We have isolated, characterized and mapped 33 dinucleotide, three trinucleotide and one
tetranucleotide repeat loci from the four major chromosomes of Drosophila pseudoobscura. Average
inferred repeat unit length of the dinucleotide repeats is 12 repeat units, similar to D. melanogaster.
Assays of D. pseudoobscura and populations of its sibling species, D. persimilis, using 10 of these
loci show extremely high levels of variation compared with similar studies of dinucleotide repeat
variation in D. melanogaster populations. The high levels of variation are consistent with an
average mutation rate of approximately 10−6 per locus per generation and an effective population
size of D. pseudoobscura approximately four times larger than that of D. melanogaster. Consistent
with allozymes and nucleotide sequence polymorphism, the dinucleotide repeat loci reveal minimal
structure across four populations of D. pseudoobscura. Finally, our preliminary recombinational
mapping of 24 of these microsatellites suggests that the total recombinational genome size may be
larger than previously inferred using morphological mutant markers.