Genetic distance and classification of domestic animals using genetic markers

Genetic distance is used to classify and elucidate the evolutionary relationship between populations, such as species, which have been diverging for a long period. The properties of genetic distance measures in livestock classification have hitherto not been investigated. We used simulation studies to compare the accuracy of eight genetic distance measures to classify recently diverged populations. The effect of varied population sizes from generation to generation were also taken into account. Comparatively better results are obtained from Nei's standard distance with two alleles at each locus and from Nei's D_A distance with four alleles at each locus under various conditions. However, the difference in accuracy among distance measures was small and very high correlations were shown. The number of alleles at each locus had a greater effect on accuracy than the number of loci or type of distance measures. It indicates that highly polymorphic markers, such as DNA microsatellite, are powerful tool to improve the accuracy in classification of domestic animals. The six distance measures had a linear relationship with generation number at constant population size. None of the distance measures, however, showed a linear relationship when population size varied. The effect of fluctuating population size on the average distance was obvious over the first few generations but declined when the number of generations was increased.