Environmental DNA analysis as a non‐invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers

Abstract

Quantitative information regarding reproduction is essential for conserving endangered animals; however, some conventional quantitative methods can be damaging to the target population and their habitats. In the present study, the reproductive migration of a threatened endemic fish, three‐lips (Opsariichthys uncirostris uncirostris), was non‐invasively monitored by quantitative PCR of species‐specific environmental DNA (eDNA), the usefulness of which has been not sufficiently explored. Water sampling and from‐shore visual inspection were performed weekly along a tributary of Lake Biwa (Japan), where adult fish seasonally migrate upstream to reproduce as well as at lake sites near the river mouth. Species‐specific eDNA was collected at all locations at times when the fish were visually observed and at certain sites where the fish were not observed. Log‐transformed individual counts from visual inspection were positively correlated with log‐transformed eDNA concentration in the river sites, indicating that eDNA analysis can be a reliable quantitative tool for fish abundance in rivers. Furthermore, distance from the lake did not influence eDNA concentration, suggesting that eDNA transport by river flow had a negligible effect on eDNA quantification. Both eDNA concentration and individual counts gradually increased from May–July, and decreased in August. Importantly, eDNA analysis showed that the fish occupied more habitats in the peak reproductive season and stayed for longer time at any given site. An additional underwater survey confirmed unexpected eDNA detections as true positives. eDNA analysis has great potential to quantitatively monitor reproductive fish migrations under certain conditions.

Environmental DNA monitoring for short‐term reproductive migration of endemic anadromous species, Shishamo smelt (Spirinchus lanceolatus)

“…In addition, eDNA concentrations can reflect the relative abundance of target species in aquatic environments (Eichmiller et al, ; Mizumoto, Urabe, Kanbe, Fukushima, & Araki, ; Takahara, Minamoto, Yamanaka, Doi, & Kawabata, ; Yates, Fraser, & Derry, ), even in streams (Doi et al, ; Lacoursière‐Roussel, Côté, Leclerc, & Bernatchez, ; Pilliod, Goldberg, Arkle, Waits, & Richardson, ; Tillotson et al, ). This technique is also useful for detecting the seasonal habitat changes of migratory fishes (Laramie, Pilliod, & Goldberg, ; Maruyama, Sugatani, Watanabe, Yamanaka, & Imamura, ; Yamanaka & Minamoto, ).…”

An Environmental DNA Survey on Distribution of an Endangered Salmonid Species, Parahucho perryi, in Hokkaido, Japan

“…Tank experiments in our previous study (Mizumoto et al, 2018) revealed a high sensitivity of the Sakhalin taimen eDNA detection system and its potential for biomass estimation in flowing waters. In general, however, the detectability of eDNA from aquatic organisms is affected by both biotic and abiotic factors such as the range from the target species, sizes and density of them, water temperature, pH, water current, flow volume and so on (e.g., Barnes et al, 2014;Song et al, 2017; Maruyama et al, 2018;Kasai et al, 2020). Therefore, actual detectability of Sakhalin taimen's eDNA in the natural river systems would rather be limited, and we are almost certain that we missed eDNA detections from some river systems, especially from large rivers or areas with low density of Sakhalin taimen.…”

“…These techniques have many advantages for detecting target species in the field, such as objectivity, high detectability, and reduced sampling effort. They have been shown to be especially useful for monitoring endangered species that are otherwise difficult to capture or observe (Fukumoto et al, 2015;Laramie et al, 2015;Pfleger et al, 2016;Carlsson et al, 2017;Maruyama et al, 2018;Atkinson et al, 2019;Iwai et al, 2019). However, the previous studies tended to apply the eDNA techniques to specific freshwater/saltwater systems or to relatively small geographical regions.…”

Aquatic suspended particulate matter as source of eDNA for fish metabarcoding

“…Recently, the use of environmental DNA (eDNA), which is the trace amounts of DNA discharged by organisms via excretion of urine, feces, body cells, eggs, etc., enables the non-invasive detection of species and their approximate relative quantification 6 – 9 . Whole fish communities can be characterized from eDNA using high throughput sequencing or specific amplicons—a process known as eDNA metabarcoding 10 – 14 .…”