Interact box Decay of gametic disequilibrium and a x test

The program PopGene.S2 has two simulation modules under the Gametic Disequilibrium menu that demonstrate two features of gametic disequilibrium covered so far.

The Magnitude of D simulation can be used to model and graph the decay in D over time given an initial value of D and a value for the recombination rate. This module can be used to produce graphs like that shown in Fig. 2.19.

The Gamete frequencies simulation can be used to conduct a hypothesis test using a x2 test that the observed level of gametic disequilibrium is significantly different than expected under random segregation. Another way to carry out this test without the aid of PopGene.S2 is to use

D 2N P1P2W2

where N is the total sample size of gametes, D is the gametic disequilibrium parameter, and p and q are the allele frequencies at two diallelic loci. The x2 value has 1 df and can be compared with the critical value found in Table 2.5.

One potential drawback of D in equation 2.24 is that its maximum value depends on the allele frequencies in the population. This can make interpreting an estimate of D or comparing estimates of D from different populations problematic. For example, it is possible that two populations have very strong association among alleles within gametes (e.g. no repulsion gametes), but the two populations differ

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