Population genetics Flashcards
What is 1 SNP considered to be?
1 position where the nucleotide can change between different haplotypes
What are the 4 factors/forces that influence allele frequencies?
- 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
What are the conditions for Hardy-Weinberg proportions in gentype frequencies?
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
How can we calculate if a population is in HW proportions?
- Calculate p and q 1st in the population by doing f(AA) + 1/2*f(Aa)
- See in 2pq = f(Aa), p^2 = f(AA), q^2 = f(aa)
What is the effect of inbreeding on genotype frequencies?
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
What is the inbreeding coefficient (F)?
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
What is inbreeding depression?
reduction in viability of inbred individual → most deleterious conditions require homozygous for mutant
Examples: cystic fibrosis, sickle cell anemia, albinisms
What is the typical rate of mutations/bp of DNA/ generation in humans?
10^-19 (1/billion) mutation/bp/generation
*We have 3 bilion nucleotides in our genome
How can migration occur?
One way or 2 ways
What are the criterias for genetic drift?
Occurs in small populations → loss of alleles
More important genetic drift in smaller populations
*Moves allele frequencies up or down with equal probability
What is Extinction vortex?
Applies to small populations:
Small population → inbreeding + random genetic drift → loss of genetic variability → reduction in individual fitness → lower reproduction + higher mortality → smaller population
What is absolut and relative fitness based on?
Absolute fitness = Percentage survival to reproductive age
Relative fitness = compared to the best survival genotype being 1
What does balancing selection vs directional selection favour?
Directional selection favours homozygous
Balancing selection favours heterozygous → brings alleles frequencies to 50/50
What is a selective sweep?
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
Are all the evolutionnary processes/forces independent?
NOPE, they interact together
How can we calculate the equilibrium frequency of a deleterious allele?
q = sqrt(u / s)
u = mutation rate
s = selection coefficient
In HW proportions: f(AA) = q^2 = u/s
What is h?
The level of dominance of the deleterious allele
For a completely recessive allele → h = 0
for h > 0 → q = u/hs
What is a complex vs simple trait?
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
What is variance?
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
What is the threshold of a complex trait?
The envrionmental / genetic presence over which the trait is shown
ex: disease is expressed
What is heritability?
H^2 = Vg/Vx
Vx = genetic variance
Vg = Vx + Ve
0 < H2 < 1
What does GWAS (genome-wide association studies) analysis allow?
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
What is QTL mapping?
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
What is the difference between GWAS and QTL?
GWAS → for many generations or recombination
QTL → single generation SNP
