Population Genetics Analysis Essay Example

through a process termed retroposition (Batzer 1994).

Alu elements comprise an estimated 5% of the human genome (Vliet 1993). Alu are inserted at specific chromosome locations and does not appear to be subject to loss or rearrangement which makes them stable genetic markers (Batzer 1994). The five conditions of the Hardy-Weinberg equilibrium were no random mating, no net mutation, infinitely large population, no movement of individuals in to or out of the population and no difference in selection against alleles.These conditions must be met in order for the Hardy-Weinberg equation p2+2pq+q2=1 to work.

In the equation p2 represents AA homozygous without Alu insertion, 2pq represents heterozygous, and q2 represents BB homozygous with Alu insertion for a given gene. In the lab cheek cells were used as a DNA source and through amplification, the PCR products were dispersed into the wells of an agarose gel. Electrophoresis was used to separate the DNA fragments. The agarose gel acts as a filter separating DNA by size, short strands move through the well in the gel more quickly then long strands.

Over time short strands will move farther away from the gel than long strands. DNA strands of same size will move at the same speed and will end up grouping together. The technique allowed rapid gene mapping and provided a simple method for the isolation and analysis of specific chromosomal region. My hypothesis was that the genotype of sample population will be in Hardy-Weinberg equilibrium.

METHODS In this experiment PCR was used to amplify particular sequences of DNA. First I labeled a 1. 5 ml of microcentrifuge tube with my initials.The 5% chelex solution was shaked thoroughly to get

the resin into the solution. Before the resin settled, 500 microliter was pipetted into the labeled microcentrifuge tube.

After the preparing the tube, I used sterile cotton swab to wipe the inside of my cheek several times. Then I placed the swab with cheek cells into the tube with chelex solution and swirled it couple of times to remove the cells from the swab. I closed the lid of the tube and placed a locking cap on the lid. I placed the tube in a 100 degree Celsius heating block for 10 minutes.After heat shocking, tube was carefully removed from the heat block and cooled it on ice for 1 minute. I spinned the tube for 2 minutes in the small microcentrifuge on the lab bench by carefully balancing the centrifuge.

20 microliter of supernatant was pipetted into a 0. 5 ml tube without disturbing the resin at the bottom of the tube because supernatant contained my DNA. I kept the DNA on ice while setting up the PCR mixture. I pipetted 40 microliter of PCR mixture which consisted of buffer, dNTP’s, primers, and Taq polymerase, into a fresh 0. 5 ml tube.

Then 5 microliter of Mg2+ was added to the PCR mixture. microliter of my template DNA was added to the side of the reaction tube because it prevented the reaction from starting until everyone in the class was ready. At the same everyone in the class centrifuged the tube for 2 minutes in the larger centrifuge. Then I placed my tube in the thermocycler to replicate the DNA. After several hours of replication, the DNA was loaded into the agarose gel. I

pipetted 10 microliter of the sample DNA into a new 0.

5 ml tube. Then added 2 microliter of loading dye to the tube and mixed by pipetting in and out several times.I pipetted 10 microliter of the mixture into a well of the agarose gel. Electrophoresis involved the use of an electrical current to separate large DNA molecules from other molecules of different size. Since DNA was negatively charged, it migrates towards the positive electrode in an electrophoresis tray.

One of the lanes of the gel was used for a ladder of DNA of known size. The ladder called Pgem was compared to each individual’s DNA to determine the size of the DNA fragments. I ran the gel at 120 volts for 20 to 30 minutes. At last I viewed the gel under a UV lamp and photographed it to determine the genotype.After that I read the gel and counted the number of individuals who had homozygous with and without Alu element and heterozygous individuals. I used Hardy-Weinberg equation p2+2pq+q2=1 to test if alleles were in equilibrium.

RESULTS The observed number of homozygous AA individuals without Alu insertion was 5, number of homozygous BB individuals with Alu element was 22 and heterozygous AB individuals were 13. Since Alu element was abundant, homozygous individuals with Alu insertion were more then homozygous individuals without Alu insertion.The total number of A alleles was 23, total number of B alleles was 57 and total number of A and B alleles was 80. The p2 represented expected proportion of A individuals which was 0. 0826, 2pq represented expected proportion of AB individuals which was 0. 4096 and q2 represented

expected proportion of B individuals which was 0.

5076. The Hardy-Weinberg statistics showed that p2+2pq+q2 was equal to 1. The expected homozygous AA was 3. 3, heterozygous AB was 16.

4, and homozygous BB was 20. 3. I calculated x2 value from x2 probability table using 1 degree freedom and the value came out to be 1. 42.

The value was greater than 0. 5 and less then 0. 1 which resulted in failure to reject the statistical decision. DISCUSSION There is equilibrium in the population for the Alu element insertion TPA-25.

The equilibrium occurred because I failed to reject the hypothesis that p2+2pq+q2 was equal to 1. The Hardy-Weinberg theory worked because our population met the conditions. The conditions included completely random mating, no net mutation, infinitely large population, no movement of individuals in or out of the population and no difference in selection against alleles.These conditions define populations in which the allele frequencies do not change. The conditions were biased because our population was small consisting of only 40 people. We formed equilibrium because our population was not big enough to perform the statistical test.

Some student’s DNA did not even run through the gel because they did not wipe the inside of the cheek hard enough which resulted in experimental error. Since our population was small and some student’s DNA could not be recognized so we had to assume that the population was in Hardy-Weinberg equilibrium.The assumption was made because not enough data was presented to know that all five conditions were true. The lab classes consisting of 100 people did not form equilibrium because the population was large which contradicts with

one of the conditions of infinitely large population. In 1990, only 30. 5% of all state residents were Florida-born, and 61.

8% were from rest of the US (city-data. com). This detail contradicts with the condition of no movement of individuals in or out of the population.Florida has one of the most diverse populations in the United States with a rich mix of different cultural, racial, and linguistic backgrounds. Hence, Florida is so diverse that it is hard for this condition to be met. LITERATURE CITED Vliet, Kent.

1993. A lab manual for integrated principles of biology: Part one- BSC 2010L. Pearson custom publishing. University of Florida. Batzer, Mark A. 1994.

African origin of human specific polymorphic Alu insertions. Vol. 91: pp 12288-12292. Florida-Migration.

http://www. city-data. com/states/Florida-Migration. html