Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel

Abstract

Environmental DNA (eDNA) analysis with species-specific primer/probe sets is promising as a tool to quantify fish abundance and distribution. Nevertheless, several factors could reduce the accuracy of this method. Here, we aimed to analyze whether intraspecific variability and diel activity rhythm affect eDNA detection in Japanese eels (Anguilla japonica). For this purpose, we performed tank experiments focusing on two points. First, we assessed the effects of base pair sequences with probe region polymorphism on eDNA detection. Next, we evaluated the influences of diel rhythm, activity, and individual differences in eDNA release rate on eDNA concentration. We examined the base pair sequences of the probe regions of 20 individuals and found genetic mismatches in two of them. The eDNA concentration was estimated to be much lower in these variants than it was in the other individuals. We conducted a rearing experiment on four non-variant individuals to explore the influences of diel activity and inter-individual differences in eDNA detection. Nocturnal eel activity was reflected in the eDNA detection but the inter-individual differences remained large. The observed weak positive correlations between eDNA concentration and activity suggest that eDNA emission is highly dependent on basal metabolism. The present study suggests that consideration of polymorphic sites at the probe region and diel activity rhythms should improve the accuracy and precision of abundance estimation through eDNA. Such fine-tuning is applicable not only for eels but also for other fishes to be targeted by eDNA technology.

Particle size distribution shift and diurnal concentration changes of environmental DNA caused by fish spawning behaviour

“…Diurnal changes in fish eDNA concentrations could be caused by simple changes in biomass or activity levels as well as spawning, but previous studies and our observations would rule out these possibilities. In the only previous study about diurnal changes in eDNA concentration, a slight increase in eDNA levels associated with nocturnal activity in nocturnal fish, Japanese eels ( Anguilla japonica ), was reported by aquarium experiments (Takahashi et al, 2021). In contrast, previous studies on nocturnal amphibians found no differences in eDNA concentrations between daytime and nighttime ( Cryptobranchus a. alleganiensis , Takahashi et al, 2018; Ascaphus montanus and Dicamptodon aterrimus , Pilliod et al, 2013).…”

“…Additionally, on day2-18:00, eDNA concentrations tended to increase again, surpassing the levels observed during the day (P<0.05). In the only previous study about diurnal changes in eDNA concentration, a slight increase in eDNA levels associated with nocturnal activity in nocturnal fish, Japanese eels (Anguilla japonica), was reported by aquarium experiments 45 . In contrast, previous studies on nocturnal amphibians found no differences in eDNA concentrations between daytime and nighttime (Cryptobranchus a. alleganiensis 16 , Ascaphus montanus and Dicamptodon aterrimus 46 ).…”

Molecular Identification of Elvers (<I>Anguilla</I> spp.) from River Estuaries in Central Java, Indonesia Using DNA Barcoding Based on <I>mt</I>DNA CO1 Sequences

“…Molecular identification of eels has been successfully conducted (Arai et al, 2020;Alter et al, 2015;Wibowo et al, 2021). Furthermore, detection of the presence and diversity of eel revealed by environmental DNA analysis (Kasai et al, 2021;Takahashi et al, 2021).…”