scholarly journals Using environmental DNA analyses to assess the occurrence and abundance of the endangered amphidromous fish Plecoglossus altivelis ryukyuensis

2020 ◽  
Vol 8 ◽  
Author(s):  
Yoshihisa Akamatsu ◽  
Gen Kume ◽  
Masuji Gotou ◽  
Takanori Kono ◽  
Takuma Fujii ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Dna Fragments ◽  
Plecoglossus Altivelis ◽  
Endangered Fish ◽  
Non Invasive ◽  
Plecoglossus Altivelis Ryukyuensis ◽  
Natural Monument ◽  
Conservation Plans ◽  
Three Rivers ◽  
Probe Set

The Ryukyu ayu Plecoglossus altivelis ryukyuensis is an endangered amphidromous fish that inhabits rivers in the Ryukyu Archipelago (Japan). Populations of the species have declined dramatically. Consequently, the Ryukyu ayu has been registered as a natural monument in Japan and monitoring surveys with direct catching are restricted legally. This restriction, unfortunately, makes monitoring of population abundances difficult and creates a barrier to both advancing understanding of the species’ status and the development of appropriate conservation plans. We developed a non-invasive monitoring methodology using eDNA analyses. We designed a specific quantitative PCR assay for the Ryukyu ayu using the mitochondrial ND4 region. Using this primer/probe set, we conducted eDNA analyses in three rivers on Amami-Ohshima Island. The DNA fragments were amplified from the eDNA extracted from natural water in each river. The numbers of DNA fragments detected were positively correlated with individual counts of fish obtained by visual snorkelling surveys. Our method does not contravene restrictions and facilitates abundance monitoring of this endangered fish species.

scholarly journals Does construction in the spawning ground improve the riverbed conditions making it suitable for spawning of the Ryukyu-ayu Plecoglossus altivelis ryukyuensis?

2020 ◽  
Vol 67 (4) ◽  
pp. 493-501
Author(s):  
Satoshi Awata ◽  
Tetsuya Tsuruta ◽  
Shin-ichiro Abe ◽  
Toshihiko Yonezawa ◽  
Kei’ichiro Iguchi
Keyword(s):  
Spawning Ground ◽  
Plecoglossus Altivelis ◽  
Plecoglossus Altivelis Ryukyuensis

Environmental DNA monitoring method of the commercially important and endangered fish Gnathopogon caerulescens

Limnology ◽  
2021 ◽  
Author(s):  
Kimiko Uchii ◽  
Kei Wakimura ◽  
Takeshi Kikko ◽  
Ryuji Yonekura ◽  
Riho Kawaguchi ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Monitoring Method ◽  
Endangered Fish ◽  
Gnathopogon Caerulescens ◽  
Commercially Important

scholarly journals Environmental DNA as a non‐invasive sampling tool to detect the spawning distribution of European anadromous shads ( Alosa  spp.)

2019 ◽  
Vol 29 (1) ◽  
pp. 148-152 ◽  
Author(s):  
Caterina Maria Antognazza ◽  
J. Robert Britton ◽  
Caitlin Potter ◽  
Elizabeth Franklin ◽  
Emilie A. Hardouin ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Non Invasive

scholarly journals Monitoring spawning migrations of potamodromous fish species via eDNA

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bettina Thalinger ◽  
Elisabeth Wolf ◽  
Michael Traugott ◽  
Josef Wanzenböck
Keyword(s):  
Fish Species ◽  
Anthropogenic Impacts ◽  
Environmental Dna ◽  
Signal Strength ◽  
Digital Pcr ◽  
Freshwater Ecosystems ◽  
Non Invasive ◽  
River Stretch ◽  
Daily Discharge ◽  
Invasive Techniques

Abstract Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.

scholarly journals Phylogenetic classification of short environmental DNA fragments

2008 ◽  
Vol 36 (7) ◽  
pp. 2230-2239 ◽  
Author(s):  
Lutz Krause ◽  
Naryttza N. Diaz ◽  
Alexander Goesmann ◽  
Scott Kelley ◽  
Tim W. Nattkemper ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Dna Fragments ◽  
Phylogenetic Classification

scholarly journals A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA under Field Conditions

2019 ◽  
Author(s):  
Clare I. M. Adams ◽  
Luke A. Hoekstra ◽  
Morgan R. Muell ◽  
Fredric J. Janzen
Keyword(s):  
Rank Order ◽  
Environmental Dna ◽  
Chrysemys Picta ◽  
Field Conditions ◽  
Painted Turtle ◽  
Freshwater Turtles ◽  
Detection Rates ◽  
Non Invasive ◽  
Painted Turtles ◽  
Current State

Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, as well as present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have been successful mostly in detecting the presence of these animals in field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored this matter by sampling lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months, attempting to detect differences in eDNA accumulation using a qPCR assay. Only one sample of the highest density pond readily amplified eDNA. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present a “shedding hypothesis”–the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms–as a potential challenge for turtle eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

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