Reports - Gene Diversity Metrics

Gene Diversity Metrics Report
Gene Diversity Metrics Report

To view this report, choose Gene Diversity Metrics from the report selector (at the top of the report pane) in the main window.

PedScope can tabulate various gene diversity metrics of a group of animals as used in the separate mate recommendations report.

Typically this would be used to study a group of animals that make up a 'current population' or otherwise a group from which future breeding is to occur.

In the description that follows, 'current population' means the group of tagged animals from the main record table.

Column Symbol Description
Mean Kinship MK

The mean kinship of an animal is the mean of its kinship coefficients with every animal in the current population, including itself. The lower the MK value, the less an animal is related to other members of the current population, 'on average'.

Informally, it makes sense to breed from such animals in order to preserve genetic diversity.

Note that two animals with low MK may nevertheless be closely related themselves, so selecting matings on this basis alone can still give rise to highly inbred offspring.

Kinship Value KV

Kinship value is simply a weighted variant of the mean kinship, weighted according to the age structure of the population.

For this to work, the program needs additional information: (a) the date of birth of each animal (from which its age is determined), and (b) the reproductive values of different aged animals, as relevant to the particular species (so-called 'Vx' values) [see Fisher, R. The Genetical Theory of Natural Selection, 1930].

Clearly, an animal in the current population that is no longer reproductive e.g. a female nearing the end of her life, is of no value in maintaining future genetic diversity, and yet calculations based on MK do not take this into account. Likewise it follows that if you have two animals with the same, low, mean kinship, but one is older than the other, then a greater priority might be given to breeding from the older animal first, to lessen the risk that its genes are lost for good.

Using KV in such mating decisions allows these factors to be incorporated into the mate ranking algorithm, whereas ranking by MK makes no distinction.

KV can be used in the mate recommendations report.

You can enter Vx data using the Document Settings window - see Vx Data.

Genome Uniqueness GU

An animal's genome uniqueness is the likelihood that it contains founder alleles that are not present in any other animal (normally) in the current population.

Informally, if an animal is the only one carrying a particular founder's genes, then you'd likely want to breed from that animal so as not to lose those genes from the population forever.

We say 'normally' here because you can actually configure what is meant by genome uniqueness, in that you can define that number of animals in the current population for which, if any given founder's alleles are only present in that number, or fewer, of the current population, then it is considered 'unique'.

A better term might be 'genome rarity' or 'founder rarity' but the term 'genome uniqueness' is already established in the literature. Genome uniqueness is determined using a gene drop analysis.

Pedigree Unknown PU

The 'pedigree unknown' value for an animal is that proportion of its founders that are unknown. This relates only to situations where an ancestor has one parent missing in the ancestry; such missing ancestors are considered to be unknown founders, missing from the pedigree.

Sometimes it can be desirable to avoid breeding from animals with a large degree of unknown pedigree, for this reason the PU value can be used in the composite mate ranking algorithm.


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