Population Genetics Lab Report
Abstract Population genetics is the study of how localized groups of individuals capable of interbreeding and creating fertile progeny change genetically over time. The Hardy-Weinberg equilibrium accounts for gene pools that do not change genetically over time. In this experiment, I intended to determine whether the sample population consisting of my fellow biology lab classmates would fall in the Hardy-Weinberg equilibrium with respect to the ALU insert from human chromosome 8. My hypothesis was that this sample population would fall in the Hardy-Weinberg equilibrium with respect to the ALU insert. To analyze whether this sample population was in the Hardy-Weinberg equilibrium or not, I amplified a sample DNA polymerase from a cheek cell
…show more content…
of each individual through PCR and electrophoresis. I then determined the allele frequency and predicted the genotype frequencies from these allele frequencies through the Hardy-Weinberg equation. Based on the chi-squared test, I found that the sample population did fall in the Hardy-Weinberg equilibrium, as my p-value was greater than .05. This is reasonable since conditions for the Hardy-Weinberg equilibrium appear to be met: inbreeding is infrequent, populations outside of our sample population have allele frequencies resembling those inside our sample population, mutation rate for the ALU insert is minimal, and selection occurs only against rare homozygotes.
Introduction Population genetics is defined as the research and analysis of a gene pool in a population.
A gene pool is the configuration of the sum of the alleles of each individual in a population. A comparison of the genotype frequencies from one generation to another indicates whether evolution has occurred. Gene pools that are not evolving are said to be in the Hardy-Weinberg equilibrium (Campbell 456). The main objective of this human population genetics experiment was to examine the allele frequencies for the sample population of my biology class and predict genotype frequencies. I wanted to calculate the proportion of individuals in the sample population with ALU inserts to determine whether the insert is in the Hardy-Weinberg equilibrium. ALU inserts are small, repetitive sequences of DNA distributed through the genomes of primates. ALU inserts from human chromosome 8 of the tissue plasminogen activator (TPA) gene were selected because they are unwavering and reliable genetic markers, as most of them show no signs of being subject to disappearance or repositioning (Batzer 12288). My hypothesis was that the ALU insert would be in the Hardy-Weinberg equilibrium because the five assumptions for the equilibrium of random mating, a large population, and no selection, mutation or migration seem to correlate with respect to the ALU insert in this random and diverse sample
population.
Materials and Methods In order to accomplish the above objectives, a lab technique known as PCR, or polymerase chain reaction, was used to amplify DNA sequences and thus genotype this sample population. To perform PCR on the sample population, a sample quantity of the template DNA was taken from each individual by use of a sterilized cotton swab placed inside the cheek and dabbed around a few times to extract cheek cells. The cotton swab was then swirled around a few times in a 1.5 ml microcentrifuge tube with 500 µL of 5% Chelex solution. The tube was then capped, placed in a 100° C heating block for 10 min., carefully removed and cooled on ice for 1 min., spun for 2 min. in a small microcentrifuge, and then finally 20 µL of the supernatant liquid was pipetted into a 0.5 ml tube. The template DNA was then left on ice while each of us set up our PCR mixture, which was a buffered solution consisting of primers (the DNA strands that are complimentary to the ends of the particular DNA sequence), Taq polymerase (the most regularly used heat-stable polymerase), dNTP’s (the four building blocks of DNA), and the added cofactor of Mg2+. In a new 0.5 ml tube, 40 µL of PCR mixture was pipetted for each individual in the sample population, followed by 5 µL of Mg2+. I then removed the template DNA from the ice and pipetted 5 µL of it onto the inner side of each 0.5 ml tube containing the PCR mixture. The tubes were then simultaneously centrifuged for 2 min., and then placed in a thermocycler. This PCR mixture then underwent 39 cycles of replication, each series including three steps: denaturing, annealing, and elongation. In the denaturing, the temperature was raised to around 94° C in order to divide the primers. Then in the annealing, the temperature was cooled to about 58° C so the complimentary DNA strands could attach to the template DNA. During the subsequent elongation, the PCR mixture was warmed to approximately 72° C to let the polymerase replicate the template DNA beginning with the primers. Once the DNA templates were amplified by PCR, we separated the different sizes through electrophoresis. To facilitate this, I pipetted 10 µL of the sample into a new 0.5 ml tube for each individual. Then, I mixed in 2 µL of loading dye into each tube and pipetted it in and out several times. I then added 10 µL of each mixture into wells of 1.6% prepared agarose gel. I then ran an electrical charge of 100 V through the gel for approximately 20 min to separate the different sizes. I then photographed the gel under a UV lamp and determined the genotype of each class member, and counted the number of individuals that have the insert (II), the number of individuals that are heterozygous (Ii), and the number of individuals that do not have the insert (ii). Two copies of 400 bp fragments indicated a presence of the ALU insert of TPA-25, one copy of a 400 bp fragment and one copy of a100 bp fragment indicated a heterozygous genotype, and two copies of 100 bp fragments indicated the absence of TPA-25. In order to determine whether the sample population was in the Hardy-Weinberg equilibrium or not, we used a chi-squared (χ2) test and the Hardy-Weinberg equation, which is also the statistical hypothesis: p2 + 2pq + q2 = 1, or (p + q) 2 = 1
Using these data, we determined the χ2 value (Σ((observed-expected)2/expected)), the degrees of freedom (n-1), and p-values based on a table of critical values of chi-squared distribution.
