Inbreeding is reproduction from the mating of pairs who are closely related genetically. Inbreeding results in 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. An individual who results from inbreeding is referred to as inbred. The avoidance of expression of deleterious recessive alleles caused by inbreeding is thought to be the main selective force maintaining the outcrossing aspect of sexual reproduction. (See also Inbreeding depression.)
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.
Inbreeding may result in a far higher phenotypic expression of deleterious recessive genes within a population than would normally be expected. As a result, first-generation inbred individuals are more likely to show physical and health defects, including:
- 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
Inbreeding can occur just because a small population has been isolated during some time, so that all breeding individuals became genetically related. It can also occur in a large population if individuals tend to mate their relatives, instead of mating at random.
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.
Island species are often very inbred, as their isolation from the larger group on a mainland allows 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.
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, brother, or 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. In general, many mammal species including humanity's closest primate relatives avoid close inbreeding possibly due to the deleterious effects.
Although there are several examples of inbred populations of wild animals, the negative consequences of this inbreeding are poorly documented.
The cheetah has very low levels of genetic variation, suggesting a population bottleneck (of unknown cause) and subsequent inbreeding sometime in the past several thousand years.  All cheetahs now come from this small gene pool. Theoretically, their lack of genetic variance could put cheetahs at greater risk from infectious diseases. One outbreak of feline infectious peritonitis in a captive cheetah population which was studied over a 5-year period had a morbidity rate of over 90%, and a mortality rate of 60%. Conversely, inbreeding can purge a population of deleterious alleles, and the cheetah is known 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 great variation in the gene pool that may help to protect the South American sea lion from extinction.
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. In fact, predators are known for low genetic variance, along with most of the top portion of the tropic levels of an ecosystem. 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 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.
Measures of Inbreeding: Definitions and some values
The inbreeding level of an individual A is defined as the probability F(A) that both alleles in one locus are derived from the same gene in an ancestor. Two alleles derived from the same gene in an ancestor are said to be identical by descent. This probability F(A) is called the "inbreeding coefficient".
Another useful measure that describes the extent to which two individuals are relatives (say individuals A and B) is their coancestry coefficient f(A,B), which gives the probability that, taking one random allele from A and another random allele from B, both are identical by descent. This is also denoted kinship coefficient between A and B.
A particular case is the self-coancestry of individual A with itself, f(A,A), which is the probability that taking one random allele from A and then, independently and with replacement, another random allele also from A, both are identical by descent. Since they can be identical by descent by sampling the same allele or by sampling both alleles that happen to be identical by descent, we have f(A,A) = 1/2 + F(A)/2.
Both the inbreeding and the coancestry coefficients can be defined for specific individuals or as average population values. They can be computed from genealogies or estimated from the population size and its breeding properties,but all methods assume no selection or are limited to neutral alleles.
Typical coancestries between relatives are as follows:
- Father/daughter, mother/son or brother/sister → 25% (1⁄4)
- Grandfather/granddaughter or grandmother/grandson → 12.5% (1⁄8)
- Half-brother/half-sister, Double cousins → 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)
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. 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. 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.
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. This method can be used to increase a particular animal's contribution to the population. 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.
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. 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.
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.
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.
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.
Children of parent-child or sibling-sibling unions are at increased risk compared to cousin-cousin unions.
Royalty and nobility
Inter-nobility marriage was used as a method of forming political alliances among elites. These ties were often sealed only upon the birth of progeny within the arranged marriage. Thus marriage was seen as a union of lines of nobility, not of a contract between individuals as it is seen today. Royal intermarriage was often practised to protect property, wealth and position, but over time some dynasties became very closely inter- and intra-linked genetically:
- In ancient Egypt, royal women carried the bloodlines and so it was advantageous for a pharaoh to marry his sister or half-sister; in such cases a special combination between endogamy and polygamy is found. Normally the old ruler's eldest son and daughter (who could be either siblings or half-siblings) became the new rulers. All rulers of the Ptolemaic dynasty from Ptolemy II were married to their brothers and sisters, so as to keep the Ptolemaic blood "pure" and to strengthen the line of succession. Cleopatra VII (also called Cleopatra VI) and Ptolemy XIII, who married and became co-rulers of ancient Egypt following their father's death, are the most widely known example.
