FastMeanKinship
FastMeanKinship is an adapted algorithm by Colleau (Genet. Sel. Evol. 34 (2002) 409-421) that calculates the mean kinship of many individuals with a group simultaneously, rather than one by one for each individual.
About Mean Kinship
Genetic diversity within populations –such as breeds, varieties, herds, zoo populations, national and local subpopulations– can be changed by the selection of breeding animals for the next generation. Consequently, the selection of animals to be removed from or added to the population is crucial to maintain genetic diversity. Especially in small populations, loss of genetic diversity can be high when all young animals, forming the future breeding pool, are highly related. The popular sire syndrome, whereby the same small group of sires and their family members are used over and over, is a strong risk factor for loss of genetic diversity. This loss of genetic diversity can increase inbreeding rates, increase inbreeding depression and increase the expression of, often severe or even lethal, genetic defects. Consequently, tools that can help to decide which animals should be selected for future breeding are required. One such tool is the use of Mean kinships.
Manual
FastMeanKinship
Factsheet
Mean Kinship: Theory and practice
Genetic diversity and kinship in populations
Two individuals can be related, and the more related they are, the more DNA variants they share. The degree of relatedness is quantified by the coefficient of relatedness (r, also coefficient of consanguinity) which can be seen as the percentage of DNA that two individuals share because of their common descent. The coefficient of kinship (f) is equal to half the relatedness coefficient (r). The reasons for using both kinship and relatedness coefficient are historical.
The kinship between two individuals can vary from 0, no DNA in common due to descent, up to 1 (or 100%) when all DNA is identical. The average kinship (or relatedness) of all the individuals in a population is a measure of the genetic diversity in a population. The higher the average kinship, the lower the genetic diversity. 1 minus average kinship in a population is a measure of the genetic diversity in the population.
Kinship coefficient of two parents is by definition the same as inbreeding coefficient (F) of each of their offspring. Consequently, the average kinship in the current group of active breeding animals largely determines the inbreeding level in the next generation in case of random mating. Selecting more related individuals for breeding thus increases the inbreeding rate of the population. The kinship and inbreeding coefficients can be calculated with pedigree data or based on DNA information. In the latter case, there are multiple methods that can be used to calculate F and f, and resulting values not only depend on the method but tend to be dependent on the marker set used as well.
Mean kinship of individuals
In general, Mean Kinship (MK) is calculated for an individual or breeding candidate to estimate how genetically related it is to the active breeding population, i.e. the individuals that are available as parents. Therefore, the Mean Kinship (MK) of an individual is the mean of the kinship coefficients of that individual with a group of other individuals. If a candidate has a low MK, its genetic variants are relatively underrepresented in the group and it contributes more to genetic diversity in the population than an individual with a high MK.