Purebred dog and pedigreed cat breeds evolved over time through selective breeding to standards. These standards may have been conformational, behavioral, or working standards. The standards were usually not organized and written at the inception of the breed, but instead written at a later date of breed organization. Written standards are often updated over time - sometimes to clarify and sometimes to accommodate changes in the breed. Changes in breed standards may change the selective pressures on what was bred for in the past, or what may be bred for in the future.

The pedigree record of a breed at its inception may be muddled with individuals of unknown ancestry, or just individuals that fit the conformational or working standard of the breed. These are the breed's foundation stock. It is only at a time after an official "establishment" of a breed that a stud book is assembled and soon closed to additional individuals of unknown ancestry. Some cat breeds maintained open stud books for a period of time that allowed for the continued registration of cats adhering to a conformational phenotype. This allowed added diversity to their gene pools.

Some breeds are formed through inbreeding on small kindreds of individuals who possess a particular phenotypic trait. When original breed records are discovered, it is found that several familial lines of ancestry during breed formation are often abandoned due to the expression of deleterious or undesirable traits. It is only the lines that produce the desired characteristics and thrive through matings and generations of breeding that become the mainstream ancestral "founders" of a breed.

Some breeds are formed through the cross-breeding of individuals from other established breeds. These individuals would be members of established breeds that have already gone through the original breeding and purging process. The new breed would still go through the typical expansion process.

The pedigree record of breeds shows that after formation, the breed will go through a significant population expansion associated with increased average inbreeding coefficients. The Birman cat breed and Cavalier King Charles Spaniel breeds are shown as examples.

Inbreeding coefficients show the genetic relatedness of the parents of individuals. Average inbreeding coefficients of breed populations show trends in breed evolution. You can look at coefficients two different ways - a total average inbreeding coefficient that accounts for all generations, and an average inbreeding coefficient based on a set number of generations. The total generational average inbreeding coefficient can only increase over time, unless importation from unrelated stock is added to the gene pool. A 10 generation average inbreeding coefficient calculated from generation to generation (based on decade of birth) will decrease in an expanding population where the average relatedness of breeding pairs is less than the previous generation. The single most important factor increasing average 10 generation inbreeding coefficients is the popular sire syndrome. With this, the breed gene pool truncates around a popular sire line, with the resultant loss of genetic influence of other quality male lines.

Molecular genetic studies of the chromosomal structure of dog breeds show large haplotype blocks (identical sections of chromosomes) and linkage disequilibrium (LD) representing the results of inbreeding and purging during breed development (vonHoldt BM, et al. Genome Res. 2011;21:1294–1305). Studies of dog breeds estimate that they lose on average 35% of their genetic diversity through breed formation (Gray MM, et al. Genetics. 2009;181:1493-1505).

Molecular genetic studies of wolf populations over time mirror those of breed formation. A study of Finnish Grey Wolves showed significant genetic diversity early on, due to migration from Russian wolves. The population then went through a significant population expansion that coincided with increased average inbreeding coefficients, decreased heterozygosity, and increases in the number of family lines as well as effective breeding population size (Jansson E, et al. Mol Ecol. 2012;21:5178-5193).

Modern breeds of cats and dogs have gone through the above-mentioned genetic selection and are in various stages of expanding their breeding population and gene pools. Some breeds may have small effective population sizes and high homozygosity. However, if their offspring are generally healthy, their population can grow and expand. They are at stages of breed development where more populous breeds were earlier in their development.

Population expansion is an important aspect of breed development and maintenance. It allows on average the successive mating of individuals less related than the prior generation. It allows the creation of new "family lines" and within-breed diversity. Population contraction is detrimental to breed maintenance due to the loss of breeding lines and genetic diversity. Maintaining adequate numbers of breeders and matings is important to breed vitality and survival.

As a consequence of breed formation, dog and cat breeds have high homozygosity. This is the nature of breed formation. Homozygosity by itself is not detrimental to breeds unless they carry a high genetic load of deleterious recessive genes. Some breeds may show decreased litter size, increased neonatal mortality, or shorter average life spans with increases in inbreeding coefficients. These "inbreeding depression" effects are due to the homozygous expression of specific deleterious genes that cause specific disease. Direct selection against these genes and phenotypes is required to improve breed health. If breed members are dying younger, what specific disease(s) is occurring in these individuals? If the breed shows issues with fertility and fecundity, then breeders should specifically select for increased fertility and fecundity.

Some advocates of dog and cat breeding call for organized outbreeding programs that mate the least-related individuals to each other. These mirror the species survival plans (SSP) formulated for rare and endangered species. The result of this effort will produce a randomized population and within-breed increases in heterozygosity regarding gene distribution. However, this will have no effect on the frequency of deleterious genes. Genes for breed-related genetic disorders that are already dispersed in the gene pool will continue to produce affected individuals in a random fashion. This type of breeding plan is also self-limiting, because as you remove the genetic differences between individuals, it becomes increasingly harder to outbreed (find mates that are genetically unlike each other). A healthy and diverse breed gene pool should have many outbred clusters as well as different linebred families.

The genetic tools of linebreeding and outbreeding should be used for specific purposes. Breeders may use different breeding tools with each mating that are either closer (linebreeding) or more distant (outbreeding) than the average in the population based on their needs. Linebreeding concentrates the genes of specific ancestors. Outbreeding brings in genes that are not present in the mate. When breeders are each performing matings that are a little different from each other - some linebreeding in one line, some outbreeding, some linebreeding in another line, etc. - it maintains a diverse breed population.

The only way to decrease the frequency of deleterious genes in a population (and increase the frequency of favorable genes) is through direct selection against (and for) those genes through genetic testing and phenotypic evaluation. The rate and degree of genetic improvement through selection is directly proportional to the amount of variation that exists between individuals within the breed. Randomizing a population through outbreeding decreases the ability to apply selective pressure for genetic improvement. Selective pressure requires lines of individuals who are unlike each other.

Some studies bemoan the homozygosity found in breeds, and call for selection to increase minor frequency alleles and haplotypes. Molecular genetic tools can identify these, but in most cases the phenotypic effects of increasing their frequency are unknown. It is possible that genetic selection for quality and against undesirable traits reduced the frequency of these genes. Blindly selecting for them without knowing their effect could significantly reverse selection-based breed improvement.

When breeds show high frequency of genetic disease, or significantly diminished fertility and fecundity, they may have too high a genetic load of disease liability genes. In extreme instances, they may require a SSP-type plan, opening the study book to importation, or crossbreeding to other related breeds. However, most breeds do not find themselves in such dire situations, and only require proper selection to improve their gene pools and genetic health.

The following conclusions can be made concerning breed evolution and health:

 The effects of inbreeding (homozygosity, large haplotype blocks and increased linkage disequilibrium) are a natural consequence of breed formation.

 Healthy breed gene pools require expanding, or large stable populations.

 Breed health should be measured based on regular surveys of health and reproduction.

 Genetic selection for breed characteristics should avoid disease-related phenotypes.

 Genetic selection for breed health should be directed against specific disease liability genes and phenotypes.

 Breeders should avoid the overuse of popular sires - the most significant factor in limiting breed genetic diversity.