Microsatellites have been widely used in studies on population genetics, ecology and evolutionary biology.
However, microsatellites are not always available for the species to be studied and their isolation could be
time-consuming. In order to save time and effort researchers often rely on cross-species amplification. We revealed a new
problem of microsatellite cross-species amplification in addition to size homoplasy by analyzing the sequences of
electromorphs from seven catfish species belonging to three different families (Clariidae, Heteropneustidae and
Pimelodidae). A total of 50 different electromorphs were amplified from the seven catfish species by using primers for 4
microsatellite loci isolated from the species
Clarias batrachus
. Two hundred and forty PCR-products representing all 50
electromorphs were sequenced and analyzed. Primers for two loci amplified specific products from orthologous loci in all
species tested, whereas primers for the other two loci produced specific and polymorphic bands from some
non-orthologous loci, even in closely related non-source species. Size homoplasy within the source species was not
obvious, whereas extensive size homoplasy across species were detected at three loci, but not at the fourth one. These data
suggest that amplification of products from non-orthologous loci and appearance of size homoplasy by cross-amplification
are locus dependent, and do not reflect phylogenetic relationship. Amplification of non-orthologous loci and appearance
of size homoplasy will lead to obvious complications in phylogenetic interference, population genetic and evolutionary
studies. Therefore, we propose that sequence analysis of cross-amplification products should be conducted prior to
application of cross-species amplification of microsatellites.
