**GENETIC DRIFT**

- Browse to http://popgensimulator.pitt.edu/graphs/allele. Simulate genetic drift in a population of 10 individuals over 100 generations with a starting allele frequency of p=0.5 using the following parameters: Base simulation model: generations = 100, p = 0.5. Finite Population Model: Population size = 10, Number of simulations = 10. Run the simulation and insert a screengrab of the output here.

- What proportion of the simulations reached fixation (P(A) = 1) after 100 generations?

1:12.00

- What proportion of the populations reach elimination (P(A)=0) after 100 generations?

0:24.43

- What was the average number of generations to reach fixation of allele A?

3

- What was the average number of generations to reach elimination of A?

7

- Repeat the simulation of Question 1, this time changing the population size to 50. Run the simulation and insert a screengrab of the output here.

- What proportion of the simulations reached fixation (P(A) = 1) after 100 generations?

1:56.00

- What proportion of the populations reach elimination (P(A)=0) after 100 generations?

0:82.00

- What was the average number of generations to reach fixation of allele A?

1

- What was the average number of generations to reach elimination of A?

1

- What conclusions can you draw about the effect of population size on genetic drift and allelic diversity?

Smaller population size will get genetic drift which might reduce allelic diversity.

** **

**NATURAL SELECTION**

Now we will use the Allele Simulator to examine the fate of advantageous and deleterious alleles over time. First, reload the webpage to ensure that only the default parameters are expected. Next, check ‘Selection’ under simulation parameters. For the exercises below, you will alter only the values of the fitness coefficient for the AA, Aa, and aa genotype. Do not alter the values for selection coefficient and dominance coefficient.

- In this exercise, we will simulate selection against the negative deleterious allele associated with chondrodystrophy in California condor. The relative fitness (fitness coefficient) values of each genotype as follows: A = 1.0, Aa = 1.0 and aa = 0.0. Commence with an allele frequency of the recessive allele of 0.17 and simulate 100 generations of selection against this condition. What do you observe?

Relative fitness represents the rate of survival and or reproduction efficiency. As the relative fitness of aa = 0.0, it means the genotype does not survive. Therefore, generation after generation the allele frequency will decrease. After 100 generations of selection, the allele frequency will nearby zero.

- In this exercise, we will simulate selection for the favoured dominant allele. associated with dark colouration in black peppered moths. The melanic (dark) allele increased in frequency from ~0.005 in 1848 to ~0.90 in 1900 (52 generations). By trial and error, find a value of the selection coefficient (s) that is adequate to explain this evolutionary event (e.g. try a relative fitness of 0.5 for aa and subsequently try other fitness values for aa). The relative fitness of each genotype is as follows: AA = 1.0, Aa = 1.0, and aa = 1-s.

* *

- Graph the allele frequency trajectories for an advantageous additive allele with selection coefficients of 0.4, 0.1, and 0.01. Begin all cases with an initial frequency of 0.01. How long does each take to go to fixation? You will need to run the simulations for 1000 generations assuming the following fitness coefficients AA = 1.0, Aa = 1 – 0.5s, and aa = 1-s. What is the effect of different sized selection coefficients on the rate of allele frequency change?

Since the selection coefficients are denoted by s, it is a measure of fitness difference. Base on the exercise, the selection coefficient is used to calculate the rate at which allele frequencies change from generation to generation within a population.

- Graph the allele frequency trajectories for an advantageous dominant, additive, and recessive allele associated with the following relative fitness values. In each case, begin with a frequency of 0.01 for the favoured allele and run for 2000 generations. What conclusions can you draw about the effect of dominance on allele frequency changes?

AA | Aa | aa | |

Dominant | 1 | 1 | 0.9 |

Additive | 1 | 0.95 | 0.9 |

Recessive | 1 | 0.9 | 0.9 |

- Simulate allele frequency trajectories for sickle-cell anaemia using the following relative fitness values: AA = 0.76, Aa = 1.0, aa = 0.20. Commence runs with an starting allele frequency of 0.1 and run for 100 generations in populations of size N = ∞, N = 100 and N=10. Use 20 replicates for each of the latter two population sizes. Compare the outcomes for the different population sizes.

- Simulate allele frequency changes for the following model of heterozygote advantage with weak selection: AA = 0.99, Aa = 1, aa=0.99. Commence runs an initial allele frequency of 0.3 and run for 100 generations for i) N = ∞, ii) N = 1000, and iii) N=10. Run 50 replicates for the latter two cases. Repeat the runs for the same population sizes with neutrality (relative fitness of all genotypes = 1). Compare the proportion of populations polymorphic at generation 100 for the neutral cases with those for balancing selection and across population sizes. Does balancing selection slow fixation, or speed it up?

**MUTATION**

- Reset all parameters. Use the mutation model to determine by how much will the frequency of the A allele will change due to mutation in 1000 generations if the allele has a current frequency of 0.5 and the mutation rate from this allele to a (forward mutation rate) is 1 x 10
^{-5}. Assuming that 1 X 10^{-5}is a typical mutation rate for different types of DNA mutations, what can you conclude about the effect of mutation on allele frequencies?

Mutation doesn’t affect allele frequencies so much.

- Reset the parameters to the default settings and change the number of generations to 10,000 and enter a low mutation rate (1 x 10
^{-4}) from allele A2 to allele A1 (backward mutation rate). What happens to the frequency of the A allele over time?

- Now make allele A1 slightly deleterious in the recessive state by changing the fitness of the A1A1 genotype to 0.9. Notice that the A allele, although harmful, is not eliminated from this population but instead is maintained at a very low frequency. Why is this?

** **

**MIGRATION**

- Reset all parameters. Now let’s assume that we have a random mating population of infinite size, with an initial frequency of the A allele of 0.5. What happens in we introduce migrants at a rate 0.01 from a population in which the frequency of the A allele (migrant allele frequency) is 0.3?

- Repeat the previous simulation, changing the migration rate from 0.01 to 0.1. What is the effect of this on frequency of the A allele over time?

- Repeat the previous simulation, changing the migrant allele frequency from 0.3 to 0.5. What is the effect of this on frequency of the A allele over time?

- Repeat the previous simulation, changing the migrant allele frequency from 0.3 to 0.1. What is the effect of this on frequency of the A allele over time?

- What can you infer about the effects of migration on allele frequencies?

**NONRANDOM MATING**

- Now let’s examine the effect of inbreeding on Allele frequencies. Reset all parameters and set the inbreeding coefficient to 0.1. How do your results compare to those of the base model (no inbreeding or other perturbing forces)?

- Open the genotype simulator at http://popgensimulator.pitt.edu/graphs/genotype. Change the starting allele frequency to 0.6 and run the base simulation model. Insert a screengrab with figure label below.

- Change the inbreeding coefficient to 0.1 and run the simulation. Insert a screengrab with figure label below.

- Change the inbreeding coefficient to 0.5 and run the simulation. Insert a screengrab with figure label below.

- What conclusions can you draw about the effect of inbreeding on allele and genotype frequencies? Why is this important with respect to the fitness of small populations?

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