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

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 a...

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Autores principales: Takahashi, Sayaka, Takada, Shingo, Yamanaka, Hiroki, Masuda, Reiji, Kasai, Akihide
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8445453/
https://www.ncbi.nlm.nih.gov/pubmed/34529685
http://dx.doi.org/10.1371/journal.pone.0255576
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author Takahashi, Sayaka
Takada, Shingo
Yamanaka, Hiroki
Masuda, Reiji
Kasai, Akihide
author_facet Takahashi, Sayaka
Takada, Shingo
Yamanaka, Hiroki
Masuda, Reiji
Kasai, Akihide
author_sort Takahashi, Sayaka
collection PubMed
description 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.
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spelling pubmed-84454532021-09-17 Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel Takahashi, Sayaka Takada, Shingo Yamanaka, Hiroki Masuda, Reiji Kasai, Akihide PLoS One Research Article 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. Public Library of Science 2021-09-16 /pmc/articles/PMC8445453/ /pubmed/34529685 http://dx.doi.org/10.1371/journal.pone.0255576 Text en © 2021 Takahashi et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Takahashi, Sayaka
Takada, Shingo
Yamanaka, Hiroki
Masuda, Reiji
Kasai, Akihide
Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel
title Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel
title_full Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel
title_fullStr Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel
title_full_unstemmed Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel
title_short Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel
title_sort intraspecific genetic variability and diurnal activity affect environmental dna detection in japanese eel
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8445453/
https://www.ncbi.nlm.nih.gov/pubmed/34529685
http://dx.doi.org/10.1371/journal.pone.0255576
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