Abstract
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.
Highlights
Freshwater ecosystems are among the most at-risk habitats in terms of anthropogenic impact and global and local species loss[1,2,3,4,5,6]
We explored sedimentary DNA spanning 100 years up to the present day in two Daphnia species, Daphnia galeata and Daphnia pulicaria, extracted from sediment cores from Lake Biwa to determine whether Daphnia sedimentary DNA could be used as an indicator to reconstruct the past population abundance and resting egg production, which were reconstructed from their remains and ephippia, respectively, preserved in sediment cores (Fig. 1b)
The sedimentary DNA of D. galeata, which was analyzed by quantitative polymerase chain reaction (qPCR) analysis, was continuously detected in three out of four replicates after the year 1940 (> 24.5-cm depth; Fig. 2a)
Summary
Freshwater ecosystems are among the most at-risk habitats in terms of anthropogenic impact and global and local species loss[1,2,3,4,5,6]. A previous study on sediment in Lake Biwa, Japan (Supplementary Fig. S2) described temporal changes in the Daphnia population abundance and resting egg production during the twentieth c entury[29]. This reconstruction of population abundance was consistent with existing time-series zooplankton monitoring data[34]. For the past several decades, Lake Biwa sediment has had a continuous record with a high time resolution of two years per 1-cm layer sample[35] These observations suggest that Daphnia in Lake Biwa is a suitable for comparing temporal changes in sedimentary DNA and its abundance and resting egg production
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