VL 6 Multilocus evolution Flashcards
What is a two-locus model in multilocus evolution?
A model considering two genetic loci with assumptions like random mating, an infinitely large population, no selection, no mutation, no gene flow, and recombination that breaks down (or not) associations between alleles at the two loci.
What is linkage diesequilibrium (LD)?
Linkage disequilibrium occurs when alleles at two loci are not independent of each other, meaning they are inherited together more often than expected by chance.
What is linkage equilibrium (LE)?
Linkage equilibrium occurs when alleles at two loci segregate independently, meaning the combination of alleles is due to random assortment.
What is a haplotype?
A haplotype is a set of alleles inherited together from a single parent. It represents the allelic combination of parental gametes.
How do you measure linkage disequilibrium?
LD is measured by the coefficient
𝐷 which quantifies the imbalance between haplotype frequencies.
For example:
𝐷 = 𝑥11𝑥22 − 𝑥12𝑥21
where 𝑥 are the frequencies of the haplotypes.
e.g. X11 = A1B1 or X12= A1B2…
What causes linkage disequilibrium?
Factors include
* non-random mating (inbreeding, assortative mating),
* genetic drift,
* gene flow,
* mutations (new point mutations, inversions), and
* natural selection. (higher fitness of certain haplotype)
What is the decay of LD by recombination?
LD decreases over time due to recombination, which breaks down associations between alleles. The decay rate depends on the recombination rate c. Will always reach LE at the ende (D=0).
decay verfall
What is additive fitness?
Additive fitness is when the fitness of an organism is the sum of the contributions from alleles at different loci. Each allele contributes independently to the overall fitness.
What is non-additive fitness (epistasis)?
Non-additive fitness, or epistasis, occurs when the fitness effect of an allele at one locus depends on the genotype at another locus.
Mimicry! HInterflügel blau und vorderflügel bau -> nicht sichtbar auf blauem background :)
HInterflügel rot und vorderflügel blau > sichtbar auf rot und auf blau :((
Alle Flügel rot -> nicht sichtbar vor rot :)
SO: two fitness peaks (all blue and all red).
But fitnessvalley prevents evolution of the other peak.
What is positive epistasis?
Positive epistasis occurs when the combined effect of two alleles results in a higher fitness than expected from their individual effects. 1+1 > 2
negative epistatsis is the opposit.
Both are called diretional epistasis
What are monogenic and complex traits?
Monogenic trait: Caused by a mutation in a single gene. Dominant or recessive.
Complex trait: Influenced by mutations in several or many genes, with most alleles having small effects. Environmental factors are also involved.
gene- gene or gene- environment interactions
Most traits!
What is heritability?
- the proportion of population variation in a phenotypic trait that is due to genetic variation
- it is a group statistic
- no information about the relative importance of genetics and environment for a specific individual
- no information about what causes the trait
- no information about the number of genes involved
- does not measure any invariant properties
How do you estimate heritability?
Heritability can be estimated through controlled experiments by comparing phenotypic similarity of genetic relatives while controlling for environmental variation, or through twin studies in natural populations.
What is Quantitative Trait Locus (QTL) analysis?
QTL analysis identifies genomic regions associated with a trait by breeding two parental lines that differ in the trait, creating a heterozygous F1 generation, and backcrossing or intercrossing to produce F2. The association between genotype and phenotype is then tested.
* statistical test: ANOVA;
* exact position cannot be determined: region is associated with variation in the trait
What is Genome-Wide Association Study (GWAS)?
GWAS is a method that tests
1. for statistical associations between genetic variants (SNPs) and phenotypes in a large number of individuals.
Significant associations (not real effect) are visualized in a Manhattan plot.
- measure significance: p-value
- correct for multiple testing, e.g., Bonferroni:
divide p-value by the number of tests
- after the statistical analyses: determining the effect size of the QTL/SNPs by odds ratio
odds of trait when risk allel is present/ odds of trait when risk allel is absent
What is missing heritability?
Missing heritability refers to the gap between the heritability estimated from genetic data and the heritability estimated from phenotype data.
It may be due to many small effect variants, rare variants with larger effects, gene-gene interactions, or gene-environment interactions.
