Population genetic 1 Flashcards
What is population genetics?
The study of genetic diversity in biological populations and the processes that cause genetic diversity to change.
Mendelian genetics lead to the rise in population genetics.
What are genetic markers?
They are genome regions that are useful for measuring and investigating genetic variation in populations.
This tends to be DNA variations (sequence variations, structural variations)
DNA polymorphisms:
You can count the proportion of variability or segregating sites and the average pairwise difference
Metrics from DNA genetic markers
Say you have 4 sample lengths of DNA
The proportion of variable sites=
Number of sites with genetic difference/ The total number of sites
Average pairwise difference= The average number of differences between samples
Average pairwise difference per site= Average PD/ the number of sites
Heterozygosity
This is the fraction of individuals in a population that are expected to be heterozygous.
If there are m alleles in a locus each with a frequency Fi then:
h= 1- the total of (frequency of each allele) sqrd
The average heterozygosity (H) can be calculated by averaging h over many loci.
HW equilibirum
H-W predicts genotype frequencies based on allele frequencies, which are stable across generations across a stable population.
H-W can also be used to compare expected values of heterozygosity from allele frequencies to observed values.
P+Q= 1
P2+Q2+2PQ=1
HW principle is a null model. Using Mendelian genetics it states that the basic principle of transmission of alleles through gametes and the formation of offspring maintains genetic variation. At equilibrium, genotype frequencies remain constant between generations.
If there is a deviation from this model, then we know an evolutionary force is acting.
Example: There are two populations with known allele frequencies.
From these allele frequencies, you can work out observed heterozygosity (Ho) and expected heterozygosity (He) from the value of p and q you have calculated (2PQ).
F= 1- (Ho/Ht) shows the departure from equilibrium.
Assumption of HW equilibrium
Assumptions of the H-W Principle
- Diploid organism with sexual reproduction (random and independent chromosome transmission to offspring)
- Non-overlapping generations (no mixing)
- Infinite population size (no random genetic drift)
- Radom mating (no inbreeding)
- Males and females have equal allele frequencies
- A close population (no migration)
- No mutation
- No selection
Evolutionary forces leading to deviations from H-W equilibrium
Molecular
- Mutation
- LD and recombination
Population
- Non-random mating
-> inbreeding
-> Positive assortative mating
- Genetic drift
Natural selection and adaptation
Evolutionary force: LD and recombination
Linkage DE arrises between genes on the same chromsome that are inherited together.
This will effect allele frequencies and equilibrium.
Recombination can break up LD unless it is preserved by selection.
Evolutionary force: Non- random mating
Individuals must mate a random with respect to a particular genotype.
What leads to non-random mating?
Inbreeding: Individuals rate with relatives more often than chance
->e.g. self fertilisatio
-> Can have inbreeding depression. (E.g. thorn apple reduced plant defence leading to 4% increase in damage from herbivores)
Positive assortative mating: Individuals with similar phenotypes are more likely to mate with each other
-> e.g. populations of trees flowering at the same time
-> e.g. birds that migrate to winter breeding sites are more likely to breed with birds that arrive at same time (from same location)
Inbreeding and positive assortment do not change allele frequencies but they change the proportion of homozygotes.
Inbreeding coefficient: measure of inbreeding
Evolutionary force: genetic drift
GEnetic drift is the fixation of alleles by chance alone.
It is greater in small populations than large populations and often occurs in populations that go through bottlenecks.
Founder effect
This is observed as a result of genetic drift and inbreeding in a subpopulation often after a population bottleneck.
Example: chilling-ham cattle
- as genetically similair as clones
Effective population size
In population genetics, the effective population size is the individuals that contribute genetically to the population.
Many approaches have been developed to calculate Ne
Evolutionary force: migration and gene flow
In nature individuals often exist in sub-populations (or demes), among which there is migration (or gene flow).
Migration often results in an increase in population heterozygosity and a reduction in overall heterozygosity. (convergence of allele frequencies in subpopulations)
The fixation index (Fst) can be used to understand the diversity between populations and migration. - fraction of difference in genetic diversity due to divergence among demes
Fst= (Average He from all demes pooled- average He across demes)/ Average He from all demes pooled)
Fst= Genetic diversity between demes/ Total genetic diversity.
Fst= 1: No migration and complete divergence
Fst= 0: Frequent migration and no divergence.
The greater the genetic diversity between demes, the lower the Fst and the greater the rate of migration.
Rate of migration can be calculated
Fst= 1/ (4Nm +1)
Lecture overview
Population genetics is important for understanding genetic diversity within populations and what causes variation in genetic diversity.
HW equilibrium is a null model for genetic diversity within populations, and if heterozygosity deviates from this null model, then you know that evolutionary forces are present.
Forces
- Mutation
- Non-random mating
- Genetic drift
- Selection
- Migration
- LD and recombination
