection is a mechanism of evolution whereby individuals that are better adapted for a particular environment are more likely to survive to reproduction and pass on their alleles to their offspring than individuals who are less suited for a particular environment. The alleles that caused this superior adaptation are therefore more likely to be passed on to the next generation and increase in frequency in the gene pool, whereas the less advantageous alleles are more likely to decrease in frequency.

Beneficial dominant alleles acted upon by natural selection often rapidly increase in frequency, but once the frequency is high they take a long time to reach fixation. Natural selection acts on phenotypes, and heterozygous and homozygous dominant individuals have the same phenotype (in complete dominance). Therefore, heterozygotes and homozygotes are equally selected for, and recessive alleles of the same gene can persist in the population through heterozygous individuals.

Beneficial recessive alleles acted upon by natural selection often take more time than dominant alleles to start increasing in frequency since they can "hide" in heterozygotes and not be phenotypically expressed. However, once they reach a certain frequency in the gene pool they tend to rapidly reach fixation.

Genetic Drift
Genetic drift is the mechanism by which allele frequencies change over time due to random sampling. Since a parent will only pass on half of its genes to its offspring, there is some element of chance regarding which alleles will be passed to the offspring. This chance causes gene frequencies in a population to naturally vary across generations, and in most populations this variation is not very noticeable. However, in small populations with small gene pools genetic drift can be very effective. The effectiveness of genetic drift decreases exponentially as the population size increases. If the gene pool is small enough, genetic drift can cause deleterious alleles to increase in frequency and become fixed. The fixation of deleterious alleles can be detrimental enough to cause the extinction of populations and even entire species.

Population Bottleneck
The term population bottleneck refers to the phenomenon where a random event causes the size of a population to drastically decrease in a relatively short period of time. It causes random changes in allele frequencies, and often decreases the genetic variation in the gene pool. After a population bottleneck event, genetic drift often acts strongly in the population, and can cause the fixation of some alleles and extinction of others. The alleles that become fixed through genetic drift are often those with the highest frequency after the bottleneck event.

The founder effect is a type of population bottleneck where part of a population is randomly isolated from the rest of the population. Like other population bottlenecks, it can also cause a large decrease in population size in the new population compared to the original one. Depending on the new gene pool and genetic variation, it can also lead to the random fixation of alleles.

Genetic Hitchhiking
When natural selection acts on a beneficial allele to increase its frequency, any alleles (beneficial, neutral, or deleterious) close to it may also increase in frequency. This effect is known as genetic hitchhiking, and it reduces the genetic variation of a population. Genetic hitchhiking can also lead to the fixation of neutral and even deleterious alleles.