Inbreeding

Inbreeding is the reproduction from the mating of two genetically related parents. Inbreeding results in increased homozygosity, which can increase the chances of offspring being affected by recessive or deleterious traits. This generally leads to a decreased fitness of a population, which is called inbreeding depression. A person who results from inbreeding is referred to as an inbred.

Livestock breeders often practice controlled breeding to eliminate undesirable characteristics within a population, which is also coupled with culling of what is considered unfit offspring, especially when trying to establish a new and desirable trait in the stock.

In plant breeding, inbred lines are used as stocks for the creation of hybrid lines to make use of the effects of heterosis. Inbreeding in plants also occurs naturally in the form of self-pollination.

Results
Inbreeding may result in a far higher phenotypic expression of deleterious recessive genes within a population than would normally be expected.[1] As a result, first-generation inbred individuals are more likely to show physical and health defects, including: Many individuals in the first generation of inbreeding will never live to reproduce. Over time, with isolation such as a population bottleneck caused by purposeful (assortative) breeding or natural environmental factors, the deleterious inherited traits are culled.
 * Reduced fertility both in litter size and sperm viability
 * Increased genetic disorders
 * Fluctuating facial asymmetry
 * Lower birth rate
 * Higher infant mortality
 * Slower growth rate
 * Smaller adult size
 * Loss of immune system function

Island species are often very inbred, as their isolation from the larger group on a mainland allows for natural selection to work upon their population. This type of isolation may result in the formation of race or even speciation, as the inbreeding first removes many deleterious genes, and allows expression of genes that allow a population to adapt to an ecosystem. As the adaptation becomes more pronounced the new species or race radiates from its entrance into the new space, or dies out if it cannot adapt and, most importantly, reproduce.[2]

The reduced genetic diversity that results from inbreeding may mean a species may not be able to adapt to changes in environmental conditions. Each individual will have similar immune systems, as immune systems are genetically based. Where a species becomes endangered, the population may fall below a minimum whereby the forced interbreeding between the remaining animals will result in extinction.

Natural breedings include inbreeding by necessity, and most animals only migrate when necessary. In many cases, the closest available mate is a mother, sister, grandmother, father, grandfather... In all cases the environment presents stresses to remove those individuals who cannot survive because of illness from the population.

There was an assumption that wild populations do not inbreed; this is not what is observed in some cases in the wild. However, in species such as horses, animals in wild or feral conditions often drive off the young of both genders, thought to be a mechanism by which the species instinctively avoids some of the genetic consequences of inbreeding.[3] In general, many mammal species including humanity's closest primate relatives avoid close inbreeding possibly due to the deleterious effects.[4]

Examples
The cheetah was once reduced by disease, habitat restriction, overhunting of prey, and competition from other predators to a very small number of individuals.[5] [6] All cheetahs now come from this very small gene pool. Should a virus appear to which none of the cheetahs has resistance, extinction is always a possibility. Currently, the threatening virus is feline infectious peritonitis, which has a disease rate in domestic cats from 1–5%; in the cheetah population it is ranging between 50% to 60%. The cheetah is also known, in spite of its small gene pool, for few genetic illnesses.

In the South American sea lion, there was concern that recent population crashes would reduce genetic diversity. Historical analysis indicated that a population expansion from just two matrilineal lines were responsible for most individuals within the population. Even so, the diversity within the lines allowed for great variation in the gene pool that may help to protect the South American sea lion from extinction.[7]