Results In the sample population of 157, we found that 21 individuals possess the insert, 61 individuals are heterozygous, and 75 individuals do not possess the insert. These data were used in executing the chi-squared test, the results of which are itemized in Table 1-1.
Table 1-1. Chi-square statistics, where I=presence of insertion and i=absence of insertion.
Genotype Observed
(o) Expected
(e) Deviation
(o-e) (o-e)2 (o-e)2 e II 21.0 17.3 3.73 13.9 0.806 Ii 61.0 69.1 8.08 65.3 0.945 ii 75.0 70.7 4.35 18.9 0.268
χ2 = 2.02; v = 2; 0.5 > p > 0.1 Discussion The p-value is significantly greater than .05, being in between .5 and .1, so we fail to reject H0. Since the results fail to reject the null hypothesis, the biological conclusion is that the sample population is in the Hardy-Weinberg equilibrium. This conclusion supports my initial hypothesis and the statistical hypothesis. It is a reasonable conclusion because the five conditions for the Hardy-Weinberg equilibrium seem to be true for the sample population. The individuals in our sample population appear to chooses their mates randomly. Any affects of gene flow from other populations, introduction of new mutations, and differential survival/reproductive success can be neglected. The sample population also represents a larger population with no genetic drift. These suppositions are reasonable since inbreeding is uncommon, populations outside of our sample population have allele frequencies similar to those inside our sample population, mutation rate for the ALU insert is low, and selection occurs only against irregular homozygotes. However, it is possible that our alternative hypothesis (HA) is true, which would state that the sample population is not in the Hardy-Weinberg equilibrium. This would be plausible because natural populations are seldom, if at all, in the Hardy-Weinberg equilibrium (Campbell 458). In many cases, populations appear to be close to the Hardy-Weinberg equilibrium because rates of evolutionary change are so slow, and the assumption of the equilibrium results only in an approximation, the actual number of carriers may be somewhat different. Also, the sample population was not infinite, but does intend to reflect random mating (with respect to the ALU insert) in an infinite population. There is also the possibility that there are inaccuracies in the data collected, possibly the result of extracting an erroneous number or kind of cheek cells, through improperly function machines (such as the thermocycler, centrifuge, camera, UV lamp, pipettes, etc.), or in having a skewed sample population.
of each individual through PCR and electrophoresis. I then determined the allele frequency and predicted the genotype frequencies from these allele frequencies through the Hardy-Weinberg equation. Based on the chi-squared test, I found that the sample population did fall in the Hardy-Weinberg equilibrium, as my p-value was greater than .05. This is reasonable since conditions for the Hardy-Weinberg equilibrium appear to be met: inbreeding is infrequent, populations outside of our sample population have allele frequencies resembling those inside our sample population, mutation rate for the ALU insert is minimal, and selection occurs only against rare homozygotes.
Introduction Population genetics is defined as the research and analysis of a gene pool in a population.
A gene pool is the configuration of the sum of the alleles of each individual in a population. A comparison of the genotype frequencies from one generation to another indicates whether evolution has occurred. Gene pools that are not evolving are said to be in the Hardy-Weinberg equilibrium (Campbell 456). The main objective of this human population genetics experiment was to examine the allele frequencies for the sample population of my biology class and predict genotype frequencies. I wanted to calculate the proportion of individuals in the sample population with ALU inserts to determine whether the insert is in the Hardy-Weinberg equilibrium. ALU inserts are small, repetitive sequences of DNA distributed through the genomes of primates. ALU inserts from human chromosome 8 of the tissue plasminogen activator (TPA) gene were selected because they are unwavering and reliable genetic markers, as most of them show no signs of being subject to disappearance or repositioning (Batzer 12288). My hypothesis was that the ALU insert would be in the Hardy-Weinberg equilibrium because the five assumptions for the equilibrium of random mating, a large population, and no selection, mutation or migration seem to correlate with respect to the ALU insert in this random and diverse sample
population.
