Comparison of traditional and novel genetic diversity metrics based on the metafounders methodology

To relate base populations in genomic evaluations, the theory of metafounders has been developed during the last decade. From this theory, relationships within and between populations can be estimated with the gamma parameter. Recently, it has been demonstrated that several genetic diversity metrics such as fixation index (Fst), Nei’s minimum genetic distance (D), and population inbreeding coefficients based on homozygosity (Fhom), drift (Fdrift) or average heterozygosity (Fb) can be estimated based on this gamma matrix. However, how these derived formulas behave in real populations, compared to their traditionally estimated counterparts, has not yet been studied. Therefore, the objective of this study is to compare traditional and gamma-based genetic diversity parameters. For this purpose, we will apply formulas found in Table 1 to different cattle populations. Formulas derived from the gamma parameter assume allelic frequencies of 0.5 in the base population. Unless the formulas are more robust to changes in allelic frequencies than expected, we should probably expect different results between the traditional and novel metrics based on gamma.