Population Genetics

Prof. Frederic Guillaume, Nov 3 2025

Related to Population Ecology

References

Primer on PopGenetics Genomics, Daniel Hartl, Oxford 2020 (background reading)

Intro

Evolutionary Dynamics of genetic variation on a population
Kind of variation, how its maintained and how it changes
- Why are individuals in a population or between populations different from each other?
- This is of course the basis of Evolution - Intro, and the result of Natural Selection

Mutation

The ultimate source of genetic variation
Due to errors in DNA replication
Mutation rate depends on the size of the geonome - more complex organisms with larger geonomes have a higher mutation rate, but more of their geonome does not code for anything. So there are more silent mutations

Structural mutations

Some mutations lead to structural changes in the chromosomes, making them bigger or smaller or splitting or joining them
- Deletion, duplication,
- "macro" mutations that are important for speciation because they stop chromosomes from recombination:
  - inversion, fission, fusion

Effects of mutation

Silent mutations effect a part of the gene sequence that doensn't translate into proteins
Neutral (or synonymous, if they don't affect protein coding) mutations might affect proteins, but don't affect fitness
Selection Coefficient $s$ describes the effect of a mutation on fitness. Higher $s$ means that a mutation will become more frequent in a population over time. Most mutations have $s$ negative or close to 0 (mildly deleterious), some neutral, and very few are positive.

Evolutionary Forces

Population genetics describes how mutation frequency changes over time and is explained by evolutionary forces:

mutation
selection
genetic drift
migration
recombination

Genotype and Allele frequencies

If we consider random mating for the alleles $A_{1}$ and $A_{2}$ (three genotypes):
!EEB-020-PopulationGenetics-2025, p.11
To convert from number to frequency: divide the number by the total population. e.g. $A_{1} A_{1}$ frequency is 0.5 and the others are 0.25.
- For allele number and and frequency, the actual number of the alleles counted

Genotype frequencies

	Num	Frq
$A_{1} A_{1}$	4	$4 / 8 = 0.5$
$A_{1} A_{2}$	2	$2 / 8 = 0.25$
$A_{2} A_{2}$	2	$2 / 8 = 0.25$

Allele frequencies

	Num	Frq
$A_{1}$	10	$p = 10 / 16 = 0.625$
$A_{2}$	6	$q = 6 / 16 = 0.375$

We use $p$ and $q$ to denote allele frequencies,
e.g. $p = \frac{\sum A_{1}}{2 N}$ , with $N = \sum (individuals)$

If you are only given genotype frequencies (and not $N$ ), you can alternatively calculate allele frequencies $p$ and $q$ directly from genotype frequencies $D, H, R$ (Dominant Homozygote, Heterozygote, Recessive Homozygote):

p = D + \frac{1}{2} H

q = R + \frac{1}{2} H = (1 - p)

Hardy-Weinberg Equilibrium

In a large population with random mating and following allele frequencies in one locus, after one generation of random mating we end up with the following distributions of genotype frequencies:
!EEB-020-PopulationGenetics-2025, p.12

Assumptions of H-W

No mutation
No selection
no migration
infinitely large population
random mating, equal number of offspring
generations are non-overlapping
meiosis is fair, no segreagation distortion.

So, if there are differences from H-W, that means that one of these is happening.

Selection

Evolution is fastest when genetic variation in fitness is largest, i.e. when p = q = 0.5
Selection will cause loss of deleterious mutations and fixation of beneficial mutations.

Migration

(refering to gene flow between populations, mediated by dispersal)

Migration works to homogenize allele frequencies between populations
It can work counter to or along with selection
Migration rate: $m$

Genetic Drift

Reproduction is a random process
Smaller population size increases genetic drift
Genetic drift reduces heterozygosity

Effective Population Size

We can calculate an effective population size for a population that is more useful for modelling

Population consequences of inbreeding

Reduction of fitness found in inbred individuals caused by expression of deleterious mutations in homozygotes
Most new mutations are mildly deleterious and recessive - increased homozygosity causes expression of more deleterious mutations that are otherwise hidden in heterozygotes
Increased homozygosity is caused by random mating in small populations, or mating among relatives in large populations.

δ = 1 - \frac{W_{F}}{W_{0}}

Mutation accumulation in small populations

In a small effective population where $N_{e} < (2 | s |)^{- 1}$ , the dynamics of mildly deleterious mutations is dominated by drift. New mutations will quickly become fixed. Since most new mutations are deleterious, small populationswill slowly accumulate them and get reduced fitness and population size. Too many accumulating mutations causes mutational meltdown.

Example: Florida Panthers and genetic rescue

Isolated panther population with high inbreeding depression. Eight pumas from Texas were introduced to fight inbreeding depression and it worked in decreasing heterozygosity.

Population Structure

We can measure genetic difference between populations with $F_{S T}$ . The rate of migration (gene flow) can be high enough to change population structure.

Linkage Disequilibrium (LD)