Size estimation of PCR products

PCR products are visualized by capillary electrophoresis and sized with an internal size-standard (e.g., using the Applied Biosystems or MegaBACE systems, both of which have extensive use for microsatellite scoring). Alleles are subsequently scored using GeneMapper v3.7 software (Applied Biosystems™). It is also possible to measure microsatellite size variants using large denaturing polyacrylamide gels (e.g., Evans, 1993) although this method has fallen from favour do to the hazards of polyacrylamide and difficulties in manually scoring allele sizes.

Once genotypes of samples have been established, microsatellite data are well suited for assessing parentage of nestmates (Evans, 1993), for standard population-genetic statistics including ecotype determination (Estoup et al., 1993; reviewed by Meixner et al., 2013), and for genome mapping (Solignac et al., 2003), among other uses.