Inbreeding depression is the reduced biological fitness in a given population as a result of inbreeding - ie., breeding of related individuals. Population biological fitness refers to its ability to survive and reproduce itself. Inbreeding depression is often the result of a population bottleneck. In general, the higher the genetic variation or gene pool 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.
Inbreeding (ie., breeding between closely related individuals) may on the 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.
Factors reducing inbreeding depression
Whilst inbreeding depression has been found to occur in almost all sufficiently studied species, some taxa, most notably the angiosperms, appear to suffer lower fitness costs than others in inbred populations. Three mechanisms appear to be responsible for this: purging, differences in ploidy and selection for heterozygosity. It must be cautioned that some studies failing to show an absence of inbreeding depression in certain species can arise from small sample sizes or where the supposedly outbred control group is already suffering inbreeding depression, which frequently occurs in populations that have undergone a recent bottleneck, such as those of the naked mole rat.
Purging selection occurs where the phenotypes of deleterious recessive alleles are exposed through inbreeding, and thus can be selected against. This theoretically can lead to such detrimental mutations being removed from the population, and has been demonstrated to occur rapidly where the recessive alleles have a lethal effect. Unfortunately, genetic drift has a strong influence on small inbred populations, which can cause the fixation of sublethal deleterious alleles where there is only a weak selective pressure against them. The fixation of a single allele for a specific gene can also reduce fitness where heterozygote advantage (where heterozygous individuals have higher fitness than homozygotes of either allele) was previously present. As a result, the influence of attempting to purge deleterious mutations from a population can either increase or decrease the fitness of a population, and is not generally recommended as a technique to improve the fitness of captive bred animals.
It has been noted that many angiosperms (flowering plants) can self-fertilise for several generations and suffer little from inbreeding depression. This is very useful for species which disperse widely and can therefore find themselves growing in a novel environment with no conspecifics present. Polyploidy (having more than two paired sets of each chromosome), which is prevalent in angiosperms, ferns and a select few animal taxa, accounts for this. By having several copies of a chromosome, as oppose to two, homozygosity is less likely to occur in inbred offspring. This means that recessive deleterious alleles are not expressed as frequently as with many copies of a chromosome, it is more likely that at least one will contain a functional allele.
Selection for heterozygosity
Inbreeding depression has also been found to occur more gradually than predicted in some wild populations, such as in the highly inbred population of Scandinavian wolves. This appears to be due to a selection pressure for more heterozygous individuals, which generally are in better condition and so are more likely to become one of the few animals to breed and produce offspring.
- Outbreeding depression
- Hybrid vigour
- Genetic purging
- Minimum viable population
- Population genetics
- Backward evolution
- Insular dwarfism
- Island gigantism
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