Morphology of cysts of fairy shrimp (Crustacea, Anostraca) is often very useful in distinguishing between genera and some morphologically distinct species. However, the cysts of many species are indistinguishable from one another due to high inter-specific morphological similarity or to extensive intra-specific variability. In addition, hybridization between some species is possible and unlikely to be detected by examining cyst morphology. We have developed an approach based on RAPD-PCR molecular markers that allows for the rapid and accurate identification of fairy shrimp species at the cyst stage. This technique can quickly differentiate between three congenic species of potentially co-occurring fairy shrimp in southern California that are known to hybridize and whose cysts are difficult or impossible to identify using morphological characters. This technique has the potential to be expanded to incorporate many more species.
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