In lions, prides are often followed by related males in bachelor groups. When the dominant male is killed or driven off by one of these bachelors, a father may be replaced with his son. There is no mechanism for preventing inbreeding or to ensure outcrossing. In the prides, most lionesses are related to one another. If there is more than one dominant male, the group of alpha males are usually related. Two lines are then being "line bred". Also, in some populations such as the Crater lions, it is known that a population bottleneck has occurred. Researchers found far greater genetic heterozygosity than expected.[8] In fact, predators are known for low genetic variance, along with most of the top portion of the tropic levels of an ecosystem.[9] Additionally, the alpha males of two neighboring prides can potentially be from the same litter; one brother may come to acquire leadership over another's pride, and subsequently mate with his 'nieces' or cousins. However, killing another male's cubs, upon the takeover, allows for the new selected gene complement of the incoming alpha male to prevail over the previous male. There are genetic assays being scheduled for lions to determine their genetic diversity. The preliminary studies show results inconsistent with the outcrossing paradigm based on individual environments of the studied groups.[8]

Calculation
Main article: Coefficient of relationshipThe inbreeding is computed as a percentage of chances for two alleles to be identical by descent. This percentage is called "inbreeding coefficient". There are several methods to compute this percentage, the two main ways are the path method[10] and the tabular method.[11] [unreliable source?]

Typical inbreeding coefficient percentages are as follows, assuming no previous inbreeding between any parents: An inbreeding calculation may be used to determine the general genetic distance among relatives by multiplying by two, because any progeny would have a 1 in 2 risk of actually inheriting the identical alleles from both parents.
 * Father/daughter, mother/son or brother/sister → 25% (1⁄4)
 * Grandfather/granddaughter or grandmother/grandson → 12.5% (1⁄8)
 * Half-brother/half-sister → 12.5% (1⁄8)
 * Uncle/niece or aunt/nephew → 12.5% (1⁄8)
 * Great-grandfather/great-granddaughter or great-grandmother/great-grandson → 6.25% (1⁄16)
 * Half-uncle/niece or half-aunt/nephew → 6.25% (1⁄16)
 * First cousins → 6.25% (1⁄16)
 * First cousins once removed or half-first cousins → 3.125% (1⁄32)
 * Second cousins or first cousins twice removed → 1.5625% (1⁄64)
 * Second cousins once removed or half-second cousins → 0.78125% (1⁄128)
 * Third cousins or second cousins twice removed → 0.390625% (1⁄256)
 * Third cousins once removed or half-third cousins → 0.1953125% (1⁄512)

For instance, the parent/child or sibling/sibling relationships have 50% identical genetics.

Domestic animals
An intensive form of inbreeding where an individual S is mated to his daughter D1, granddaughter D2 and so on, in order to maximise the percentage of S's genes in the offspring. D3 would have 87.5% of his genes, while D4 would have 93.75%.[12] Breeding in domestic animals is assortative breeding primarily (see selective breeding). Without the sorting of individuals by trait, a breed could not be established, nor could poor genetic material be removed. Homozygosity is the case where similar or identical alleles combine to express a trait that is not otherwise expressed (recessiveness). Inbreeding, through homozygosity, exposes recessive alleles. Inbreeding is used to reveal deleterious recessive alleles, which can then be eliminated through assortative breeding or through culling.

Inbreeding is used by breeders of domestic animals to fix desirable genetic traits within a population or to attempt to remove deleterious traits by allowing them to manifest phenotypically from the genotypes. Inbreeding is defined as the use of close relations for breeding such as mother to son, father to daughter, brother to sister.

