Comparisons of Different Colonies

Breeders often want to maintain the same outbred stock at different locations and need some way of testing whether the colonies have drifted apart. The above protocol could be used to compare colonies. Assuming a set of background and segregating markers has been chosen, then samples of about 20 animals could be taken from each colony and tested at the same 10 loci. The invariant loci should be the same in both colonies. The segregating loci could be used to compare the total number of heterozygous animals in the two samples, using a contingency chi-squared test or comparing two proportions using the normal approximation of the binomial distribution. These tests are described in most statistical textbooks and are available in several computer statistical packages, such as MINITAB.

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