E X E R C I S E S
IV. Genetic Drift
1. Consider a time, say 150,000 years ago, when the entire race totaled only about 50,000 individuals. At this time, humans likely resembled the Bushmen of the Kalahari Desert. They existed as nomadic hunter-gatherers, whose unit of social and population structure was a clan of perhaps 20-100 individuals. Occasional ice ages, volcanic eruptions, and plagues reduced the overall numbers - extinguished some populations, isolated some populations, and forced some populations to share the same range. These population bottlenecks provide ideal conditions for genetic drift - the random effect of mating within small, isolated populations. Fixing an Alu - from an initial jump on a single chromosome of a single human to both chromosomes of every person in a population - becomes a statistically probable event. Allele frequencies of unfixed Alus change rapidly within isolated groups. Gene flow from immigrants or between groups with overlapping ranges introduces new Alus and alters frequencies of existing ones. Bottlenecks are then released, and populations grow in size until Alu frequencies stabilize, according to Hardy-Weinberg equilibrium.
Theoretically, each Alu insertion is the result of a unique transposition event that occurred once in human evolutionary history. In this question, you will use a Hardy-Weinberg Simulator to explore the fate of a single Alu jump to a new location on a single chromosome of a member of a hunter-gatherer group.
The Hardy-Weinberg simulator allows you to study Hardy-Weinberg population equilibrium and how it is affected by changes in genotype survival rates, initial allele percentages, population size, and the number of generations. At each generation, two parents are chosen at random from a population and a child's genotype is generated from its parents' genotypes, using an approach similar to performing a Punnet Square analysis. The probability that the child survives to the age of reproduction is determined by the survival rate for the child's genotype. If the child does survive, then that child is added to the gene pool for the next generation. This process is repeated, starting with choosing parent pairs, until enough children are generated so that the number surviving is the same as the number of parents.
Because of chance and varying survival rates for different genotypes, the percentage of "+" and "-" alleles may vary from generation to generation. You can study this phenomenon through repeated simulation runs or by varying genotype survival rates, initial allele percentage, population size, and number of generations.
a. Point your web browser to http://www.bioservers.org/sim/.
b. On the Simulation Server page, your goal is to set parameters that simulate a nomadic population of hunter-gatherers in which a new Alu insertion event occurs. The Simulator will let you follow that insertion event to see whether it is lost from - or spreads throughout - the population over time.
c. The key parameters you will need to enter, then, are population size and "+" allele frequency. Say you chose a population size of 50 individuals. Because each individual in this population has two copies of each chromosome, there are 2 X 50 = 100 total alleles for any given locus. If a single Alu insertion event occurs in this population, then the "+" allele frequency will be 1 out of 100 alleles, or 1%.
d. To configure Simulation Server for this scenario, first move and click the mouse in the white area of the upper window pane. This will "deposit" a circle-shaped population node onto the workspace. Next, with this node still highlighted (the circle will be outlined in bold), type 250 into the # Runs text box. Type 100 into the # Generations text box. Type 50 into the Starting Population text box. Type 1 into the Starting % "+" box. Finally, save your work by clicking on "Enter Values."
e. Now we will "release" this first population from the bottleneck, allowing it to grow to 1,000 individuals in each generation. To do this, move and click the mouse somewhere to the right of Population 1's node. As before, this will "deposit" a circle-shaped population node(#2) onto the workspace. Next, with this node still highlighted, type 100 into the # Generations text box. Type 1000 into the Population text box. Type 0 into the Starting % "+" box. Save this Population's configuration by clicking on "Enter Values."
f. Finally we will compare the population release scenario with a parallel population that is kept at the original, small population size. To do this, move and click the mouse somewhere to the right of Population 1's node. With the new Population 3's node still highlighted, type 100 into the # Generations text box. Type 50 into the Population text box. Type 1 into the Starting % "+" box. Save this Population's configuration by clicking on "Enter Values."
g. Now we will link the populations, so that Population 1 "feeds into" Populations 2 and 3. To do this, first select 1 from the first popup menu next to the Link/Unlink buttons. Select 2 from the other popup menu. Click Link. A line should appear, connecting Population 1 to 2. To link Population 1 to 3, select 1 from the first popup menu and 3 from the second. Click Link. Another line should appear, connecting Population 1 with 3.
h. Start the simulation by clicking on the Begin Run button. Wait until the Simulation Progress reports 100% complete. (Depending on the speed of your computer, this may take anywhere from 2 to 10 minutes.)
i. To view the results of the simulation, scroll down to the bottom pane. Click on the "Graph" tab.
j. Click on the checkboxes labeled Node #1, Node #2 and Node #3. Click the "Linked" checkbox. Click the "Press here to graph" button.
k. Look at your results. You should see a line for each of the 250 populations you started. Most of these lines will go to 0, meaning the "+" allele was lost from the population. Some lines will continue and then bifurcate into two new lines. These new lines represent the effects of releasing the population size, and holding the population size small. How do they compare?
l. Examine the graph that shows the frequency of the "+" allele versus generation number. In general, what happens to the "+" allele (i.e., the Alu insertion) over time? Are there any runs in which the Alu insertion begins to spread throughout the population during the first 100 generations? Is this a common or rare occurrence? For the runs where the Alu allele is not lost from the population, what happens to the allele frequency when the population size "explodes" (generation 101-200 in Population 2)? Conversely, what happens to the Alu allele when the population is kept small (generation 101-200 in Population 3)? In addition to population size, can you think of any other factors that would help an Alu insertion event spread? (Hint: What would happen if inheriting an Alu insertion conferred a selective advantage to the individual carrying the insertion?)
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