Isolation and characterization of microsatellite loci for use in population genetic analysis in the small-bodied cladoceran Ceriodaphnia cornuta along a riverscape

Population genetic analyses with DNA molecular markers provide insights into population genetic structure and local adaptation. Microsatellite markers for a common small-bodied cladoceran, Ceriodaphnia cornuta, were developed using high-throughput sequencing. Their effectiveness and practicability were tested by investigating the genetic structure of six populations, radiating about 60 kilometers in space and 70 years in time along a subtropical riverscape. Specifically, 26 microsatellites with high polymorphism were successfully isolated. Rarefaction analysis showed that a sample size of greater than 15 individuals genotyped at 10 microsatellite markers provided sufficient resolution for estimating the genetic diversity. Based on a subset of 12 randomly selected loci, all the populations displayed comparably high genetic diversity, but the downstream populations were significantly differentiated from the upstream populations. However, the genetic structure was homogeneous for three historical populations within a lake over decades. Bayesian estimation of recent migration rates among geographic sites was limited. The effective population size steeply decreased from upstream to downstream. Finally, one microsatellite locus was under positive selection, indicating a divergent selection process among different geographic sites. These results indicate that C. cornuta had the significant population genetic differentiation in a local riverscape. This finescale genetic structure may be the result of local adaptation.