Inbreeding
Inbreeding is breeding between close relatives, whether plant or animal. If practiced repeatedly, it often leads to a reduction in genetic diversity, and the increased gene expression of recessive traits, resulting in inbreeding depression. This may result in inbred individuals exhibiting reduced health and fitness and lower levels of fertility.
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.
In plant breeding, inbred lines are used as stocks for the creation of hybrid lines to make use of the heterosis effect. Inbreeding in plants also occurs naturally in the form of self-pollination.

# Results of inbreeding
Inbreeding may result in a far higher 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.
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 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.

# Inbreeding in domestic animals
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 (#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 problematical 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.
Inbreeding is also deliberately induced in laboratory mice in order to guarantee a consistent and uniform animal model for experimental purposes.

# Inbreeding in humans
The taboo of incest has been discussed by many social scientists. Anthropologists attest that it exists in most cultures. As inbreeding within the first generation often produces expression of recessive traits, the prohibition has been discussed as a possible functional response to the requirement of culling those born deformed, or with undesirable traits.  The eugenicists used breeding techniques to promulgate their ideas of human perfection and "illness" on all humans. Some anthropologists like Charles Davenport advocated the traditional forms of assortative breeding to form "better" human stock. Geneticists and other medical professionals have studied the effects of inbreeding in humans, noting considerable medical consequences even in the first generation.

## Royalty and nobility
The royal and noble families of Europe have close blood ties which are strengthened by royal intermarriage; the most discussed instances of interbreeding relate to European monarchies. Examples abound in every royal family; in particular, the ruling dynasties of Spain and Portugal were in the past very inbred. Several Habsburgs, Bourbons and Wittelsbachs married aunts, uncles, nieces and nephews. Even in the British royal family, which is very moderate in comparison, there has scarcely been a monarch in 300 years who has not married a (near or distant) relative. Indeed, Queen Elizabeth II and her husband Prince Philip, Duke of Edinburgh are second cousins once removed, both being descended from King Christian IX of Denmark. They are also third cousins as great-great-grandchildren of Queen Victoria of the United Kingdom. European monarchies did avoid brother-sister marriages, though Jean V of Armagnac was an exception.
It is not necessarily the case that there was a greater amount of inbreeding within royalty than there is in the population as a whole: it may simply be better documented. Among genetic populations that are isolated, opportunities for exogamy are reduced. Isolation may be geographical, leading to inbreeding among peasants in remote mountain valleys. Or isolation may be social, induced by the lack of appropriate partners, such as Protestant princesses for Protestant royal heirs. Since the late Middle Ages, it is the urban middle class that has had the widest opportunity for outbreeding.
There were at times serious long-term health and political consequences to multi-generational interbreeding in royal families between persons who were closely related.  Most notable was Charles II of Spain, who had multiple, severe disabilities largely linked to inbreeding.  Not only was he developmentally disabled and could not chew his food properly, he also could not produce children, thus leading to the collapse of his bloodline and the War of the Spanish Succession.
Other examples of royal family intermarriage include:
- Some Egyptian Pharaohs and Peruvian Sapa Incas married their sisters; in both cases we find a special combination between endogamy and polygamy. 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. He then had to marry his sister (not half-sister), which ultimately led to the catastrophic Huascars reign, culminating in a civil war and then fall of the empire.
- Cleopatra VII and Ptolemy XIII, married and named co-rulers of ancient Egypt following their father's death, were brother and sister.  Not only this, but all rulers of the Ptolemaic dynasty from Ptolemy II on engaged in inbreeding among brothers and sisters, so as to keep the Ptolemaic blood "pure".
- The House of Habsburg inmarried particularly often. Famous in this case is the Habsburger (Unter) Lippe (Habsburg jaw/Habsburg lip/"Austrian lip"), typical for many Habsburg relatives over a period of six centuries. The condition progressed through the generations to the point that last of the Spanish Habsburgs, Charles II of Spain, could not properly chew his food. (See mandibular prognathism.)
- Charles V, Holy Roman Emperor, King of Spain and Infanta Isabella of Portugal were first cousins.
- John, Crown Prince of Portugal and Joan of Habsburg were double first cousins.
- Mary, Queen of Scots and Henry Stuart, Lord Darnley were half first cousins, and 3rd cousins once removed.
- King Louis XIV of France and Infanta Maria Theresa of Spain were double first cousins.
- King William III and Queen Mary II of England were first cousins.
- King George I of Great Britain and Princess Sophia Dorothea of Celle were paternal first cousins.
- King Philip V of Spain and Princess Maria Luisa of Savoy were double second cousins.
- King Gustav III of Sweden and Princess Sophia Magdalena of Denmark were second cousins.
- King Christian VII of Denmark and Princess Caroline Matilda of Great Britain were first cousins
- King George IV of the United Kingdom and Princess Caroline of Brunswick were first cousins.
- William I, German Emperor and Princess Augusta of Saxe-Weimar were second cousins.
- Queen Victoria of the United Kingdom and Prince Albert of Saxe-Coburg and Gotha were first cousins.
- Emperor Franz Joseph I of Austria and Princess Elisabeth of Bavaria were first cousins.
- King George V of the United Kingdom and Princess Mary of Teck were second cousins once removed.
- Prince Gustav Adolf, Duke of Vasterbotten and Princess Sibylla of Saxe-Coburg and Gotha, parents of the present King Carl XVI Gustaf of Sweden, were second cousins.
- Prince Nicola Pignatelli (16481730) and Princess Giovanna Pignatelli (16661723) were half great-granduncle and half great-grandniece, representing a peculiar alliance between two relatives. Nicola was a son of Giulio Pignatelli, Prince of Noia (1587-1658) through his third wife and Giovanna a great-great-granddaughter through his first marriage.
- A similar alliance was the marriage between Princess Sophie of Sweden and Grand Duke Leopold of Baden, half-brother of her maternal grandfather.
Intermarriage in European royal families is no longer practiced as often as in the past. This is likely due to changes in the importance of marriage as a method of forming political alliances through kinship ties between nobility, as well as an awareness of modern medical science. 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. More marry for "love", best illustrated by the second marriage of Prince Charles of the United Kingdom. During the tumult of the removal, sometimes by revolution, of most lines of nobility from state government, it became less important to marry for the good of the respective monarchies and the states they governed.