Environmental DNA (eDNA) is currently developing as a powerful tool for assessing aquatic species dynamics. However, its utility as an assessment tool for quantification remain under debate as the sources of eDNA for different species is not always known. Therefore, accumulating information about eDNA sources from different species is urgently required. The objective of our study was to evaluate whether sedimentary DNA targeting two Daphnia species, D. galeata and D. pulicaria, could track Daphnia population dynamics and resting egg production. Applying a quantitative PCR targeting the mitochondrial 12S rRNA gene on sediment cores collected in Lake Biwa, Japan, we compared sedimentary DNA concentration of Daphnia with the abundance of remains and ephippia, reflecting their abundance and resting egg production, respectively. We found that the sedimentary DNA concentrations of Daphnia for the past century were inconsistent with their population abundance. However, the concentration was highly correlated with the resting egg production. Our results provide evidence that ephippia with resting eggs, released during spawning activities, was a significant source of Daphnia DNA archived in sediments. Our work provides critical insights for using sedimentary DNA as a monitoring tool for egg production dating back 100 years.

Copepods play a key trophic role as secondary producers in transferring primary production to higher trophic levels such as fish. Copepod production significantly contributes to successful fish recruitment. Despite their importance, knowledge of their dynamics over several decades remains limited due to the difficulty to obtain long-term data series with exhaustive sampling and analysis. However, an understanding long-term copepod dynamic is urgently required to head toward better management for sustainable aquatic ecosystems and fish recruitment. Sedimentary DNA (sedDNA) has been developing a useful tool for reconstructing past plankton dynamics. This study evaluates whether sedDNA targeting the pelagic copepod, Eodiaptomus japonicus, in Lake Biwa (Japan) can be an effective tool for elucidating its past population dynamics. It was applied a quantitative polymerase chain reaction method targeting the mitochondrial cytochrome c oxidase subunit I gene on sediment cores and compared the detected sedDNA concentrations with the unique long-term dataset of demographic traits, biomass, specific growth rate, production, subitaneous eggs, and resting eggs of E. japonicus. The sedDNA concentration of E. japonicus recovered from sediment layers did not correlate significantly with its resting eggs and its specific growth rate but with in situ production, biomass, and subitaneous egg production. The results provided the evidence for the sedDNA as a tracking tool for assessing copepod past production dynamics.

Copepods play a key trophic role as secondary producers, transferring primary production to higher trophic levels such as fish. Copepod production contributes significantly to successful fish recruitment. Despite their importance, knowledge of copepod dynamics over several decades remains limited due to the lack of long‐term data series with adequate sampling and analysis. However, an understanding of long‐term copepod dynamics is urgently required to strive toward better management for sustainable aquatic ecosystems and fish recruitment. Sedimentary DNA (sedDNA) has been developing as a useful tool for reconstructing past plankton dynamics. This study evaluates whether sedDNA targeting the pelagic copepod, Eodiaptomus japonicus, in Lake Biwa (Japan) can be an effective tool for elucidating its past population dynamics. We applied a quantitative polymerase chain reaction method targeting the mitochondrial cytochrome c oxidase subunit I gene on two sediment cores and compared the detected sedDNA concentrations with the unique long‐term dataset of demographic traits, biomass, specific growth rate, production, subitaneous eggs, and resting eggs of E. japonicus. The sedDNA concentration of E. japonicus recovered from sediment layers correlated significantly with in situ production, biomass, and production of immediately hatching eggs but not with resting eggs or specific growth rate. Our study provides evidence for the effective use of sedDNA as a tracking tool for assessing past copepod production dynamics.