Population Genetics Flashcards
Overall Population Genetics
All about Frequency – Frequency of alleles + Frequency of genotypes
Why is it important to know Frequency (Ex)
Example – Important to know the Frequency of a disease causing allele
Example – calculating Genotype Frequency
RR = 1
Rr = 3
rr = 6
Sum of all genotype Frequency
1.0 – sum of all Frequency should add up to 1.0
Example – calculating Allele Frequency
RR = 1
Rr = 3
rr = 6
Calculating Allele Frequency (Overall)
Allele/Total # of alleles in population
Sum of all allele Frequency
1.0 – sum of all allele = 1
Crash Course Video
Look at notes
H-W (Overall)
Describes that under the right circumstances mendelian genetics works at the whole populations
What does H-W show?
Shows the Frequency with which to expect to find different alleles within the population thats not evolving
- States the equilibrium
- Frequncey of alleles in the popultions = remaining constant from generation to generation
Allele frequency change in H-W
Frequency of alleles in the population = remain constant from generation to generation
- If the assumptions of H-W are met –> allele frequencies don’t change over time
Requirements for H-W
- No Natural Selection – no alleles are beneficial than any other
- No Sexual selection – mating in population is random
- No individual can have a better chance
- No Mutations
- Need huge population because smaller population have more genetic drift
- No Gene flow – would mess with allele Frequency
H- W equation
P^2 + 2pq + q^2 = 1.0
Deriving H-W
Have P and Q
P = Frequncey of one allele
Q = Frequency of another allele
P + Q = 1.9
Frequncey of AA = P X P
- Multiple two because each individual has two alleles
Frequncey of Aa = 2pq
Frequncey of aa = q X q
What does H-W show
Can see mendle’s laws ay work in a population
What happens if frequencies don’t like up with equilibrium
If things don’t line up with equilibrium = know that there are some factors at work
T/F – Dominant alleles will increase in frequency over time
False – Dominance has no influence in increase unless it has selective pressure
History
1905 – Punnet have punnets square to describe mendelian ratios
- Looked at way to predict mendelian ratios with punnet square
–> Student asked Punnet – If brown eyes are dominant to blue then why isn’t all of population becoming brown eyed –> He didn’t know the answer
1915 – TH Morgan looking at white eyed flies and sex linkage
Issue Punnet had
He could not answer question of why Dominant traits do not always increase in Frequency over time
Didn’t know why dominant alleles don’t take over populations
Why did people push against Mendle
People pushed against Mendle because thought traits should increase in frequency that didn’t
Questions people had after mendle
- Why don’t dominant alleles take over populations
- What will happen to the genotype and allele Frequencies in the next generation
Adjusting Punnet Square
A = 0.3
a = 0.7
Can add allele Frequency into punnet square
Freq of AA = 0.3 X 0.3 = 0.09
- Because Frequency of sperm A and Frequency of egg will A combing
Finding genotype Frequencies P/Q
P = Freq A
q = Freq of a
Freq of AA = P^2
Freq of Aa = 2pq (P X Q OR Q X P)
Freq of aa = q^2
What does H-W show
Shows how Frequencies of dominant allele can stay low
H-W example
AA = 9
Aa = 42
aa = 49
Show allele and genotype Frequency
Adjusting Punnet Square (shematic)
Can add in P and Q
P and Q in punnet square
Shows how H-W is derived
P and P = P^2
P and Q OR Q and P = 2pq
Q and Q = Q^2
Can add in P and Q into punnet square – show how H-W is derived
What does H-W describe
H-W describes allele frequency in population
H-W (Details)
Allele frequencies –> Sum of all allele frequencies add to 1 (P + Q = 1.0)
Genotype frequencies = dictated by punnet square
P^2 + 2pq + q^2 = 1.0
In H-W the allele frequencies don’t change over time
Assumptions of H-W
Population that allele/genotype frequencies don’t change has assumptions
- No Migrations in or out of population
- No Mutation
- No natural Selection (natural or artificial) –> No one genotype is better than the other
- Random mating
- Infinite population size
What does H-W work for?
P^2 + 2pq + q^2 = 1 –> assumption that only works for organisms that are diploid – works for diploid
Evolution
Change in allele frequency over time
What do we get from H-W
Get expected values
Why would expected values be different than observed values
If expected don’t matched observed values – need to ask why not –> population must be in violation of one of the assumptions
What do allele frequencies reflect in a population
In a population allele frequencies are a reflection of genetic diversity
Example – Is Pleibald spotting likely in H-W –> Do you think that pleiblad spotting with have evolution
Look at all of the assumptions:
1. Is theer selection –> No
2. is there reanodm mating –> Yes there is no difefrnce is mating because of pleibald
3. Is there migration – No –> no one is leaving because of Pleibald
4. Is there increased or decreased mutations –> No – Pleibald won’t increase or decrease mutations
5. Is there reduced population size because of being pleibald –> NO – pleibald would not affect popultion size
Calculating Expected values Example
SS – 151
Ss – 131
ss – 44
Find P and Q from genotype frequncies
Once have P and Q can find expected genotype frequencies (P^2 + 2pq + q^2 = 1.0 – gives genotype frequencies)
Multiply expected genotype frequency by total individuals in populations
How can we test whether a popultion is under H-W
Do a Chi Square GOF test – Look at the observed vs. expected values
Null Hypothesis
Differences between observed and expected values is due to random chance/sampling error
Pleibald Spotting Example
SS – 151
Ss – 131
ss – 44
Take observed –> get allele frequencies (find p/q) –> Find expected genotype frequencies
Determining Df in H-W
df = # of genotype classes - # of alleles
Example:
3 genotype classes (AA + Aa + aa)
2 Alleles
df = 3 - 2 = 1
***We lose an extra degree of freedom because the frequencies of p and q are not independent
NO – because don’t know AA or Aa – can’t count a – don’t know allele frequencies
Don’t know how many are AA or Aa = can’t count frequency of a or A alleles
IF CAN’T CALCULATE ALLELE FREQUNCIES = CAN’T TEST IF POPULATION IS IN H-W
What do you know to test whether a population is in H-W
Allele frequencies mist be known
NO – because don’t know allele frequency – don’t know TT vs tt = don’t know allele frequency
Evolution + PTC
PTC is not found in nature but the ability to taste PTC correlates with the ability to taste other bitter compounds – there may have been selective advantage for tasters in early evolutionary history
- May have helped individuals choose what to eat
- Sequence analysis of modern human populations show that TAS alleles are under H-W –> they are no longer being selected for if it is under H-W
Answer – 0.2
Allele 1 + Allele 2 + Allele 3 = 1.0
100% of alleles are 1, 2 or 3
Because still diploid organism = only one egg and one sperm
H-W for more than 2 alleles per locus
Can do H-W with more than two alleles
