An assessment of zooplankton assemblages with high-throughput DNA sequencing

Marine zooplankton comprise a major component of marine ecosystems, and accurate assessment of their constantly changing diversity and abundances is necessary for successful fisheries management and the design of marine reserves. Zooplankton are also instrumental in quantifying the effects of environmental variation. Traditional morphological taxonomic identification by microscopy remains essential to such studies, but is time-consuming and taxonomic specialization varies among researchers. High-throughput DNA sequencing (HTS) is an alternative method being applied to the assessment zooplankton assemblages in a growing number of studies. In this contribution, we apply HTS for mitochondrial COI and nuclear 28S to plankton net samples form the northern Monterey bay, California, and demonstrate its utility for detecting variation in zooplankton assemblages between two, 4–5 day sampling periods in the fall of 2013.