## Interact box Assortative mating and genotype frequencies

The impact of assortative mating on genotype frequencies can be simulated in PopGene.S2. The program models several non-random mating scenarios that can be selected under the Mating Models menu. The results in each case are presented on a De Finetti diagram, where genotype and allele frequencies can be followed over multiple generations.

Start with the Positive w/o dominance model of mating. In this case only like genotypes are able to mate (e.g. AA mates only with AA, Aa mates only with Aa, and aa mates only with aa). Take the time to write out Punnett squares to predict progeny genotype frequencies for each of the matings that takes place. Enter initial genotype frequencies of P(AA) = 0.25 and P(Aa) = 0.5 (P(aa) is determined by subtraction) as a logical place to start. At first, run the simulation for 30 generations. With these values and mating patterns, what happens to the frequency of heterozygotes? What happens to the allele frequencies? Next try other initial genotype frequencies that vary the allele frequencies and that are both in and out of Hardy-Weinberg proportions.

Next run both the Positive with dominance and Negative (Dissassortative matings) models. In the Positive with dominance model, the AA and Aa genotypes have identical phenotypes. Mating can therefore take place among any pairing of genotypes with the dominant phenotype or between aa individuals with the recessive phenotype. In the Negative mating model, only unlike genotypes can mate. Take the time to write out Punnett squares to predict progeny genotype frequencies for each of the matings that takes place. In each case, use a set of the same genotype frequencies that you employed in the Positive w/o dominance mating model. How do all types of non-random mating affect genotype frequencies? How do they affect allele frequencies?

observed heterozygosity by the expected heterozygosity expresses the difference in the numerator as a percentage of the expected heterozygosity. Even if the difference in the numerator may seem small, it may be large relative to the expected heterozygosity. Dividing by the expected heterozygosity also puts F on a convenient scale of -1 and +1. Negative values indicate heterozygote excess and positive values indicate homozygote excess relative to Hardy-Weinberg expectations. In fact, the fixation index can be interpreted as the correlation between the two alleles sampled to make a diploid genotype (see the Appendix for an introduction to correlation if necessary). Given that one allele has been sampled from the population, if the second allele tends to be identical there is a positive correlation (e.g. A and then A or a and then a), if the second allele tends to be different there is a negative correlation (e.g. A and then a or a and then A), and if the second allele is independent there is no correlation (e.g. equally likely to be A or a). With random mating, no correlation is expected between the first and second allele sampled to make a diploid genotype.

of biparental inbreeding (mating between two related individuals) or sexual autogamy (self-fertilization).

Fixation index (F) The proportion by which heterozygosity is reduced or increased relative to the heterozygosity in a randomly mating population with the same allele frequencies.

Let's work through an example of genotype data for one locus with two alleles that can be used to estimate the fixation index. Table 2.8 gives observed counts and frequencies of the three genotypes in a sample of 200 individuals. To estimate the fixation index from these data requires an estimate of allele frequencies first. The allele frequencies can then be used to determine expected heterozygosity under the assumptions of Hardy-Weinberg. If p represents the frequency of the B allele,

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