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Long-distance dispersal of diapausing eggs by migratory waterfowl is one factor thought to be responsible for the macrogeographical homogeneity of allozyme frequencies in species of the Daphnia pulex complex. If so, populations on either side of the Rocky Mountains are expected to be divergent because few major flyways cross them. To test this prediction, Daphnia populations from lakes and ponds across eastern Oregon were surveyed for mtDNA and allozyme variation. The data were analysed with previously collected data from populations in the midwest U.S. Phenetic analysis of the allozyme data clustered the populations into four discrete groups, which correspond to habitat: permanent lakes, ponds in the midwest, coastal and valley ponds in Oregon and sand dune ponds in Oregon. A recent taxonomic revision by Hebert suggests that these groups correspond to D. pulicaria, D. pulex, D. arenata and D. melanica, respectively. Cladistic analysis of mtDNA variation revealed the same groups except that mtDNA haplotypes from the D. pulex and D. pulicaria populations formed a single clade. All four species were significantly subdivided with respect to allozyme markers, but there were no clear differences between D. pulicaria populations on either side of the Rocky Mountains, suggesting that they are not a barrier to gene flow in this species. Whereas mtDNA differentiation among D. pulicaria populations was not significant, the pond-dwelling species, D. pulex and D. arenata, showed even greater differentiation for mtDNA than for allozymes. It is suggested that extinction/recolonization events occur more frequently in pond vs. lake habitats and have a greater impact on the subdivision of mtDNA variation because of the haploid, maternal inheritance of the mitochondrial genome. [ABSTRACT FROM AUTHOR]