Livestock breeders often practice inbreeding to "fix" desirable characteristics within a population. However, they must then cull unfit offspring, especially when trying to establish the new and desirable trait in their stock.
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:
Natural selection works to remove individuals who acquire the above types of traits from the gene pool. Therefore, many more 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 stresses, the deleterious inherited traits are culled.
The cheetah once was reduced by disease, habitat restriction, overhunting of prey, competition from other predators (primarily lions, competition from human land use, etc.) to a very small number of individuals. All cheetahs now come from this very small gene pool. Should a virus appear that none of the cheetahs have resistance to, 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.
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.
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.
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 inoculate the South American sea lion from extinction.
Natural breedings include inbreeding by necessity, and most animals only migrate when necessary. In many cases, the closest living mate is a mother, sister, grandmother, father, grandfather... In all cases the environment presents stresses to select or remove those individuals who cannot survive because of illness from the population.
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 then are being "line bred". Also, in some populations such as the Crater lions, it is known that a population bottleneck has occurred. Far greater genetic heterozygosity than what was expected was found. 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 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.
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.
The 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 and the tabular method .
Typical inbreeding percentages are as follows:
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.
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 quote 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 (http://aipl.arsusda.gov/main/data.html#gtrend). 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, a specific form of inbreeding, is accomplished through breedings of cousins, aunt to nephew, half brother to half sister. This was used to isolate breeds within the companion and livestock industry. For instance an animal with a desirable colour is bred back within the lines with identified selection traits whether it be milk production or adherence to breed standard of appearance or behavior. Breeders must then cull unfit individuals, and in some cases the breeders will then outbreed to increase the level of genetic diversity. Again casual breeding is problematic as it is without the requisite culling of individuals who are either maladaptive, not to breed standard or carriers of poor genetic material that must be removed from a healthy breeding program.
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's 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.
The two dog sites above also point out that in the registered dog population, the onset of large numbers of casual breeders has cooresponded 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 also was cited in the quotes above on cattle raising.
There is a greater amount of inbreeding within royalty than there is in the population as a whole. Among genetic populations that are isolated, opportunities for exogamy are reduced, however may not intend to inbreed. Isolation may be geographical, leading to inbreeding among people in remote mountain valleys. Or isolation may be social, induced by the lack of appropriate partners, such as Protestant princesses for Protestant royal heirs, in which case inbreeding is desired. Since the late Middle Ages, it is the urban middle class that has had the widest opportunity for outbreeding and the least desire to inbreed.
It has long been debated on whether inbreeding caused some of the problems among some of the family members of some royal lines, most notably centered around Charles II of Spain, who was mentally retarded. It is thought that his genetic makeup was so thoroughly degenerated that he could not properly chew food.
Other examples of royal family inbreeding include:
Inbreeding in European royal families has declined slightly in relation to the past. This is likely due to clear scientific evidence of genetic degeneration. Instead, inter-nobility marriage as a method of forming political alliances among elite power-brokers has taken precedence. These ties were often sealed only upon the birth of progeny within the arranged marriage. Marriage was seen as a union of lines of nobility, not of a contract between individuals as it is seen today. However, inbreeding within Royal bloodlines is still alive and well.
A recent study in Iceland by the deCODE genetics company, published by the journal Science, found that third cousins had the highest rate of genetic success & children, suggesting a minimal relationship to each other is favorable in humans pairing off and reproducing.