Inbreeding depression

Inbreeding depression is the reduced biological fitness caused by loss of genetic diversity as a consequence of inbreeding, the breeding of individuals closely related genetically. This loss of genetic diversity results from small population size, often stemming from a population bottleneck.

Biological fitness refers to an organism's ability to survive and perpetuate its genetic material. In general, the higher the genetic variation or gene pool within a breeding population, the less likely it is to suffer from inbreeding depression, though inbreeding and outbreeding depression can simultaneously occur.

Inbreeding depression seems to be present in most populations of organisms, but varies across mating systems. Remarkably, hermaphroditic species often exhibit lower degrees of inbreeding depression than outcrossing species, as repeated generations of selfing is thought to purge deleterious alleles from populations. For example, the outcrossing nematode (roundworm) Caenorhabditis remanei has been demonstrated to suffer severely from inbreeding depression, unlike its hermaphroditic relative C. elegans, which experiences outbreeding depression.

Inbreeding (i.e., breeding between closely related individuals) results in more recessive traits manifesting themselves, as the genomes of pair-mates are more similar. Recessive traits can only occur in an offspring if present in both parents' genomes. The more genetically similar the parents are, the more often recessive traits appear in their offspring. This normally has a positive effect, as most genes are undergoing purifying selection (the homozygous state is favored). However, for very closely related individuals, there is an increased likelihood of homozygous deleterious genes in the offspring which can result in less-fit individuals. For the alleles that confer an advantage in the heterozygous and/or homozygous-dominant state, the fitness of the homozygous-recessive state may even be zero (meaning sterile or unviable offspring).

In inbred populations, especially small ones, genetic drift causes alleles to become fixed in a population. Drift load is the decline in fitness in a population due to the fixation of deleterious alleles.

An example of inbreeding depression is shown in the image. In this case, a is the recessive allele which has negative effects. In order for the a phenotype to become active, the gene must end up as homozygous aa because in the geneotype Aa, the A takes dominance over the a and the a does not have any effect. Some recessive genes result in detrimental phenotypes by causing the organism to be less fit to its natural environment.

Another mechanism responsible for inbreeding depression is the fitness advantage of heterozygosity, which is known as overdominance. This can lead to reduced fitness of a population with many homozygous genotypes, even if they are not deleterious or recessive. Here, even the dominant alleles result in reduced fitness if present homozygously (see also hybrid vigour).

Overdominance is rare in nature. For practical applications, e.g. in livestock breeding, the former is thought to be more significant – it may yield completely unviable offspring (meaning outright failure of a pedigree), while the latter can only result in relatively reduced fitness.