Population Genetics

Question 1

Hardy-Weinberg Equation

Answer 1

1 = p^2 + 2pq + q^2

Question 2

P(AA) =
P(Aa) =
P(aa) =

Answer 2

P(AA) = p^2
P(Aa) = 2pq
P(aa) = q^2

Question 3

Allele frequency

Answer 3

The percentage of alleles in a whole population (2 per person) that are of a particular type

Question 4

Allele Frequency equation

Answer 4

(# of A alleles in the population)/(Total # of alleles in the population)

Question 5

Hardy-Weinberg Assumptions

Answer 5

• diploid organism
• sexual reproduction
• nonoverlapping generations
• random mating
• large population size
• equal allele frequencies in the sexes
• no migration
• no mutation
• no selection

Question 6

If a locus is in HWE, does that mean all the assumptions are true?

Answer 6

No

Question 7

Penetrance

Answer 7

P(disease/”disease genotype”)

e.g. P(breast cancer/BRCA1 mutation)

Question 8

q =

Answer 8

sqrt(disease frequency)

Question 9

Sample 2000 people in the population. Observe 20 with a Mendelian recessive disease. What is the allele frequency?

Answer 9

q = sqrt (20/2000) = 0.1

Question 10

Sample 1000 people in the population. Observe 60 with a rare Mendelian dominant disease. What is the allele frequency?

Answer 10

p = (disease frequency)/2 = (60/1000)/2 = 0.03

Question 11

Unilineal relatives (definition and examples)

Answer 11

• Related through only one parent

- Examples: first cousins, aunts/uncles, grandparents

Question 12

Bilineal relatives (definition and examples)

Answer 12

• Related through both parents

- Examples: siblings, double cousins, inbreeding loop

Question 13

Identity-by-descent (IBD)

Answer 13

• Two alleles are IBD if they are inherited from a common ancestor (any two alleles of the same variant are not necessarily IBD, they may just be identical by state (IBS))

Question 14

Coefficient of kinship

Answer 14

• describes the average genetic sharing between 2 people
• Probability that two random alleles in 2 different people are IBD
• Meaning: measure of how closely related two people are
• 0 means that people are unrelated
• 1/2 means people are genetically identical

Question 15

Coefficient of kinship vs. coefficient of inbreeding

Answer 15

• Coefficient of inbreeding = F
• F is the probability of two alleles IBD in an individual
• F for a person = the coefficient of kinship for the person’s parents

Question 16

Cotterman’s k

Answer 16

• Describes the average genetic sharing between two people (does not distinguish unilineal vs. bilineal sharing)

Question 17

True or False: Genotype frequencies at any specific locus are in HWE as long as HWE assumptions hold

Answer 17

True (in particular, random mating)

Question 18

Why are chromosomes inherited in pretty large chunks?

Answer 18

• Chromosomes are inherited in pretty large chunks due to recombination during meiosis

Question 19

True or False; when every locus is in HWE, different loci are inherited independently

Answer 19

False: even in a random-mating population with every locus in HWE, different loci are not inherited independently (this is true in families and across the population)

Question 20

% of offspring that are non-parental types is the _______________

Answer 20

“distance” between the genes

Question 21

Example:

• Suppose traits A and B have a ‘distance’ of 5%
• Suppose traits B and C have a ‘distance’ of 30%
• What will the distance between A and C be?

Answer 21

A-----B-----C = 35%
C-----A-----B = 25%

Question 22

Genes stay together during meiosis unless there is ______________________

Answer 22

Recombination

Question 23

Probability of recombination is _________

Answer 23

theta (recombination fraction, Sturtevant’s distance, “Morgans”)

Question 24

The pace of mixing depends on _______________

Answer 24

the recombination fraction, theta

The larger the theta, means faster mixing

Question 25

Theta = 0 when ___________

Answer 25

the loci are in the same place

Question 26

Theta = 1/2 when _________________

Answer 26

the loci are on different chromosomes (or VERY far apart on the same chromosome)

Question 27

Linkage Disequilibrium (LD) is ______________

Answer 27

correlation between genotypes at different loci (in a population)

Question 28

2 important sources of LD in human populations

Answer 28

1) Admixture: mixing (interbreeding) of two populations | 2) New mutation

Question 29

Linkage vs. LD

Answer 29

- Linkage: if two genes are "linked," they are on the same chromosomes (theta

Question 30

The only relationship between linkage and LD is that _______________________

Answer 30

LD goes away more slowly if linkage is tight (genes are close together)

Question 31

Addition Rule

Answer 31

If two events are MUTUALLY EXCLUSIVE (can't both happen at the same time); then their probabilities add P(A v B) = P(A or B) = P(A) + P(B)

Question 32

Addition Rule Example

Answer 32

Roll an even number or roll a "1" on a die | P = (1/2) + (1/6) = 2/3

Question 33

Independence

Answer 33

Two events are independent if one happening does not affect the likelihood of the other happening

Question 34

Multiplication Rule for Independent Probabilities

Answer 34

P(A ^ B) = P(A and B) = P(A)P(B)

Question 35

Multiplication Rule Example

Answer 35

- Roll a "1" on the first die and roll an even number on the second - (1/6) * (1/2) = 1/12

Question 36

Binomial Distribution

Answer 36

- Experiment with only two outcomes - n = number of times experiment performed - X = number of "successes" out of n trials - The distribution of X is binomial (n,p) where p is the probability of "success" in each experiment

Question 37

Interpretation of p values

Answer 37

- The p value is NOT the probability that the null hypothesis is true - A large p value does not necessarily mean the null hypothesis is true. It just means that there isn't enough evidence to reject the null hypothesis (possibly because of too small of a sample)

Question 38

When we reject the null hypothesis, we say ________________________________________

Answer 38

the result is statistically significant

Question 39

Statistically significant does not necessarily mean _________________________________

Answer 39

SCIENTIFICALLY SIGNIFICANT

Question 40

Definition of drift

Answer 40

- Random changes in allele frequency by chance in finite populations - Particularly important for small populations - Due to the random sampling of gametes - Cause: random sampling of alleles

Question 41

How does drift operate in real human populations?

Answer 41

- Bottleneck: large population is reduced, then re-expands - Founder effect: genetic effects on a population started by a small group of individuals (as a result, alleles in the founder group becomes the alleles in the population)

Question 42

Which processes drive evolution?

Answer 42

- Mutation - natural selection - genetic drift

Question 43

Selection

Answer 43

differing viability and/or fertility of different genotypes

Question 44

Mutation

Answer 44

- Change in the genetic material - Significance: mutation changes allele frequencies because it creates new alleles - mutation is the ultimate source of all genetic variation