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This overview of methodology and applications of sediment archives of living dinoflagellates and other protists examines their potential to study ecology and evolution of unicellular eukaryotes through time. Sediment cores from Koljö Fjord on the west coast of Sweden and from Mariager Fjord in Northern Denmark, both enclosed embayments with recurring anoxic bottom water, provide a virtually undisturbed sediment record. Cultures of dinoflagellates (and other protists) were established by individually isolating specimens from dated sediment layers. Twelve sediment cores were used from which over 500 dinoflagellate strains from 20 different taxa, as well as numerous strains of diatoms, haptophytes, prasinophytes and heterotrophic protists, were established. Model dinoflagellate species included Pentapharsodinium dalei and Scrippsiella trochoidea. The culture strains were used to test for intraspecific variation through time in morphology, genotypes and physiology. In this paper we discuss the potential for using the sediment archive for temporal population studies, including applications relevant to palaeoecological studies.

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