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SL12003 - Genetics > Lecture 12&13 - Allele Frequency > Flashcards

Lecture 12&13 - Allele Frequency Flashcards

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1
Q

What is a population

A

Interbreeding groups of organisms (of the same species)

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2
Q

Where does genetic variation come from

A

Mutation and recombination

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3
Q

What is an allele

A

Alternative DNA sequences at a locus (version of a gene) inherited as a unit

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4
Q

What is a locus

A

The position in the genome being considered

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5
Q

Way is a single nucleotide polymorphism (SNPs)

A

variation at a single position in a DNA sequence among individuals

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6
Q

What is genetic variation for a trait

A

Genetically based phenotypic differences between individuals arise
from sequence differences

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7
Q

Why may a gene have no effect on traits

A

If all individuals have the same allele, the locus does not contribute variation
– i.e., the gene does not contribute to phenotypic differences between
individuals
– The nature of phenotypic variation contributed by a gene depends on the
nature of the allelic variants at the locus

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8
Q

What produces genetically-based phenotypic variation

A

Genes with different alleles that lead to different phenotypes

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9
Q

How is frequency of an allele calculated

A

Frequency of allele A = Number of A alleles/ Total number of alleles

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10
Q

How is the number of alleles in a diploid population calculated

A

Total number of A alleles = 2x the number of AA homozygotes
(nAA) + the number of Aa heterozygotes (nAa)
(slide 13)

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11
Q

Why do we care about change in allele frequencies

A

Evolution
Can be used to understand migration/gene flow
– Different alleles may be favoured in different environments
– Infer how some types of phenotype variation are associated with
genetic differences
* E.g., compare frequency of alleles at some loci in a group suffering from
a genetic disorder to a group that does not.

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12
Q

What is a genotype frequency

A

Number of individuals with the genotype divided by total number of individuals

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13
Q

How is genotype frequency (f) calculated

A

f (AA) = Number of AA individuals / Number of individuals§

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14
Q

What is the Hardy-weinberg model

A

Two alleles in a diploid individual are randomly and independently
sampled from an infinitely large pool of gametes
Probability of sampling the A allele is p
Probability of sampling the a allele is (slide 20)

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15
Q

What are some assumptions of the Hardy-weinberg model

A

Population is very large
Random mating
No migration in or out of the population
No selection
No mutation

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16
Q

What does a large population mean for the H-W model

A

Eliminates sampling error
* You expect the frequency of A in your population to be p, but
it would not necessarily be p in a finite sample
* No sampling error means allele frequencies are constant
* Allows for mathematically simple model

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17
Q

What does Random mating for the H-W model mean

A

All individuals have an equal chance of mating with each
other
* No assortative mating, no inbreeding, no outbreeding

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18
Q

What does No migration in or out of the population for the H-W model mean

A

Closed population, no alleles entering leaving through
migration
* So, the allele frequencies are not influenced by
variation entering from other populations

19
Q

What does no selection mean for the H-W model

A

Alleles do not affect fitness, so survival and
reproduction are not associated with the genotype of
an individual
* So, genotype frequencies are not altered by differential
fitness
* And allele frequencies are not changing over time due
to differences in their ‘success’

20
Q

What does no mutation mean for the H-W model

A

Mutations do not ‘add’ or ‘subtract’ copies of an allele
from the population
* No new alleles are introduced

21
Q

What does the H-W model offer

A

Idealised reference
Reference point against which real population genetic data can be compared
Can be considered a null model

22
Q

What are the predictions of the H-W model

A

Prediction: the allele frequencies of a population do not change
solely due to random mating.

  • Prediction: genotypic frequencies are the product of allele
    frequencies and will return to these frequencies after a single
    generation of random mating.
23
Q

What are the predicted genotype frequencies for the H-W model

A

Freq. homozygous A (AA)= p2
Freq. homozygous a (aa)= q2
Freq. heterozygote (Aa)= 2pq

24
Q

What is the main violation of the H-W assumptions

A

Non-random mating
Finite population
Natural selection

25
Q

What is the effect of non-random mating on the H-W model

A

Non-random mating affects genotype frequencies in a
population
- Some combinations of alleles will occur at higher
frequency than expected, others at lower frequency

26
Q

What are the types of non-random mating

A

Assortive mating
Disassortative mating
Inbreeding

27
Q

What is assortative mating

A

genetically or phenotypically similar
individuals tend to mate with each other

28
Q

What is negative assortative mating

A

genetically or phenotypically dissimilar
individuals tend to mate with each other

29
Q

What is inbreeding

A

Individuals mating with relatives

30
Q

What is the affect of asssortative mating on H-W model

A

Phenotype-biased mating means frequencies of certain
genotypes, in loci underlying the phenotype, will be altered
* Can affect heterozygosity, increasing or decreasing it depending
on the pattern
* This effect is not genome-wide, though it can be multiple loci
* Traits are generally shaped by multiple loci instead of one,
more on this later

31
Q

What is the affect of inbreeding

A

Relatives share alleles, so offspring produced by matings between
relatives are more likely to have two copies of the same allele
* Can measure this by considering whether an individual has a pair of
alleles that are identical by descent (IBD)
* Inbreeding increases the likelihood of alleles being IBD
* These individuals are homozygous so inbreeding increases
homozygosity and reduces heterozygosity

32
Q

What is the effect of inbreeding on the H-W equation

A

F(AA) = p2 + pqF
F(Aa) = 2pq − 2pqF
F(aa) = q2 + pqF
F = proportional reduction in the frequency of heterozygotes
compared to that expected in the Hardy-Weinberg model

33
Q

What is inbreeding depression

A

Occurs when inbreeding leads to reduced viability and/or fecundity (‘fitness’)

Must be caused by a general pattern of lower fitness of
homozygotes compared to heterozygotes

34
Q

What is the most likely result of inbreeding and why

A

Deleterious recessive mutations
Harmful genetic variants that cause negative effects only in
homozygotes
* Heterozygotes are “carriers”
* Examples include lots of genetic diseases, e.g. cystic fibrosis

Rare, hidden in heterozygotes, cannot be removed by selection

35
Q

Why do allele frequencies change

A

Genetic Drift
Natural selection
Migration

36
Q

What is genetic drift

A

Random changes in allele frequencies
(slides 3-8 PPT 2)

37
Q

How does a finite population violate the H-W population

A

Randomly sample alleles from a ‘gamete pool’ to make the next
generation of individuals
* In a finite population, the frequencies of alleles you sample to
create a population can (and will) differ from the actual
frequencies in the gamete pool
* For any allele frequency, the expected amount of ‘error’ is
proportional to 1/2N (where 2N is the total number of alleles)

38
Q

What is a bottleneck

A

When populations go through drastic reductions in population
size, it can produce huge ‘drift events’ (slides 9-11 ppt 2)

39
Q

What is a founder event

A

Similar to bottlenecks, when a new
population is founded by very few
individuals, the allele frequencies
can be very different from the original population (slides 12-17 ppt 2)

40
Q

How does Natural selection violate H-W

A

Selection favours one allele
Overdominance

41
Q

What is migration (gene flow)

A

Movement of alleles from one
population to another

42
Q

How does migration violate H-W model

A

Isolated populations will tend to become more different from
each other in allele frequencies over time
- differences in local pattern of selection
- differences caused by drift
* Migration opposes this process and reduces genetic
differences between populations, through exchange (slide 24-25 PPT 2)

43
Q

Reading:

A

Genetics: a conceptual approach Chapter 25

How life works chapter 20.1-20.5

SL12003 - Genetics (12 decks)

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