Conclusions
We have shown that copper tolerance has evolved in a small subset of strains in a local mining-exposed population of S. marinoi , and that the resting stage population have retained these strains even though the mining activity and pollution level has declined. Our artificial evolution experiment highlights that selection from such standing genetic variation in phytoplankton enables populations to respond to environmental stress much faster than through de-novomutations. It also suggests that extensive species dynamics might be due to evolutionarily important strains that sometimes occur in low frequency but can be swept to high frequencies by directional selection under specific conditions. Importantly, our experimental approach exemplifies how strain-specific metabarcoding can be employed to track selection and quantify strain fitness during co-cultivation, enabling incorporation of higher amounts of strains than other approaches permit. With careful experimental design, future strain-specific metabarcoding experiments should be able to track selection processes in diverse populations inhabiting dynamic and complex environments, more similar to the challenges that phytoplankton face in their natural habitat. Although further development and evaluations of the analytical approaches in mixed DNA samples of unknown allele composition are warranted, it should in theory be possible to track selection processes in natural populations based in situ sampling of environmental DNA from monitoring programs or targeted sampling efforts. Collectively such approaches will yield important new insight into how the intraspecific diversity enables phytoplankton to adapt to life in a dynamic environment.