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

Atsushi Maruyama,Akio Imamura,Hiroki Yamanaka,Kazuki Watanabe,Kousuke Sugatani

doi:10.1002/ece3.4653

Atsushi Maruyama, Akio Imamura + Show 3 more

Open Access

https://doi.org/10.1002/ece3.4653

Copy DOI

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.

Highlights

Information regarding reproduction is essential for effectively and ef‐ ficiently conserving rare and endangered animal species (Sutherland, 1998)
Environmental DNA analysis was proposed as a non‐invasive, quick approach to monitoring aquatic macro‐organisms (Ficetola, Miaud, Pompanon, & Taberlet, 2008; Jerde, Mahon, Chadderton, & Lodge, 2011; Lodge et al, 2012). This technique can reveal the distribution of target species by detecting species‐specific DNA fragments in water samples. environmental DNA (eDNA) analysis can be performed non‐invasively and simultaneously at several sites with more repetition than conventional methods, such as capture and direct observation, because the only fieldwork necessary is the collection of water samples (Darling & Mahon, 2011; Nakagawa et al, 2018; Yamamoto et al, 2016)
When the 89 positive eDNA data points were analyzed, it emerged that the probability of observing three‐lips during visual inspection was significantly correlated with the log10‐transformed eDNA concentration (GLM with a logit link function, z = 4.12, p < 0.001; Figure 3) and was significantly different between the river and lake sites (z = 3.18, p < 0.01)

Summary

| INTRODUCTION

Information regarding reproduction is essential for effectively and ef‐ ficiently conserving rare and endangered animal species (Sutherland, 1998). Environmental DNA (eDNA) analysis was proposed as a non‐invasive, quick approach to monitoring aquatic macro‐organisms (Ficetola, Miaud, Pompanon, & Taberlet, 2008; Jerde, Mahon, Chadderton, & Lodge, 2011; Lodge et al, 2012) This technique can reveal the distribution of target species by detecting species‐specific DNA fragments in water samples. To assess whether animal density can be predicted by eDNA analysis, we selected a cyprinid fish, three‐lips (Opsariichthys un‐ cirostris uncirostris, Temminck et Schlegel), in a river as a model to test whether eDNA analysis can quantitatively monitor fish popu‐ lations (Figure 1) This fish grows in lakes and large adult individuals (14–25 cm standard length; 2+–4+ age) only seasonally migrate up‐ stream into tributaries for reproduction (Nakamura, 1951; Tanaka, 1970).

| MATERIALS AND METHODS

Results of visual inspection

| DISCUSSION

| CONCLUSION

Findings

CONFLICT OF INTEREST