Breeders must cull unfit breeding suppressed individuals and/or individuals who demonstrate either homozygosity or heterozygosity for genetic based diseases.[13] The issue of casual breeders who inbreed irresponsibly is discussed in the following quotation on cattle: ''Meanwhile, milk production per cow per lactation increased from 17,444 lbs to 25,013 lbs from 1978 to 1998 for the Holstein breed. Mean breeding values for milk of Holstein cows increased by 4,829 lbs during this period.[14] High producing cows are increasingly difficult to breed and are subject to higher health costs than cows of lower genetic merit for production'' (Cassell, 2001). Intensive selection for higher yield has increased relationships among animals within breed and increased the rate of casual inbreeding. ''Many of the traits that affect profitability in crosses of modern dairy breeds have not been studied in designed experiments. Indeed, all crossbreeding research involving North American breeds and strains is very dated (McAllister, 2001) if it exists at all''.<sup class="reference" id="cite_ref-14">[15] Linebreeding is a form of inbreeding. There is no clear distinction between the two terms, but linebreeding may encompass crosses between individuals and their descendants or two cousins.<sup class="reference" id="cite_ref-TaveInbreeding_11-1">[12] <sup class="reference" id="cite_ref-UMissouri_15-0">[16] This method can be used to increase a particular animal's contribution to the population.<sup class="reference" id="cite_ref-TaveInbreeding_11-2">[12] While linebreeding is less likely to cause problems in the first generation than does inbreeding, over time, linebreeding can reduce the genetic diversity of a population and cause problems related to a too-small genepool that may include an increased prevalence of genetic disorders and inbreeding depression.<sup class="Template-Fact" style="white-space:nowrap;">[citation needed]

Outcrossing is where two unrelated individuals have been crossed to produce progeny. In outcrossing, unless there is verifiable genetic information, one may find that all individuals are distantly related to an ancient progenitor. If the trait carries throughout a population, all individuals can have this trait. This is called the founder effect. In the well established breeds, that are commonly bred, a large gene pool is present. For example, in 2004, over 18,000 Persian cats were registered.<sup class="reference" id="cite_ref-16">[17] A possibility exists for a complete outcross, if no barriers exist between the individuals to breed. However it is not always the case, and a form of distant linebreeding occurs. Again it is up to the assortative breeder to know what sort of traits both positive and negative exist within the diversity of one breeding. This diversity of genetic expression, within even close relatives, increases the variability and diversity of viable stock.<sup class="reference" id="cite_ref-17">[18]

The two dog sites above also point out that in the registered dog population, the onset of large numbers of casual breeders has corresponded with an increase in the number of genetic illnesses of dogs by not understanding how, why and which traits are inherited. The dog sites indicate that the largest percentage of dog breeders in the US are casual breeders. Therefore the investment in a papered animal,with an expected short term profit, motivates some to ignore the practice of culling. Casual breeders in companion animals often ignore breeding restrictions within their contracts with source companion animal breeders. The casual breeders breed the very culls that a genetics based breeder has released as a pet. The casual breeder was also cited in the quotes above on cattle raising.

Laboratory animals
Systematic inbreeding and maintenance of inbred strains of laboratory mice and rats is of great importance for biomedical research. The inbreeding guarantees a consistent and uniform animal model for experimental purposes and enables genetic studies in congenic and knock-out animals. The use of inbred strains is also important for genetic studies in animal models, for example to distinguish genetic from environmental effects.

Genetic disorders
Autosomal recessive disorders occur in individuals who have two copies of the gene for a particular recessive genetic mutation. Except in certain rare circumstances, such as new mutations or uniparental disomy, both parents of an individual with such a disorder will be carriers of the gene. These carriers do not display any signs of the mutation and may be unaware that they carry the mutated gene. Since relatives share a higher proportion of their genes than do unrelated people, it is more likely that related parents will both be carriers of the same recessive gene, and therefore their children are at a higher risk of a genetic disorder. The extent to which the risk increases depends on the degree of genetic relationship between the parents: The risk is greatest when the parents are close relatives and lower for relationships between more distant relatives, such as second cousins, though still greater than for the general population.<sup class="reference" id="cite_ref-18">[19]

Children of parent-child or sibling-sibling unions are at increased risk compared to cousin-cousin unions.

Some inbreeding may enhance fertility rate
A recent study in Iceland by the deCODE genetics company, published by the journal Science, found that third cousins produced more children and grandchildren, suggesting that "in spite of the fact that bringing together two alleles of a recessive trait may be bad, there is clearly some biological wisdom in the union of relatively closely related people".<sup class="reference" id="cite_ref-28">[29] For hundreds of years, inbreeding was historically unavoidable in Iceland due to its then tiny and isolated population.