Fatty acid‐based diet estimation method and long‐term monitoring data reveal generalist and selective feeding behaviors in herbivorous cladocerans and copepods

Zooplankton play an essential role in lake ecosystems by linking primary producers to higher trophic levels. While herbivorous cladocerans are well studied, the diets and population dynamics of herbivorous copepods remain less understood. We created fatty acid reference profiles for the calanoid copepod Eudiaptomus gracilis through controlled 13 C‐labeled feeding experiments and compound‐specific stable isotope analysis. We then analyzed 8 years of biochemical data from Lake Vesijärvi, Finland, and utilized quantitative fatty acid signature analysis (QFASA) to estimate phytoplankton composition and the assimilated diets of herbivorous cladocerans and calanoid copepods. These estimates, alongside zooplankton biomass measurements, allowed us to examine links between food availability, assimilation, and population dynamics. Different feeding strategies were found: calanoid copepods fed selectively, with a clear preference for golden algae and avoidance of cyanobacteria, whereas cladocerans behaved as generalists, with diets tracking phytoplankton composition. Cladoceran biomass showed weak but detectable responses to phytoplankton composition, whereas calanoid copepod biomass remained detached, likely due to its longer life cycle and selective feeding. These patterns suggest that calanoid copepods' selectivity may help maintain fish productivity under eutrophication by focusing on nutritionally rich phytoplankton. By estimating phytoplankton assimilated by zooplankton with QFASA, our approach provides a complementary perspective to traditional phytoplankton sampling, exposing the unseen, assimilated fraction of phytoplankton. Furthermore, substantial interannual variability underscores the value of long‐term monitoring for capturing key trophic interactions in boreal lakes.