The null hypothesis (see Chapter 19) with Hardy-Weinberg equilibrium testing is that the genotype frequencies are identical to the proportions expected
Table 20.6 Assumptions with Hardy—Weinberg equilibrium.
No natural selection No restriction on mating so all alleles have equal chance of becoming part of next generation
No mutation No new alleles being introduced
No immigration/emigration No new alleles being introduced or leaving
Random mating Any allele combination is possible
Large population Lots of possible allele combinations based on the allele frequencies. In other words, perfect independence of the alleles at the measured locus exists in the population under examination. Thus, small /»-values cast doubt on the validity of the null hypothesis. The Bonferroni correction is often applied to lower the /-value and thus make results with multiple comparisons not statistically significant (see D.N.A. Box 19.2). It is important to keep in mind that since the perfect conditions for HWE and linkage equilibrium (LE) cannot exist in real human populations (random mating, no migration, etc.), therefore the null hypothesis cannot be true by definition.
If minor departures are seen from HWE, there is generally no major cause for concern with using a particular database. Some authors will do little more than note that there is a statistically significant departure from HWE for a particular locus in their population data set. It is important to keep in mind that there are three principal reasons for observations of major differences (departures) from Hardy-Weinberg equilibrium: (1) parents might be related leading to inbreeding and a higher than expected number of homozygotes, (2) population substructure, and (3) selection because persons with different genotypes might survive and reproduce at different rates (NRCII 1996, p. 98).
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