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Spring Semester Classes - Boards Studying > Population Genetics > Flashcards

Population Genetics Flashcards

1
Q

Hardy-Weinberg Equation

A

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

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2
Q

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

A 
P(AA) = p^2
P(Aa) = 2pq
P(aa) = q^2
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3
Q

Allele frequency

A

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

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4
Q

Allele Frequency equation

A

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

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5
Q

Hardy-Weinberg Assumptions

A
  • diploid organism
  • sexual reproduction
  • nonoverlapping generations
  • random mating
  • large population size
  • equal allele frequencies in the sexes
  • no migration
  • no mutation
  • no selection
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6
Q

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

A

No

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7
Q

Penetrance

A

P(disease/”disease genotype”)

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

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8
Q

q =

A

sqrt(disease frequency)

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9
Q

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

A

q = sqrt (20/2000) = 0.1

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10
Q

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

A

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

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11
Q

Unilineal relatives (definition and examples)

A
  • Related through only one parent

- Examples: first cousins, aunts/uncles, grandparents

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12
Q

Bilineal relatives (definition and examples)

A
  • Related through both parents

- Examples: siblings, double cousins, inbreeding loop

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13
Q

Identity-by-descent (IBD)

A
  • 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))
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14
Q

Coefficient of kinship

A
  • 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
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15
Q

Coefficient of kinship vs. coefficient of inbreeding

A
  • 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
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16
Q

Cotterman’s k

A
  • Describes the average genetic sharing between two people (does not distinguish unilineal vs. bilineal sharing)
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17
Q

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

A

True (in particular, random mating)

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18
Q

Why are chromosomes inherited in pretty large chunks?

A
  • Chromosomes are inherited in pretty large chunks due to recombination during meiosis
19
Q

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

A

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)

20
Q

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

A

“distance” between the genes

21
Q

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?
A 
A-----B-----C = 35%
C-----A-----B = 25%
22
Q

Genes stay together during meiosis unless there is ______________________

A

Recombination

23
Q

Probability of recombination is _________

A

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

24
Q

The pace of mixing depends on _______________

A

the recombination fraction, theta

The larger the theta, means faster mixing

25
Q

Theta = 0 when ___________

A

the loci are in the same place

26
Q

Theta = 1/2 when _________________

A

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

27
Q

Linkage Disequilibrium (LD) is ______________

A

correlation between genotypes at different loci (in a population)

28
Q

2 important sources of LD in human populations

A

1) Admixture: mixing (interbreeding) of two populations

2) New mutation

29
Q

Linkage vs. LD

A
  • Linkage: if two genes are “linked,” they are on the same chromosomes (theta
30
Q

The only relationship between linkage and LD is that _______________________

A

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

31
Q

Addition Rule

A

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)

32
Q

Addition Rule Example

A

Roll an even number or roll a “1” on a die

P = (1/2) + (1/6) = 2/3

33
Q

Independence

A

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

34
Q

Multiplication Rule for Independent Probabilities

A

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

35
Q

Multiplication Rule Example

A
  • Roll a “1” on the first die and roll an even number on the second
  • (1/6) * (1/2) = 1/12
36
Q

Binomial Distribution

A
  • 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
37
Q

Interpretation of p values

A
  • 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)
38
Q

When we reject the null hypothesis, we say ________________________________________

A

the result is statistically significant

39
Q

Statistically significant does not necessarily mean _________________________________

A

SCIENTIFICALLY SIGNIFICANT

40
Q

Definition of drift

A
  • 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
41
Q

How does drift operate in real human populations?

A
  • 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)
42
Q

Which processes drive evolution?

A
  • Mutation
  • natural selection
  • genetic drift
43
Q

Selection

A

differing viability and/or fertility of different genotypes

44
Q

Mutation

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

Spring Semester Classes - Boards Studying (1 decks)

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