scholarly journals Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling

2020 ◽  
Author(s):  
Keiichi Fukaya ◽  
Hiroaki Murakami ◽  
Seokjin Yoon ◽  
Kenji Minami ◽  
Yutaka Osada ◽  
...  
Keyword(s):  
Quantitative Data ◽  
Environmental Dna ◽  
Fish Population ◽  
Hydrodynamic Modelling ◽  
Population Abundance

scholarly journals Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling

2018 ◽  
Author(s):  
Keiichi Fukaya ◽  
Hiroaki Murakami ◽  
Seokjin Yoon ◽  
Kenji Minami ◽  
Yutaka Osada ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Cost Effective ◽  
Population Monitoring ◽  
Fish Population ◽  
Abundance Estimation ◽  
Population Abundance ◽  
Jack Mackerel ◽  
Non Invasive ◽  
Quantitative Measurements ◽  
Japanese Jack Mackerel

AbstractWe propose a general framework of abundance estimation based on spatially replicated quantitative measurements of environmental DNA in which production, transport, and degradation of DNA are explicitly accounted for. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. These findings indicate the ability of environmental DNA to reliably reflect population abundance of aquatic macroorganisms and may offer a new avenue for population monitoring based on the fast, cost-effective, and non-invasive sampling of genetic information.

scholarly journals Transect sampling promotes higher detection rates compared to discrete sampling for environmental DNA applications

2021 ◽  
Vol 4 ◽  
Author(s):  
Thiago Sanches
Keyword(s):  
Detection Probability ◽  
Environmental Dna ◽  
Common Species ◽  
Fish Population ◽  
Probability Of Detection ◽  
Detection Rates ◽  
Indirect Measure ◽  
Real Distribution ◽  
Transect Sampling ◽  
The Impact

The use of environmental DNA (eDNA) to monitor species in aquatic environments has rapidly increased over the past decade. eDNA has consistently outperformed other methods of detection, yet eDNA relies on an indirect measure to estimate the real distribution of a species. Therefore, understanding the environmental factors that disperse eDNA is of major importance. Here we modeled the use of transect sampling for eDNA studies and also model the impact of river advection on detection radius and the expected probability of detection. Our model suggests that transect sampling: 1) increases the detection probability for both rare and common species, thus reducing the frequency of false negatives, 2) diminishes the standard deviation of the detection probability, which in most cases means higher reproducibility of eDNA studies, 3) better estimates systemwide trends of fish population distinguishing zones of multiple fishes from zones where few fishes are present, and 4) diminishes the effects of eddies and river velocity on the detection probability and detection radius. We propose the use of transect sampling as an alternative method of eDNA sampling with benefits that surpass the disadvantages of not being able to pinpoint the exact fish location. Our model also suggests that even short transects (less than 100 m) can yield considerable benefits compared to point sampling.

Hierarchical model detects decadal changes in calibration relationships of single-pass electrofishing indices of abundance of Atlantic salmon in two large Canadian catchments

2019 ◽  
Vol 76 (4) ◽  
pp. 523-542 ◽  
Author(s):  
Guillaume J.R. Dauphin ◽  
Gérald Chaput ◽  
Cindy Breau ◽  
Richard A. Cunjak
Keyword(s):  
Atlantic Salmon ◽  
Fish Population ◽  
Sampling Procedure ◽  
Population Abundance ◽  
New Techniques ◽  
Single Pass ◽  
Sampling Protocols ◽  
Using Data ◽  
The Relationship ◽  
Index Of Abundance

Electrofishing is a commonly used technique to assess freshwater fish population abundance, and in many programs, there has been a shift in the sampling methodologies towards less laborious techniques. These new techniques usually only provide an index of abundance and require calibration with other sampling methods such as successive removal to be used for absolute abundance estimation. Using data for juvenile Atlantic salmon (Salmo salar) collected in 400 sites sampled over 21 years in two large Canadian river catchments with a single sampling protocol, we developed a hierarchical Bayesian model to account for effort, day of sampling, area of the site, and catchment effects on the relationship between the single-pass index of abundance and the fish densities, thereby illustrating the importance of carrying out a calibration exercise on a regular basis. Our work indicates that calibration relationships can change over time even with standardized sampling protocols and that these directional changes in important components of the sampling procedure can bias the estimate of population abundance and misinform the understanding of population dynamics.

