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Background  The population structure of cyclical parthenogens such as water fleas is strongly influenced by the frequency of alternations between sexual and asexual (parthenogenetic) reproduction, which may differ among populations and species. We studied genetic variation within six populations of two closely related species of water fleas of the genus  Daphnia  (Crustacea, Cladocera).  D. galeata  and  D. longispina  both occur in lakes in the Tatra Mountains (Central Europe), but their populations show distinct life history strategies in that region. In three studied lakes inhabited by  D. galeata , daphnids overwinter under the ice as adult females. In contrast, in lakes inhabited by  D. longispina , populations apparently disappear from the water column and overwinter as dormant eggs in lake sediments. We investigated to what extent these different strategies lead to differences in the clonal composition of late summer populations.    Results  Analysis of genetic variation at nine microsatellite loci revealed that clonal richness (expressed as the proportion of different multilocus genotypes, MLGs, in the whole analysed sample) consistently differed between the two studied species. In the three  D. longispina  populations, very high clonal richness was found (MLG/N ranging from 0.97 to 1.00), whereas in  D. galeata  it was much lower (0.05 to 0.50). The dominant MLGs in all  D. galeata  populations were heterozygous at five or more loci, suggesting that such individuals all represented the same clonal lineages rather than insufficiently resolved groups of different clones.    Conclusions  The low clonal diversities and significant deviations from Hardy-Weinberg equilibrium in  D. galeata  populations were likely a consequence of strong clonal erosion over extended periods of time (several years or even decades) and the limited influence of sexual reproduction. Our data reveal that populations of closely related  Daphnia  species living in relatively similar habitats (permanent, oligotrophic mountain lakes) within the same region may show strikingly different genetic structures, which most likely depend on their reproductive strategy during unfavourable periods. We assume that similar impacts of life history on population structures are also relevant for other cyclical parthenogen groups. In extreme cases, prolonged clonal erosion may result in the dominance of a single clone within a population, which might limit its microevolutionary potential if selection pressures suddenly change.

Strong differences in the clonal variation of two Daphnia species from mountain lakes affected by overwintering strategy