Allozyme analysis – the investigation of allelic variation at enzyme loci, accessible through gel electrophoresis - was the first type of molecular marker to be applied in the field of honey bee research (Mestriner 1969, Mestriner and Contel 1972). The majority of allozyme studies in honey bee diversity appeared in the 80’s and 90’s of the past century (Garstide, 1980; Nunamaker et al., 1984; Sheppard and Berlocher, 1984, 1985; Badino et al., 1988; Lobo et al., 1989; Kandemir and Kence, 1995; Dedej et al., 1996). Allozyme studies have contributed to our understanding of gene flow, population structure and hybridization (Badino et al., 1983, 1985, 1988; Sheppard and McPheron, 1986; Del Lama et al., 1990; Meixner et al., 1994) and revealed founder effects (Cornuet and Fresnaye, 1979; Sheppard, 1988).

One of the most polymorphic and most widely used enzyme loci in studies of population variation of honey bees has been the Mdh1 (malate dehydrogenase) locus. Its variation has been particularly useful, because its allele frequencies differ greatly between different the lineages of the honey bee. Therefore, Mdh variation has been extensively used in studies about the spread of Africanized honey bees, or in studies on differentiation of European lineages (Cornuet, 1982; Cornuet et al., 1986; Lobo et al, 1989; Del Lama et al., 1990). However, as there is evidence that variation of the Mdh1 locus can be interpreted as consequence of physiological adaptation to different climates and thus may not necessarily reflect gene flow (Coelho and Mitton, 1988; Nielsen et al., 1994, Cornuet et al., 1995), phylogeographic conclusions should be drawn with caution, since the Mdh1 Locus is obviously not selectively neutral.

Comparatively few loci are polymorphic in honey bees and there are no fixed allelic differences between subspecies; therefore, variation within A. mellifera consists exclusively of differences in allele frequencies between populations. This limitation renders allozymes less suitable for the purpose of identification of a small sampling or a single colony; however, the marker may still be employed usefully in population studies. As an advantage, the method is easy to use and scoring the data is comparatively unproblematic and straightforward. In addition, the method is economical in setup and running, since it does not require too much expensive laboratory equipment. The most commonly studied enzyme systems and polymorphic loci, together with the most common alleles and recommendations for staining are summarized in Table 5. Data analysis