In molecular ecology the analysis of large microsatellite data sets is becoming increasingly popular. Here we introduce a new software tool, which is specifically designed to facilitate the analysis of large microsatellite data sets. All common microsatellite summary statistics and distances can be calculated. Furthermore, the microsatellite analyser (msa) software offers an improved method to deal with inbred samples (such as Drosophila isofemale lines). Executables are available for Windows and Macintosh computers.

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We surveyed microsatellite distribution in 10 completely sequenced genomes. Using a permutation-based statistic, we assessed for all 10 genomes whether the microsatellite distribution significantly differed from expectations. Consistent with previous reports, we observed a highly significant excess of long microsatellites. Focusing on short microsatellites containing onlya few repeat units, we demonstrate that this repeat class is significantly underrepresented in most genomes. This pattern was observed across different repeat types. Computer simulations indicated that neither base substitutions nor a combination of length-dependent slippage and base substitutions could explain the observed pattern of microsatellite distribution. When we introduced one additional mutation process, a length-independent slippage (indel slippage) operating at repeats with few repetitions, our computer simulations captured the observed pattern of microsatellite distribution

Aspergillus nidulans rcoA encodes a member of the WD repeat family of proteins. The RcoA protein shares sequence similarity with other members of this protein family, including the Saccharomyces cerevisiae Tup1p and Neurospora crassa RCO1. Tup1p is involved in negative regulation of an array of functions including carbon catabolite repression. RCO1 functions in regulating pleiotropic developmental processes, but not carbon catabolite repression. In A. nidulans, deletion of rcoA (ΔrcoA), a recessive mutation, resulted in gross defects in vegetative growth, asexual spore production and sterigmatocystin (ST) biosynthesis. Expression of the asexual and ST pathway‐specific regulatory genes, brlA and aflR, respectively, but not the signal transduction genes (i.e. flbA, fluG or fadA) regulating brlA and aflR expression was delayed (brlA) or eliminated (aflR) in a ΔrcoA strain. Overexpression of aflR in a ΔrcoA strain could not rescue normal expression of downstream targets of AflR. CreA‐dependent carbon catabolite repression of starch and ethanol utilization was only weakly affected in a ΔrcoA strain. The strong role of RcoA in development, vegetative growth and ST production, compared with a relatively weak role in carbon catabolite repression, is similar to the role of RCO1 in N. crassa.

Drosophila melanogaster originated in Africa and colonized the rest of the world only recently (approximately 10,000 to 15,000 years ago). Using 151 microsatellite loci, we investigated patterns of gene flow between African D. melanogaster populations representing presumptive ancestral variation and recently colonized European populations. Although we detected almost no evidence for alleles of non-African ancestry in a rural D. melanogaster population from Zimbabwe, an urban population from Zimbabwe showed evidence for admixture. Interestingly, the degree of admixture differed among chromosomes. X chromosomes of both rural and urban populations showed almost no non-African ancestry, but the third chromosome in the urban population showed up to 70% of non-African alleles. When chromosomes were broken into contingent microsatellite blocks, even higher estimates of admixture and significant heterogeneity in admixture was observed among these blocks. The discrepancy between the X chromosome and the third chromosome is not consistent with a neutral admixture hypothesis. The higher number of European alleles on the third chromosome could be due to stronger selection against foreign alleles on the X chromosome or to more introgression of (beneficial) alleles on the third chromosome.