Inbreeding depression is the reduced fitness in a given population as a result of breeding of related individuals. It is often the result of a population bottleneck. In general, the higher the genetic variation within a breeding population, the less likely it is to suffer from inbreeding depression. Inbreeding depression seems to be present in most groups of organisms, but varies across mating systems. 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 Caenorhabditis remanei has been demonstrated to suffer severely from inbreeding depression, unlike its hermaphroditic relative C. elegans, which experiences outbreeding depression.
Breeding between closely related individuals, called inbreeding, may on one hand result in more recessive deleterious traits manifesting themselves, because the genomes of pair-mates are more similar: recessive traits can only occur in offspring if present in both parents' genomes, and the more genetically similar the parents are, the more often recessive traits appear in their offspring. Consequently, the more closely related the breeding pair is, the more homozygous deleterious genes the offspring may have, resulting in very unfit individuals. For 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).
An example of inbreeding depression is shown to the right. In this case, a is a recessive allele which has negative effects. In order for the a phenotype to become active, the gene must end up as aa because in the geneotype Aa, the A takes dominance over the a and the a does not have any effect. Due to evolutionary causes, recessive genes are, more often than not, 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 heterozygous, which is known as overdominance. This can lead to reduced fitness of a population with many homozygous genotypes, even if they are not deleterious. Here, even the dominant alleles result in reduced fitness if present homozygously (see also hybrid vigour).
Currently, it is not known which of the two mechanisms is more prevalent in nature. For practical applications, e.g. in livestock breeding, the former is probably more significant – it may yield completely unviable offspring (meaning outright failure of a pedigree), while the latter can only result in relatively reduced fitness.
Inbreeding depression and natural selection
Natural selection cannot effectively remove all deleterious recessive genes from a population for several reasons. First, deleterious genes arise constantly through mutation within a population. Second, in a population where inbreeding occurs frequently, most offspring will have some deleterious traits, so few will be more fit for survival than the others. It should be noted, though, that different deleterious traits are extremely unlikely to equally affect reproduction – an especially disadvantageous recessive trait expressed in a homozygous recessive individual is likely to eliminate itself, naturally limiting the expression of its phenotype. Third, recessive deleterious alleles will be "masked" by heterozygosity, and so in a dominant-recessive trait, heterozygotes will not be selected against.
When recessive deleterious alleles occur in the heterozygous state, where their potentially deleterious expression is masked by the corresponding wild-type allele, this masking phenomenon is referred to as complementation (see Complementation (genetics).
In general, sexual reproduction in eukaryotes has two fundamental aspects: recombination during meiosis, and outcrossing. It has been proposed that these two aspects have two natural selective advantages respectively. A proposed adaptive advantage of meiosis is that it facilitates recombinational repair of DNA damages that are otherwise difficult to repair (see Meiosis – section: Theory that DNA repair is the adaptive advantage of meiosis). A proposed adaptive advantage of outcrossing is complementation, which is the masking of deleterious recessive alleles  (see hybrid vigor or heterosis). The selective advantage of complementation may largely account for the general avoidance of inbreeding (see Kin recognition).
Managing inbreeding depression
Introducing alleles from a different population can reverse inbreeding depression. Different populations of the same species have different deleterious traits, and therefore their crossbreeding will not result in homozygosity in most loci in the offspring. This is known as outbreeding enhancement, practiced by conservation managers and zoo captive breeders to prevent homozygosity.
However, intermixing two different populations may give rise to unfit polygenic traits in outbreeding depression, yielding offspring which lack the genetic adaptations to specific environmental conditions. These, then, will have a lowered fitness than pure-bred individuals e.g. of a particular subspecies that has adapted to its local environment.
Although severe inbreeding depression in humans seems to be highly uncommon and not widely known, there have been several cases of apparent forms of inbreeding depression in human populations. Charles Darwin, through numerous experiments, was one of the first scientists to demonstrate the effects of inbreeding depression. Charles's wife, Emma was his first cousin. He attempted to study the theory of inbreeding within his own children. Of the ten Darwin children, three died before the age of ten. Of the rest, three had child-less long-term marriages. As with animals, this phenomenon tends to occur in isolated, rural populations that are cut off to some degree from other areas of civilization.
A notable example is the Vadoma tribe of western Zimbabwe, many of whom carry the trait of having only two toes due to a small gene pool. Another example is Fumarase deficiency, a rare genetic disorder that leads to severe mental retardation. Over half of the known cases are in the isolated and adjoining polygamous Reformed Mormon communities of Hilldale, Utah and Colorado City, Arizona.
Species not subject to inbreeding depression
Inbreeding depression is not a phenomenon that will inevitably occur. Given enough time and a sufficiently (but not too) small gene pool, deleterious alleles may be eliminated by natural selection and genetic drift.
Under most circumstances, this is a rare occurrence though, as the gene pool cannot become too large (thereby increasing the odds of new deleterious alleles appearing through mutation) nor too small (resulting in outright inbreeding depression). Among island endemic populations, however, a high resistance to inbreeding depression is often seen. These derive from very small initial populations that must have been viable, and panmixia in the early stages of speciation was usually thorough. This will result in a very comprehensive elimination of deleterious recessive alleles at least.[verification needed] The second type of inbreeding depression—caused by overdominant heterozygous alleles—is impossible to eliminate by panmixia. However, local conditions may result in an altered selective advantage, so that the fitness of the heterozygous genotype is lowered.
- Chatham Islands Robin
- Laysan Duck (data equivocal; severe population fluctuations probably natural)
- Mauritius Kestrel
- Naked Mole Rat (mammal displaying eusocial reproductive structure and low genetic variation)
- Stegodyphus dumicola and some other social spiders (live in highly inbred colonies)
- Thai Ridgeback, a dog breed
- Yellow Crazy Ant
- Outbreeding depression
- Hybrid vigour
- Genetic purging
- Minimum viable population
- Population genetics
- Backward evolution
- Insular dwarfism
- Island gigantism
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