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Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel
- Source :
- PLoS ONE, Vol 16, Iss 9, p e0255576 (2021), PLoS ONE
- Publication Year :
- 2021
- Publisher :
- Public Library of Science (PLoS), 2021.
-
Abstract
- 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.
- Subjects :
- Marine and Aquatic Sciences
Artificial Gene Amplification and Extension
Polymerase Chain Reaction
Biochemistry
Environmental DNA
Marine Fish
Japanese eel
DNA extraction
Energy-Producing Organelles
Multidisciplinary
Eels
Eukaryota
Mitochondria
Circadian Rhythm
Freshwater Fish
Osteichthyes
Vertebrates
Freshwater fish
Medicine
Cellular Structures and Organelles
Research Article
Environmental Monitoring
Fish Biology
Science
Zoology
Marine Biology
Biology
Nocturnal
Bioenergetics
Research and Analysis Methods
Intraspecific competition
Extraction techniques
Species Specificity
Surface Water
Genetic variation
Fish Physiology
Animals
Animal Physiology
Genetic variability
Molecular Biology Techniques
Diel vertical migration
Molecular Biology
Organisms
Biology and Life Sciences
Genetic Variation
Cell Biology
biology.organism_classification
Anguilla
DNA, Environmental
Vertebrate Physiology
Fish
Earth Sciences
Hydrology
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 16
- Issue :
- 9
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....8f725703a4564b387cbbe72720f659f3