3.3.2.DNA microsatellites

DNA microsatellites are a type of variable number of tandem repeats (VNTR), also known as short tandem repeats (STR) and simple sequence repeats (SSR). Microsatellites are segments of DNA with a sequence motif ranging from 1 to 6 bases, repeated from 4 to probably 100 or more times (Tautz, 1990). It seems that most eukaryotes carry these elements, whose role is not particularly clear. Honey bees and bumble bees were the first social insects for which DNA microsatellites were developed (Estoup  et al., 1993). The aim of the original project was to determine the zone of introgression between A. m. mellifera and A.m. ligustica in the region of the French-Italian Alps. For each microsatellite locus, a specific set of primers is used for PCR. A valuable source for loci in honey bees was published by Solignac et al. (2003), including information on subspecies variation and possible amplification in three other species of Apis.

DNA microsatellites offer variation useful for inferring population differentiation, originating from a high mutation rate (Levinson and Gutman, 1987) during replication, by adding or removing repeat units compared to the original microsatellite element. Estoup et al. (1995a) described the process of allelic evolution and used these markers to separate 9 populations of honey bees with seven microsatellite loci. The approaches used for inferring population differentiation at this early stage were mainly based on F-statistics and tree drawing methods from phylogeny. The first studies were done with a sample size of approximately 40 individuals per population, which since then has been found an effective number (Cornuet at al., 1999). A detailed study of the west European honey bees used 11 loci to differentiate the M lineage bees from C lineage bees of Greek origin and to demonstrate a high amount of introgression into the French population (Garnery et al., 1998b). The statistical analysis used were Fst values and phylogenetic trees, indicating a marked interest in grouping samples, based not on their sampling origin, but based on their similarity. This method does cluster the Iberian honey bees separate from the rest. The paper was important, as the data were used to suggest methods to define conservation strategies of local honey bee populations.

Franck et al. (1998) analysed the origin of west European honey bees with 8 microsatellite loci and mtDNA. The analysis demonstrated that the Iberian bees were rather pure, with limited influence from Northern Africa, drawing strength from the combination of two independent marker types. Similar methods were used to determine variation in honey bees from the Middle East that led to the hypothesis of a fourth lineage based on molecular data (Franck et al., 2000) (see Annex on lineages). A time related study concerning the Africanization process of the Yucatan peninsula demonstrated the strength of DNA microsatellites in finding hybrids (Clarke et al., 2002).

3.3.2.2. Problems and potential pitfalls with using microsatellites