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

Interspecific comparisons of microsatellite loci have repeatedly shown thatthe loci are longer and more variable in the species from which they arederived (the focal species) than are homologous loci in other (nonfocal)species. There is debate as to whether this is due to directional evolutionor to an ascertainment bias during the cloning and locus selectionprocesses. This study tests these hypotheses by performing a reciprocalstudy. Eighteen perfect dinucleotide microsatellite loci identified from aDrosophila simulans library screen and 18 previously identified in anidentical Drosophila melanogaster library screen were used to surveynatural populations of each species. No difference between focal andnonfocal species was observed for mean PCR fragment length. However,heterozygosity and number of alleles were significantly higher in the focalspecies than in the nonfocal species. The most common allele in theZimbabwe population of both species was sequenced for 31 of the 36 loci.The length of the longest stretch of perfect repeat units is, on average,longer in the focal species than in the non-focal species. There is apositive correlation between the length of the longest stretch of perfectrepeats and heterozygosity. The difference in heterozygosity can thus beexplained by a reduction in the length of the longest stretch of perfectrepeats in the nonfocal species. Furthermore, flanking-sequence lengthdifference was noted between the two species at 58% of the loci sequenced.These data do not support the predictions of the directional-evolutionhypothesis; however, consistent with the ascertainment bias hypothesis, thelower variability in nonfocal species is an artifact of the microsatellitecloning and isolation process. Our results also suggest that the magnitudeof ascertainment bias for repeat unit length is a function of themicrosatellite size distribution in the genomes of different species.