Parameters based on probabilities of gene origin were used to evaluate the genetic variability of four Austrian cattle breeds. Effective numbers of founders, ancestors and remaining founder genomes showed that all four populations investigated are rather small genetically. Effective numbers of remaining founder genomes were 94 for Simmental, 41 for Braunvieh (Brown Swiss), 32 for Pinzgauer and 21 for Grauvieh (Grey cattle, a small mountain breed). As the value of 94 for Simmental was rather large in comparison with estimates from other populations in previous studies, the effect of population structure was investigated. A cosine measure of similarity based on differences in individual founder contributions to different subpopulations was defined and used for analysis. Subpopulations defined by regions were clearly more distinct for Simmental than for Braunvieh. The size of the cosine values depended on the method of calculating founder contributions and was overestimated when choosing the method not accounting for drift and bottlenecks (effective number of founders).
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