Population genetics

Question 1

What is 1 SNP considered to be?

Answer 1

1 position where the nucleotide can change between different haplotypes

Question 2

What are the 4 factors/forces that influence allele frequencies?

Answer 2

• Mutation → source of genetic variation, occurs rarely, not rapid change in allele frequencies
• Migration → frequent or infrequent, when frequent → homogenizes populations between them
• Natural Selection
• Genetic Drift

Question 3

What are the conditions for Hardy-Weinberg proportions in gentype frequencies?

Answer 3

Random matin, no mutation, no selection, no migration, no drift
AA = p^2
Aa = 2pq
aa = q^2
*Takes 1 generation → proprtions remain unchanged afterwards if same conditions

Question 4

How can we calculate if a population is in HW proportions?

Answer 4

1. Calculate p and q 1st in the population by doing f(AA) + 1/2*f(Aa)
2. See in 2pq = f(Aa), p^2 = f(AA), q^2 = f(aa)

Question 5

What is the effect of inbreeding on genotype frequencies?

Answer 5

Type of non-random mating
Increases homozygosity in the next generation:
F(AA) = p^2 + Fpq
F(Aa) = 2pq(1-F)
F(aa) = q^2 + Fpq

*DOES NOT CHANGE ALLELE FREQUENCIES

Question 6

What is the inbreeding coefficient (F)?

Answer 6

F quantifies the overall probability that the 2 alleles inherited by 1 given individual will be indentical by descent

F = (1/2)^2 * (1+Fa) + F for every path
More inbreeding → probability or identity by descent → increasing probability of homozygosity

Question 7

What is inbreeding depression?

Answer 7

reduction in viability of inbred individual → most deleterious conditions require homozygous for mutant
Examples: cystic fibrosis, sickle cell anemia, albinisms

Question 8

What is the typical rate of mutations/bp of DNA/ generation in humans?

Answer 8

10^-19 (1/billion) mutation/bp/generation
*We have 3 bilion nucleotides in our genome

Question 9

How can migration occur?

Answer 9

One way or 2 ways

Question 10

What are the criterias for genetic drift?

Answer 10

Occurs in small populations → loss of alleles
More important genetic drift in smaller populations

*Moves allele frequencies up or down with equal probability

Question 11

What is Extinction vortex?

Answer 11

Applies to small populations:
Small population → inbreeding + random genetic drift → loss of genetic variability → reduction in individual fitness → lower reproduction + higher mortality → smaller population

Question 12

What is absolut and relative fitness based on?

Answer 12

Absolute fitness = Percentage survival to reproductive age
Relative fitness = compared to the best survival genotype being 1

Question 13

What does balancing selection vs directional selection favour?

Answer 13

Directional selection favours homozygous
Balancing selection favours heterozygous → brings alleles frequencies to 50/50

Question 14

What is a selective sweep?

Answer 14

When 1 new nucleotide mutation is strongly favoured → strong dip in allelic diversity

Can reduce diversity in genomic region, espacially those with low rates of recombinations
Leave behind past events that have influenced the genome

Question 15

Are all the evolutionnary processes/forces independent?

Answer 15

NOPE, they interact together

Question 16

How can we calculate the equilibrium frequency of a deleterious allele?

Answer 16

q = sqrt(u / s)

u = mutation rate
s = selection coefficient

In HW proportions: f(AA) = q^2 = u/s

Question 17

What is h?

Answer 17

The level of dominance of the deleterious allele
For a completely recessive allele → h = 0

for h > 0 → q = u/hs

Question 18

What is a complex vs simple trait?

Answer 18

Simple trait → controlled by 1 or 2 genes
Complex trait → quantitative trait → controlled by many many genes and external factors → follows a bell-shaped distribution of phenotypic states

Question 19

What is variance?

Answer 19

A measurement of how far each data is from the mean
- It is additive for all different variances of different influencing factors

(1/# data) * sum of (data - mean)^2

Question 20

What is the threshold of a complex trait?

Answer 20

The envrionmental / genetic presence over which the trait is shown
ex: disease is expressed

Question 21

What is heritability?

Answer 21

H^2 = Vg/Vx
Vx = genetic variance
Vg = Vx + Ve
0 < H2 < 1

Question 22

What does GWAS (genome-wide association studies) analysis allow?

Answer 22

Allows us to map genes to influence complex trait variation, assess their effect
Relies on population surveys that look for correlation between markers and phenotypic trait values in samples taken from large populations

Question 23

What is QTL mapping?

Answer 23

One way to discover underlying genes controlling for complex phenotypes
Co-segregation (co-inheritance) of phenotypes and marker alleles → usually SNPs

*Look at different chromosomes and see if common segments for all members of a specific phenotype

Question 24

What is the difference between GWAS and QTL?

Answer 24

GWAS → for many generations or recombination
QTL → single generation SNP