Simulation guidelines: Demographic History

Comments:
Laura: The further the frequency is from the 0.5 in either direction the more heterozygosity decreases since there is a
higher frequency of one allele over the other. This also means that variation decreases as well. The variation will be
dependent on what random variability effects occurred by genetic drift during the generation/generations of the
bottleneck. These frequencies will set the stage for the frequency of the alleles after the bottleneck event is over which will
dictate variation. If a pretty high p or pretty high q allele is present, then variation and heterozygosity will be low.

Kiara: You can include how natural selection favors certain alleles before the bottleneck as a way to further explain why the
results differ when the starting allele frequencies are changed from p=q to p=0.8 and p=0.6.

Angel: I think that you can also add how the frequencies are affected during the bottle neck and how that compares to
before and after, for each of the main graphs. Maybe for questions 1 and 2 add how the set parameters for allele
frequencies could show what happened after the bottleneck of each graph.

Simulation 3: What happens when the starting allele frequencies are manipulated?

Timing & duration of founding event: 55-60

Number of founders = 20

Starting allele freq = 0.5 (p = q)

Run this three times, by clicking “new plot”. Is the output always the same? What general pattern emerges?
The general pattern is that the A allele will go back to a frequency of 0.5 after the bottleneck event, or they will normalize
around 0.6 or 0.4, but generally, the A allele does not go to fixation or loss. As Angel pointed out, before the bottleneck, the
allele frequencies were around 0.5, steadily rising, then the population experienced a bottleneck, which caused a jump in
the allele frequency of A, before normalizing to around 0.4-0.6.
 Starting allele freq = 0.6 (p = 0.6, q = 0.4)
Run this three times, by clicking “new plot”. Is the output always the same? What general pattern emerges?
The plot generally follows the same pattern, the frequency of the A allele starts off at 0.6, a bottleneck occurs which causes
a small spike, then the population returns to an A allele frequency of 0.6 or around 0.6.

Starting allele freq = 0.8 (p = 0.8, q = 0.2)

Run this three times, by clicking “new plot”. Is the output always the same? What general pattern emerges?
There is no general pattern. The frequency of the A allele starts off at 0.8, which causes it to sometimes go to fixation after
the bottleneck event, or drop significantly.
Step 1: Keep the graph default plot p(A). Briefly discuss the graphical output. Explain how the frequency of the p allele
changes over time as a result of changing the parameters. Explicitly discuss how particular values increase or
decrease the strength of genetic drift.
When the starting frequency is set to 0.5, there is a 50/50 chance that the A allele will go to fixation or loss, and
occasionally it will; for the most part, the frequency of the A allele remains at the 0.5 after the bottleneck event. When the
starting frequency is set to 0.8, the chances of the allele going to fixation or loss is 80%, which strengthens the effects of
genetic drift. As the starting allele frequency rises, the strength of genetic drift rises as well. Angel pointed out that it
would be helpful to include the results as a function of the parameters set, so generally, the higher the starting frequency,
the higher the chances of an allele going to fixation or loss, which is exactly what the results depict.
 Step 2: Without changing any other parameter, change the default plot to genetic variance. On the Y axis you can see that
genetic variance = pA (1-pA). This is a population estimate of heterozygosity. Explain how the change in the
relative frequency of p and q influences population genetic variance over time. This will remind you of an
important concept you learned in lecture: in a HW model population, the frequency of heterozygote genotypes is
maximal when p=q=0.5. Any departure from that (if p is more abundant, or if q is more abundant) will decrease H.
Expand this basic premise to encompass an interpretation of how H should change as parameter values change.
When the starting frequency is set to 0.5, genetic variance is more likely to be at 0.25, or to be maximized, but as the
starting frequency is set to higher and higher numbers, the variance gets lower and lower. For instance, when the A allele
starts at a frequency of 0.8, the genetic variance starts at around 0.14 and rises and falls as the frequency of the A allele
gets closer and further from 0.5. As Laura pointed out, variance and changes of allele frequency are negatively correlated,
so as the allele frequency of A grows further away from 0.5, the genetic variance drops.