1. Lab 6: Genetic Drift and Effective Population Size

2. Goals To calculate the probability of fixation or loss of an allele.
To estimate mean time until fixation of an allele.
To estimate effective population size affected by past cataclysms.
To learn how genetic drift and selection interact in populations of various Ne.

3. What is MC method?
The (pseudo-random) number generator has certain characteristics (e.g., a long "period" before the sequence repeats)
The (pseudo-random) number generator produces values that pass tests for randomness
There are enough samples to ensure accurate results
It simulates the phenomenon in question.

4. p = ?
p = ?

5. Probability of fixation or loss
Genetic drift results from chance changes in allele frequencies that result from sampling of gametes from generation to generation in a finite population.

6. 2. Exact probability of fixation of an allele is equal to the initial frequency of that allele in absence of selection.
3. Probability of fixation of an allele can be calculated empirically by using Monte Carlo simulations as implemented in Populus.

7. Important assumption for Genetic Drift model in Populus
Population size is assumed to remain constant from generation to generation
Allelic frequency changes result only from the random sampling process

8. Problem 1 (15 minutes). The frequencies of alleles A1 and A2 are
p = 0.7 and q = 0.3, respectively.
Use Populus to empirically estimate the probabilities of fixation and loss for each of these alleles.
What do you think are the exact probabilities of fixation and loss for each allele?
Do these probabilities depend on the population size?

9. Problem 2 (15 minutes). Consider a population with the following genotype counts:
Case
A1A1
A1A2
A2A2 1 18 4 3 2 7 21
Use Populus to empirically estimate the mean time (in number of generations) until fixation for allele A1 for each case.
Show the mean time until fixation of A1 calculated using the diffusion approximation (given above) for each case.
Discuss the reasons for the differences (if any) between the two types of estimates. What are some of the assumptions underlying each method?

10. Mean time until fixation of an allele depends on population size and initial frequency of that allele.
A1A1(N11)
A1A2
(N12)
A2A2(N22) N p q
T(p)
T(p) in terms of N 16 2 20
0.85
0.15
26.78
1.34N 18
0.05
0.95
77.96
3.90N

11. Effective population size
Effective Population Size: Effects of Different Numbers of Males and Females
Table courtesy of K. Ritland

12. Problem 3 (15 minutes). The census population size of an isolated population of finches on the Galapagos Islands is as follows. What is the effective population size in 2010?
Year
Females
Males
1930
120
250
1950 15
290
1970
350
1990
1500
2500
2010
3500
5000
Dr. Robert Rothman, Rochester Institute of Technology

13. When time is discontinuous, a transition matrix can be used to determine the probability of fixation in the next generation.

14. Fitness in terms of s and h (adaptive Darwinian selection) 1 + s
Genotype
A1A1
A1A2
A2A2
Fitness
ω11
ω12
ω22
Fitness in terms of s and h
(adaptive Darwinian selection)
1 + s
1 + hs 1
(purifying selection)
1 − hs
1 − s
Using traditional setup for adaptive Darwinian (positive) selection
These can be easily converted to terms for purifying selection

15. Problem 4 (15 minutes). If adaptive Darwinian selection (characterized by h = 0.5 and s = 0.25) is operating on a locus and the frequency of allele A1 at that locus is p = 0.25, predict whether A1 is more likely to get lost or to become fixed:
In a population with Ne = 10.
In a population with Ne = 30.
For each of the two cases, calculate the probability of fixation of A1 empirically (i.e., using Populus).
If Ne affects the probabilities of fixation and loss of A1, explain why. If not, explain why not.

16. Problem 5. GRADUATE STUDENTS ONLY: Starting with the conditions in Problem 4-a), calculate the probability that:
The frequency of A1 becomes 0.1 in the next generation.
A1 becomes fixed in the next generation.
If the two transition probabilities differ dramatically, explain why. If not, explain why not.