Deviations from expected values may be due to a variety of causes. If an excess of heterozygotes is observed this may indicate the presence of overdominant selection or the occurance of outbreeding. Alternatively, if an excess of homozygotes is detected it may be due to four factors. First, the locus is under selection. Second, 'null alleles' may be present which are leading to a false observation of excess homozygotes. Third, inbreeding may be common in the population. Fourth, the presence of population substructure may lead to Wahlunds' effect. The likelihood of each of these explanations must be assessed from additional data, such as demographic information, i.e. population distribution.
The analysis of known pedigrees will aid in this regard. Examination of the inheritance of alleles will allow for the identification of null alleles (Callen et al. 1993; Paetkau and Strobeck 1995; Pemberton et al. 1995). Null alleles are usually caused by a mutation in the primer binding site leading to an allele that will not amplify (Callen et al. 1993; Paetkau and Strobeck 1995). Traditional linkage analysis can be performed to ensure that independent assortment of alleles at different loci is occurring.
The analysis of a large number of loci will increase the power of detecting population substructure because each locus will contain an independent history of the population depending on the amounts of random drift, mutation, and migration that have occurred. If this information is not independent (i.e. the loci are genetically linked) then the results may be biased towards the events of a single linkage group since this information will be over represented in the combined data set. If a substantial amount of pedigree information is not available, linkage analysis may not be useful. In this situation an analysis of gamete phase equilibrium (Chakraborty 1984) can be performed to test for the random association of alleles at different loci (e.g. Edwards et al. 1992).