- Among European monarchies Jean V of Armagnac formed a rare brother-sister relationship. Also other royal houses, such as the Wittelsbachs had marriages among aunts, uncles, nieces and nephews. The British royal family had several marriages as close as the first cousin, but none closer.
- One of the most famous examples of a genetic trait aggravated by royal family intermarriage was the House of Habsburg, which inmarried particularly often and is known for the mandibular prognathism of the Habsburger (Unter) Lippe (otherwise known as the 'Habsburg jaw', 'Habsburg lip' or 'Austrian lip'"). This was typical for many Habsburg relatives over a period of six centuries. The condition progressed through the generations to the point that the last of the Spanish Habsburgs, Charles II of Spain, could not properly chew his food.
- Besides the jaw deformity, Charles II also had a huge number of other genetic physical, intellectual, sexual, and emotional problems. It is speculated that the simultaneous occurrence in Charles II of two different genetic disorders: combined pituitary hormone deficiency and distal renal tubular acidosis could explain most of the complex clinical profile of this king, including his impotence/infertility which in the last instance led to the extinction of the dynasty.
- Francis II from the house of Habsburg-Lorraine married his double cousin Maria Theresa of Naples and Sicily, and several of their children had potentially genetic health problems. Their daughter Marie Anne is said to have suffered from a hideous facial deformity and also being mentally deficient. Their son Ferdinand who became an emperor was also mentally deficient and suffered from Hydrocephalus (meaning water head) which resulted in an enlarged head. He also had several seizures daily. Of course he never was capable of leading the empire and relied on others and abdicated during the difficulties of the Revolutions of 1848. When informed of the revolution he supposedly asked “But are they allowed to do that?” (Viennese German: Ja, dürfen's denn des?) Also five of the children of Francis II died in infancy or early childhood.
- Another famous genetic disease that circulated among European royalty was hemophilia. This spread to the royal families of Russia and Spain, and was a factor in the overthrow of both. Because the progenitor, Queen Victoria, was in a first cousin marriage, it is often mistakenly believed that the cause was consanguinity (inbreeding). However, this disease (in males) is generally not aggravated by cousin marriages, although rare cases of hemophilia in girls (though not including Victoria) can occur from the union of hemophiliac men and their cousins.
- Some Peruvian Sapa Incas married their sisters; in such cases a special combination between endogamy and polygamy is found. Normally the son of the old ruler and the ruler's oldest (half-)sister became the new ruler. The Inca had an unwritten rule that the new ruler must be a son of the Inca and his wife and sister.
- The Chakri Dynasty of Thailand has included marriages between cousins as well as more close relatives. The current king, Bhumibol Adulyadej is a first-cousin once removed of his wife, Sirikit, the two being respectively a grandson and a great-granddaughter of Chulalongkorn. The parents of the king's father, Mahidol Adulyadej, were half-siblings, both being children of Mongkut by different mothers.
- Queen Elizabeth II and her husband Prince Philip, Duke of Edinburgh are third cousins as a result of both being directly descended from Queen Victoria; as well as second cousins once removed as a result of being directly descended from Christian IX of Denmark.
Today, intermarriage within European royal families has declined in relation to the past along with the power and prevalence of noble families and their importance in international affairs.
Possible increase of fertility
A recent study in Iceland by the deCODE genetics company, published by the journal Science, found that third cousins produced more children and grandchildren than more distant marriages, suggesting that "in spite of the fact that bringing together two alleles of a recessive trait may be bad, there may be some biological wisdom in the union of relatively closely related people". For hundreds of years, inbreeding was historically unavoidable in Iceland due to its then tiny and isolated population.
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- Coefficient of relationship
- Cousin marriage
- Evolution of sexual reproduction
- Genetic purging
- Genetic sexual attraction
- Heterozygote advantage
- Identical ancestors point
- Inbreeding depression
- Insular dwarfism
- Intellectual inbreeding
- List of coupled cousins
- Outbreeding depression
- Prohibited degree of kinship
- Selective breeding
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