Materials and Methods In order to accomplish the above objectives, a lab technique known as PCR, or polymerase chain reaction, was used to amplify DNA sequences and thus genotype this sample population. To perform PCR on the sample population, a sample quantity of the template DNA was taken from each individual by use of a sterilized cotton swab placed inside the cheek and dabbed around a few times to extract cheek cells. The cotton swab was then swirled around a few times in a 1.5 ml microcentrifuge tube with 500 µL of 5% Chelex solution. The tube was then capped, placed in a 100° C heating block for 10 min., carefully removed and cooled on ice for 1 min., spun for 2 min. in a small microcentrifuge, and then finally 20 µL of the supernatant liquid was pipetted into a 0.5 ml tube. The template DNA was then left on ice while each of us set up our PCR mixture, which was a buffered solution consisting of primers (the DNA strands that are complimentary to the ends of the particular DNA sequence), Taq polymerase (the most regularly used heat-stable polymerase), dNTP’s (the four building blocks of DNA), and the added cofactor of Mg2+. In a new 0.5 ml tube, 40 µL of PCR mixture was pipetted for each individual in the sample population, followed by 5 µL of Mg2+. I then removed the template DNA from the ice and pipetted 5 µL of it onto the inner side of each 0.5 ml tube containing the PCR mixture. The tubes were then simultaneously centrifuged for 2 min., and then placed in a thermocycler. This PCR mixture then underwent 39 cycles of replication, each series including three steps: denaturing, annealing, and elongation. In the denaturing, the temperature was raised to around 94° C in order to divide the primers. Then in the annealing, the temperature was cooled to about 58° C so the complimentary DNA strands could attach to the template DNA. During the subsequent elongation, the PCR mixture was warmed to approximately 72° C to let the polymerase replicate the template DNA beginning with the primers. Once the DNA templates were amplified by PCR, we separated the different sizes through electrophoresis. To facilitate this, I pipetted 10 µL of the sample into a new 0.5 ml tube for each individual. Then, I mixed in 2 µL of loading dye into each tube and pipetted it in and out several times. I then added 10 µL of each mixture into wells of 1.6% prepared agarose gel. I then ran an electrical charge of 100 V through the gel for approximately 20 min to separate the different sizes. I then photographed the gel under a UV lamp and determined the genotype of each class member, and counted the number of individuals that have the insert (II), the number of individuals that are heterozygous (Ii), and the number of individuals that do not have the insert (ii). Two copies of 400 bp fragments indicated a presence of the ALU insert of TPA-25, one copy of a 400 bp fragment and one copy of a100 bp fragment indicated a heterozygous genotype, and two copies of 100 bp fragments indicated the absence of TPA-25. In order to determine whether the sample population was in the Hardy-Weinberg equilibrium or not, we used a chi-squared (χ2) test and the Hardy-Weinberg equation, which is also the statistical hypothesis: p2 + 2pq + q2 = 1, or (p + q) 2 = 1
Using these data, we determined the χ2 value (Σ((observed-expected)2/expected)), the degrees of freedom (n-1), and p-values based on a table of critical values of chi-squared distribution.
Results In the sample population of 157, we found that 21 individuals possess the insert, 61 individuals are heterozygous, and 75 individuals do not possess the insert. These data were used in executing the chi-squared test, the results of which are itemized in Table 1-1.
Table 1-1. Chi-square statistics, where I=presence of insertion and i=absence of insertion.
Genotype Observed
(o) Expected
(e) Deviation
(o-e) (o-e)2 (o-e)2 e II 21.0 17.3 3.73 13.9 0.806 Ii 61.0 69.1 8.08 65.3 0.945 ii 75.0 70.7 4.35 18.9 0.268
χ2 = 2.02; v = 2; 0.5 > p > 0.1 Discussion The p-value is significantly greater than .05, being in between .5 and .1, so we fail to reject H0. Since the results fail to reject the null hypothesis, the biological conclusion is that the sample population is in the Hardy-Weinberg equilibrium. This conclusion supports my initial hypothesis and the statistical hypothesis. It is a reasonable conclusion because the five conditions for the Hardy-Weinberg equilibrium seem to be true for the sample population. The individuals in our sample population appear to chooses their mates randomly. Any affects of gene flow from other populations, introduction of new mutations, and differential survival/reproductive success can be neglected. The sample population also represents a larger population with no genetic drift. These suppositions are reasonable since inbreeding is uncommon, populations outside of our sample population have allele frequencies similar to those inside our sample population, mutation rate for the ALU insert is low, and selection occurs only against irregular homozygotes. However, it is possible that our alternative hypothesis (HA) is true, which would state that the sample population is not in the Hardy-Weinberg equilibrium. This would be plausible because natural populations are seldom, if at all, in the Hardy-Weinberg equilibrium (Campbell 458). In many cases, populations appear to be close to the Hardy-Weinberg equilibrium because rates of evolutionary change are so slow, and the assumption of the equilibrium results only in an approximation, the actual number of carriers may be somewhat different. Also, the sample population was not infinite, but does intend to reflect random mating (with respect to the ALU insert) in an infinite population. There is also the possibility that there are inaccuracies in the data collected, possibly the result of extracting an erroneous number or kind of cheek cells, through improperly function machines (such as the thermocycler, centrifuge, camera, UV lamp, pipettes, etc.), or in having a skewed sample population.