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Elucidating the relationships between the resting cysts of dinoflagellates (studied mostly by palaeontologists) and their corresponding motile stages (studied mostly by biologists) allows a wealth of biological and palaeontological information to be combined. It enables the presence of living cysts in modern sediments to predict the seasonal appearance of motile stages in the water column, and of fossil cysts in the geological record to test molecular phylogenetic relationships, calibrate molecular clocks and facilitate palaeoenvironmental reconstructions. The morphology of the living cysts, in conjunction with motile-stage morphology and ultrastructure and molecular studies, can also be useful for constructing phylogenetic relationships. Dinoflagellate resting cysts were first recorded in plankton surveys in the 1870s and 1880s, although their significance as such was not then recognized. Much later, in the 1940s and 1950s, they were encountered in cultures of motile cells and in the 1960s were shown to be hypnozygotic cysts. From the 1960s there was a rapid increase in the knowledge of cyst–motile stage equivalencies based on cyst incubation experiments, but the limitations of this method including taxonomic uncertainties for both motile stages and cysts required new approaches. The advent of molecular characterization of dinoflagellates in the 1980s and 1990s, and the desire to analyse individual cells, led the way in the 2000s to the single-cell (cyst) polymerase chain reaction (PCR) technique. The historical development of cyst–theca relationship studies is examined, the successes and limitations of the various methods are illustrated with examples, and the impact of single-cell PCR is assessed in detail.

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