Population Genetics

Population genetics

Aims to understand the genetic composition of a population and the forces that determine and change that composition.

Hardy-Weinberg equilibrium

The null hypothesis of population genetics, what happens when there is no evolution.

How to calculate with hardy-weinberg

Observed frequency

• numbers of one group / total number

Allele frequency

• observed frequency added together

• P = AA + 0.5(Aa)

Expected genotype frequency

• for AA = P²

• for Aa = 2 x p x q

• for aa = q²

Expected counts

• genotype frequency x total number

Heterozygosity

Total frequency of heterozygotes - represented by H

What causes loss of heterozygosity

Inbreeding - does not change allele frequencies

Genetic drift - changes allele frequencies at random

How does inbreeding stop heterozygosity

For example - self fertilization.

A/A can only make A/A, a/a can only make a/a

If a generation consists of one AA, Aa, and aa, all AA make AA, all aa make aa, and Aa makes ¼ AA and aa each, therefore there is more AA and aa than Aa.

Inbreeding coefficient

Represented by F. It is the degree of inbreeding.

Brother sister = ¼

Half siblings = 1/8

First cousin = 1/16

Second cousin = 1/64

Recessive deleterious alleles in inbreeding

Since there is more homozygosity, this increases recessive diseases.

Relative risk of this can be calculated by F / q

F = inbreeding coefficient and q = recessive allele frequency.

Calculating how much heterozygosity will remain after a certain amount of time relating to genetic drift

Ht = H0(1-1(2N))^t

H = heterozygosity

t = number of generations

N = population size

H0 = initial heterozygosity

Migration

Permanent movement of alleles from one population to another. Recipient population initial frequency is pr. Donor population initial frequency is pd. M is migrant population.

Pr’ = pr + m(pd - pr)

Gene flow and population differentiation

Gene flow is a force acting against genetic drift, only a few migrants are necessary to keep the population differentiation at a low level.

Measuring fitness when it comes to selection

fitness = observed frequency / expected frequency

fitness = observed count / expected count

Directional selection

Allele with highest average fitness increases in frequency

Balanced polymorphism / stabilising selection

Heterozygote has more fitness

Disruptive selection

Homozygotes have more than heterozygote. Population will either keep dominant or recessive.

Quantitative traits

Phenotype is a scale, often few at extremes and lots at intermediates

How to test for heritability

Two short individuals and two tall are mated. If offspring are the same then the trait is not heritable.

Additive variance

Going from aa to Aa to AA increases phenotype by the same amount

Dominant variance

A is dominant to a. Aa does not equal intermediate phenotype but rather dominant phenotype.

Broad sense heritability

H² = genetic variance / phenotypic variance.

If H² is 0.5, 50% of variation is explained by genetic differences.

Narrow sense heritability

h² = additive genetic variance / phenotypic variance

If h² is close to 1, parents appearance is a good indication of offspring appearance.

Directional selection

The selection differential is the difference between the optimum and current mean of a trait.

Selection response is the difference between the mean trait value for offspring and the previous generation

Response = h² x selection differential

Phylogenetic tree

Hypothesis for evolutionary relationships between species

Polotomy

A mother species split into three or more daughter species at the same time on a phylogenetic tree, it is unlikely in most cases and is due to not enough data being used to make the tree.

Monophyletic group

A common ancestor and all descendants

Paraphyletic group

A common ancestor and most of its descendants

Polyphyletic group

Grouping derived from two or more distant ancestors

How to find the nearest relative through a phylogenetic tree

The tree with the fewest substitutions is the preferred tree