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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Sayaka Takahashi, Shingo Takada, Hiroki Yamanaka, Reiji Masuda, Akihide Kasai
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f80261cfd750447481931948a00a0ea7
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:f80261cfd750447481931948a00a0ea7
record_format	dspace
spelling	oai:doaj.org-article:f80261cfd750447481931948a00a0ea72021-12-02T20:08:13ZIntraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel.1932-620310.1371/journal.pone.0255576https://doaj.org/article/f80261cfd750447481931948a00a0ea72021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0255576https://doaj.org/toc/1932-6203Environmental 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.Sayaka TakahashiShingo TakadaHiroki YamanakaReiji MasudaAkihide KasaiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 9, p e0255576 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sayaka Takahashi Shingo Takada Hiroki Yamanaka Reiji Masuda Akihide Kasai Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel.
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.
format	article
author	Sayaka Takahashi Shingo Takada Hiroki Yamanaka Reiji Masuda Akihide Kasai
author_facet	Sayaka Takahashi Shingo Takada Hiroki Yamanaka Reiji Masuda Akihide Kasai
author_sort	Sayaka Takahashi
title	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_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_sort	intraspecific genetic variability and diurnal activity affect environmental dna detection in japanese eel.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/f80261cfd750447481931948a00a0ea7
work_keys_str_mv	AT sayakatakahashi intraspecificgeneticvariabilityanddiurnalactivityaffectenvironmentaldnadetectioninjapaneseeel AT shingotakada intraspecificgeneticvariabilityanddiurnalactivityaffectenvironmentaldnadetectioninjapaneseeel AT hirokiyamanaka intraspecificgeneticvariabilityanddiurnalactivityaffectenvironmentaldnadetectioninjapaneseeel AT reijimasuda intraspecificgeneticvariabilityanddiurnalactivityaffectenvironmentaldnadetectioninjapaneseeel AT akihidekasai intraspecificgeneticvariabilityanddiurnalactivityaffectenvironmentaldnadetectioninjapaneseeel
_version_	1718375217907105792

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

Ejemplares similares