BIOL 4250 BU The Effects of Population Size & Differences Discussion

Biol 4250 – Assignment #2
Instructions: For this assignment you need to use the population genetic simulation tool
available on the following website: https://faculty.washington.edu/herronjc/a1/
For each question that involves a simulation, you just need to record the final frequency
of the allele. For example, if the allele is lost you would just record “0” for that run. You
can see the frequency for each generation (and the final frequency at the end) by
clicking on the “table” tab. You do not need to save the graphs, but you must turn in the
final frequency data for each run.
Background
Since real populations are always of finite size, both selection and genetic drift can
potentially influence whether a an allele reaches fixation or is lost from the population.
Which evolutionary force (GD or NS) is more important depends on a number of
parameters including: population size, the strength of selection (given by the selection
coefficient), and starting frequency. We will examine the influence of these factors in the
simulations.
Part I. For this problem, we are going to look at the effects of population size on whether
a beneficial allele will reach fixation in a population. Use the following starting
parameters:
Starting frequency of A1: 0.01
Fitness of A1A1 = 1
Fitness of A1A2 = .95
Fitness of A2A2 = 0.90
Population size 10
(a) Carry out this simulation for 500 generations. Do this 15 times and record the final
frequency of A1 for each run (you can click on the page icon to see the frequency data in
the final generation).
(b) Now, change the population size to 200 and do 15 simulations. Record your data.
(c) Now, change the population size to 1000 and do 15 simulations. Record your data.
(d) Now, change the population size to 10,000 and do 15 simulations. Record your data.
1. The A1 allele is beneficial and should be favored by natural selection. Why doesn’t it
always reach fixation in a population?
2. Is the allele more likely to reach fixation in a small or large population? Why?
Part II. For this problem, we are going to look at the effects of the size of the selection
coefficient on whether a beneficial allele reaches fixation in a population. We will
change the size of the selection coefficient by entering different values for the relative
fitness of the three genotypes:
Starting frequency of A1: 0.01
Fitness of A1A1 = 1
Fitness of A1A2 = 0.8
Fitness of A2A2 = 0.6
Populations size = 200
(e) Carry out the simulation for 500 generations 15 times and record your data.
3. How do the results from this simulation compare with those from “b” above (which has
the same population size)? What does this tell you about the effects of the size of the
selection coefficient on the probability that a beneficial allele will reach fixation?
Part III. For this problem, we are going to look at the effects of the starting frequency of
a beneficial allele on the probability that it will reach fixation in a population. We are
going to change the starting frequency to make the A1 allele less common to start:
Starting frequency of A1: 0.001
Fitness of A1A1 = 1
Fitness of A1A2 = 0.95
Fitness of A2A2 = 0.90
Populations size = 1000
(f) Carry out the simulation for 500 generations 15 times and record your data.
4. At the start, what is the probability that the A1 allele will reach fixation by drift alone?
5. How do the results of this simulation compare with those of “c” above? What does
this tell you about the effect of the starting frequency of a beneficial allele on the
probability that it will reach fixation?
6. Considering the last several exercises, what conditions are most favorable for fixing a
beneficial allele in a population in terms of population size (large or small), size of the
selection coefficient (large or small), and starting frequency (high or low)?
Part IV. Now, let’s consider dominant/recessive alleles. We are going to look at what
happens to a deleterious A1 allele in the population. Input the following parameters:
Starting frequency of A1: 0.1
Fitness of A1A1 = 0.90
Fitness of A1A2 = 1
Fitness of A2A2 = 1
Populations size = Infinite (just type this in the box)
7. Based on the input parameters is the A1 allele dominant or recessive? How can
you tell?
8. By assuming an infinite population size, what evolutionary force are we ensuring
does not have an effect?
(g) Carry out the simulation one time for 500 generations and then once for 10,000
generations. Record your data.
9. Is the deleterious recessive allele eliminated from the population in either of the
simulations? Please explain why or why not?
(h) Now, change the population size to 100 (leave other parameters the same) and carry
out the simulation for 500 generations 15 times. Record your data.
10. Compare the results of these simulations with those from “g” above. If there is a
difference, please explain what accounts for the difference.