Lecture 12&13 - Allele Frequency Flashcards
What is a population
Interbreeding groups of organisms (of the same species)
Where does genetic variation come from
Mutation and recombination
What is an allele
Alternative DNA sequences at a locus (version of a gene) inherited as a unit
What is a locus
The position in the genome being considered
Way is a single nucleotide polymorphism (SNPs)
variation at a single position in a DNA sequence among individuals
What is genetic variation for a trait
Genetically based phenotypic differences between individuals arise
from sequence differences
Why may a gene have no effect on traits
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
What produces genetically-based phenotypic variation
Genes with different alleles that lead to different phenotypes
How is frequency of an allele calculated
Frequency of allele A = Number of A alleles/ Total number of alleles
How is the number of alleles in a diploid population calculated
Total number of A alleles = 2x the number of AA homozygotes
(nAA) + the number of Aa heterozygotes (nAa)
(slide 13)
Why do we care about change in allele frequencies
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.
What is a genotype frequency
Number of individuals with the genotype divided by total number of individuals
How is genotype frequency (f) calculated
f (AA) = Number of AA individuals / Number of individuals§
What is the Hardy-weinberg model
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)
What are some assumptions of the Hardy-weinberg model
Population is very large
Random mating
No migration in or out of the population
No selection
No mutation
What does a large population mean for the H-W model
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
What does Random mating for the H-W model mean
All individuals have an equal chance of mating with each
other
* No assortative mating, no inbreeding, no outbreeding
What does No migration in or out of the population for the H-W model mean
Closed population, no alleles entering leaving through
migration
* So, the allele frequencies are not influenced by
variation entering from other populations
What does no selection mean for the H-W model
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’
What does no mutation mean for the H-W model
Mutations do not ‘add’ or ‘subtract’ copies of an allele
from the population
* No new alleles are introduced
What does the H-W model offer
Idealised reference
Reference point against which real population genetic data can be compared
Can be considered a null model
What are the predictions of the H-W model
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.
What are the predicted genotype frequencies for the H-W model
Freq. homozygous A (AA)= p2
Freq. homozygous a (aa)= q2
Freq. heterozygote (Aa)= 2pq
What is the main violation of the H-W assumptions
Non-random mating
Finite population
Natural selection
What is the effect of non-random mating on the H-W model
Non-random mating affects genotype frequencies in a
population
- Some combinations of alleles will occur at higher
frequency than expected, others at lower frequency
What are the types of non-random mating
Assortive mating
Disassortative mating
Inbreeding
What is assortative mating
genetically or phenotypically similar
individuals tend to mate with each other
What is negative assortative mating
genetically or phenotypically dissimilar
individuals tend to mate with each other
What is inbreeding
Individuals mating with relatives
What is the affect of asssortative mating on H-W model
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
What is the affect of inbreeding
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
What is the effect of inbreeding on the H-W equation
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
What is inbreeding depression
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
What is the most likely result of inbreeding and why
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
Why do allele frequencies change
Genetic Drift
Natural selection
Migration
What is genetic drift
Random changes in allele frequencies
(slides 3-8 PPT 2)
How does a finite population violate the H-W population
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)
What is a bottleneck
When populations go through drastic reductions in population
size, it can produce huge ‘drift events’ (slides 9-11 ppt 2)
What is a founder event
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)
How does Natural selection violate H-W
Selection favours one allele
Overdominance
What is migration (gene flow)
Movement of alleles from one
population to another
How does migration violate H-W model
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)
Reading:
Genetics: a conceptual approach Chapter 25
How life works chapter 20.1-20.5
