We present 32 polymorphic microsatellite markers for species of the European Daphnia longispina group: D. galeata, D. hyalina, D. rosea, D. cucullata and D. curvirostris. Microsatellite markers were either isolated from genomic libraries or optimized based on previously published sequence information of sister taxa. Cross‐species tests revealed that all but one of the polymorphic markers are applicable to more than one species, which allows intra‐ and interspecific genetic studies on, i.e. population structure, hybridization events and introgression.

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Cyclic parthenogenesis, the alternation of parthenogenetic and sexual reproduction, can lead to a wide scope of population structures, ranging from almost monoclonal to genetically highly diverse populations. In addition, sexual reproduction in aquatic cyclic parthenogens is associated with the production of dormant stages, which both enhance potential gene flow among populations as well as impact local evolutionary rates through the formation of dormant egg banks. Members of the cladoceran genus Daphnia are widely distributed key organisms in freshwater habitats, which mostly exhibit this reproduction mode. We assessed patterns of genetic variation within and among populations in the eurytopic and morphologically variable species Daphnia longispina, using data from both nuclear (13 microsatellite loci) and mitochondrial (partial sequencing of the 12S rRNA gene) markers from a set of populations sampled across Europe. Most populations were characterized by very high clonal diversity, reflecting an important impact of sexual reproduction and low levels of clonal selection. Among-population genetic differentiation was very high for both nuclear and mitochondrial markers, and no strong pattern of isolation by distance was observed. We also did not observe any substantial genetic differentiation among traditionally recognized morphotypes of D. longispina. Our findings of high levels of within-population genetic variation combined with high among-population genetic differentiation are in line with predictions of the monopolization hypothesis, which suggests that in species with rapid population growth and potential for local adaptation, strong priority effects due to monopolization of resources lead to reduced levels of gene flow.

Summary1. Molecular genetic methods continuously uncover cryptic lineages harboured by various species. However, from an applied perspective, it remains unclear whether and to which extent such a genetic diversity affects biological traits (e.g. ecological, behavioural and physiological characteristics) and environmental management. 2. We assessed potential deviations regarding the trait 'environmental stress tolerance' using individuals from five field populations of each of two cryptic lineages (called A and B) comprised under the nominal species Gammarus fossarum. We used ammonia as a chemical stressor while assessing the feeding rate on leaf discs as a measure of sublethal response. In this context, we established a restriction fragment length polymorphism assay to allow a rapid identification of the lineages. 3. We observed a biologically meaningful and statistically significant twofold higher overall tolerance of one cryptic lineage, lineage B, over the other. Confounding factors that may have the potential to influence the test results, such as life stage, sex, season of collection, parasitism, physiological status of organisms and upstream land-use patterns of the river catchments, were either controlled for or displayed only minor deviations between lineages. 4. Synthesis and applications. The trait differences observed in the present study seem to be mainly explained by the considerable genetic differentiation between cryptic lineages of one nominal species. Although traits other than tolerance have been minimally investigated in this context, this study indicates implications in the reliability and quality of environmental monitoring and management if cryptic lineage complexes are ignored.

BackgroundGenetically divergent cryptic species are frequently detected by molecular methods. These discoveries are often a byproduct of molecular barcoding studies in which fragments of a selected marker are used for species identification. Highly divergent mitochondrial lineages and putative cryptic species are even detected in intensively studied animal taxa, such as the crustacean genus Daphnia. Recently, eleven such lineages, exhibiting genetic distances comparable to levels observed among well-defined species, were recorded in the D. longispina species complex, a group that contains several key taxa of freshwater ecosystems. We tested if three of those lineages represent indeed distinct species, by analyzing patterns of variation of ten nuclear microsatellite markers in six populations.ResultsWe observed a discordant pattern between mitochondrial and nuclear DNA, as all individuals carrying one of the divergent mitochondrial lineages grouped at the nuclear level with widespread, well-recognized species coexisting at the same localities (Daphnia galeata, D. longispina, and D. cucullata).ConclusionsA likely explanation for this pattern is the introgression of the mitochondrial genome of undescribed taxa into the common species, either in the distant past or after long-distance dispersal. The occurrence of highly divergent but rare mtDNA lineages in the gene pool of widespread species would suggest that hybridization and introgression in the D. longispina species complex is frequent even across large phylogenetic distances, and that discoveries of such distinct clades must be interpreted with caution. However, maintenance of ancient polymorphisms through selection is another plausible alternative that may cause the observed discordance and cannot be entirely excluded.Electronic supplementary materialThe online version of this article (10.1186/s12862-017-1070-4) contains supplementary material, which is available to authorized users.