Microsatellite variation in Drosophila melanogaster and Drosophila simulans: A reciprocal test of the ascertainment bias hypothesis

Interspecific comparisons of microsatellite loci have repeatedly shown that the loci are longer and more variable in the species from which they are d erived (the focal species) than are homologous loci in other (nonfocal) spe cies. There is debate as to whether this is due to directional evolution or to an ascertainment bias during the cloning and locus selection processes. This study tests these hypotheses by performing a reciprocal study. Eighte en perfect dinucleotide microsatellite loci identified fr um a Drosophila s imulans library screen and 18 previously identified in an identical Drosoph ila melanogaster library screen were used to survey natural populations of each species. No difference between focal and nonfocal species was observed for mean PCR fragment length. However, heterozygosity and number of allele s were significantly higher in the focal species than in the nonfocal speci es. The most common allele in the Zimbabwe population of both species was s equenced for 31 of the 36 loci. The length of the longest stretch of perfec t repeat units is, on average, longer in the focal species than in the non- focal species. There is a positive correlation between the length of the lo ngest stretch of perfect repeats and heterozygosity. The difference in hete rozygosity can thus be explained by a reduction in the length of the longes t stretch of perfect repeats in the nonfocal species. Furthermore, flanking -sequence length difference was noted between the two species at 58% of the loci sequenced. These data do nor support the predictions of the direction al-evolution hypothesis; however consistent with the ascertainment bias hyp othesis, the lower variability in nonfocal species is an artifact of the mi crosatellite cloning and isolation process. Our results also suggest that t he magnitude of ascertainment bias for repeat unit length is a function of the microsatellite size distribution in the genomes of different species.