Exploring the Genetic Diversity and Population Structure of <i>Daphnia cucullata</i> Sars, 1862 in Boreal Lakes (Latvian Lakeland) Based on Microsatellites

We have used <i>Daphnia cucullata</i> (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most appropriate microsatellite markers for future genetic studies of <i>Daphnia cucullata</i> populations of lakes Svente, Riča, Dridzis and Geraņimovas-Ilzas in the Boreal biogeographical region. Based on these microsatellite markers, we determined the genetic diversity of these populations. The loci Dgm105 and Dgm101 had the maximum number of alleles and the maximum number of private alleles. The specific locus Dgm105 had five private alleles (62% of all detected alleles), and locus Dgm101 had four private alleles (57% of all detected alleles) in these loci. We determined the observed heterozygosity (H_obs) and the expected heterozygosity (H_exp) level (via Hardy–Weinberg equilibrium), the number of polymorphic loci, the number of detected alleles in each analyzed microsatellite locus, the average number of alleles at the locus (N_a), the average effective number of alleles at the locus (N_e), the F_ST of the population’s genetic differentiation, the genetic distance (D) (following Nei) and the significance (χ²-test) of differences between the levels of observed and expected heterozygosity. It was shown that <i>Daphnia cucullata</i> populations from lakes with a low number of zooplankton taxa (Riča and Geraņimovas-Ilzas) have a higher genetic diversity compared to lakes with a high number of zooplankton taxa (Dridzis and Svente). It was found that <i>Daphnia cucullata</i> populations from lakes Dridzis and Svente have the least genetic distance, and these populations form a single genetic group, as confirmed via clustering.