scholarly journals Lake sediment DNA as a proxy in fish population studies: analytical challenges and opportunities

2021 ◽  
Author(s):  
Doreen Yu-Tuan Huang ◽  
Richard Bindler ◽  
Christian Bigler ◽  
Sofia Ninnes ◽  
Fredrik Olajos ◽  
...  
Keyword(s):  
Population Studies ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Extraction Methods ◽  
Fish Population ◽  
Mountain Lakes ◽  
Ecological Studies ◽  
Conventional Pcr ◽  
Challenges And Opportunities ◽  
Dna Extraction Methods

Abstract Sedimentary environmental DNA (sed-eDNA) coupled with metabarcoding is increasingly exploited for ecological studies, but application of the method to resolve fish dynamics in lakes still needs better validation. This study (1) evaluated the sed-eDNA yields from the commonly used DNeasy PowerSoil DNA Kit from mineral-rich and organic-rich sediments and (2) examined the viability of fish sed-eDNA recovery and detection in surface sediment samples from 13 Swedish mountain lakes, with organic contents of 18–52%, by using conventional PCR and droplet digital PCR. Based on concurrent fish-population surveys these lakes contain arctic char and brown trout. We show that, compared to other specifically designed lysis buffers, the DNeasy PowerSoil DNA Kit is less effective to recover DNA from organic-rich sediments and almost 50% of the extracted DNA was lost during purification steps. The amplification of fish sed-eDNA using conventional PCR with teleo primers failed to detect positive signals; whereas ddPCR assays enabled quantification of amplifiable DNA in all the extracts. However, further molecular cloning of the positive ddPCR droplets from one sediment sample revealed amplified sequences of unidentified origin that cannot be aligned well to fish. Thus the performance of the teleo primers for quantification of fish sed-eDNA detection requires further examination. For detection of fish sed-eDNA for ecological studies, we suggest that DNA extraction methods and primers should be carefully selected and the performance of ddPCR to detect DNA at low quantities needs to be further scrutinized to circumvent the pitfalls of false positives.

Statistical Processing of Different Sounds of Vocalizing Fish and Mammals to Estimate Their Population Size With Two Acoustic Sensors

2019 ◽  
Vol 53 (4) ◽  
pp. 68-80 ◽  
Author(s):  
Shaik Asif Hossain ◽  
Monir Hossen
Keyword(s):  
Population Size ◽  
Statistical Processing ◽  
Environmental Dna ◽  
Marine Species ◽  
Statistical Signal Processing ◽  
Fish Population ◽  
Processing Technique ◽  
Population Estimation ◽  
Human Interaction ◽  
Signal Processing Technique

AbstractFish and mammals have an enormous impact on marine ecosystems. A proper estimation of their population size is necessary, not only for their ecological values but also for commercial purposes. Most conventional techniques for estimating fish population are visual sampling techniques, the environmental DNA (eDNA) technique, minnow traps, the removal method of population estimation, and echo integration techniques, all of which are sometimes complex and costly, require human interaction, and can be harmful for marine species. In order to overcome these limitations, in this paper, a passive acoustic fishery monitoring technique is proposed as an alternative. The method is based on a statistical signal processing technique called “cross-correlation” and different types of sounds—namely, chirps, grunts, growls, clicks, and so forth—produced by fish and mammals. Our goal was not only to propose an efficient technique for fish population estimation but also to measure its performance for different fish sounds by using numerical simulations. From the analyses of simulated results, we found that the chirp sound-generating species produced better results than the other two types of sound-generating species—the grunt- and growl-generating species.

Application of a Multispecies Approach for Assessing the Population Abundance and the Age–Structure of Fish Stocks

1981 ◽  
Vol 38 (4) ◽  
pp. 424-431 ◽  
Author(s):  
Jacek Majkowski
Keyword(s):  
Fish Species ◽  
Age Structure ◽  
Cohort Analysis ◽  
Laboratory Data ◽  
Single Species ◽  
Fish Predation ◽  
Fish Population ◽  
Natural Mortality ◽  
Population Abundance ◽  
Fish Stocks

Application of a multispecies approach for assessing the population abundance and the age-structure of fish stocks is proposed. The main objective of this approach is to eliminate a bias in the results of cohort analysis (the most frequently used single-species procedure for assessing the fish population age-structure) caused by uncertainties in the external estimates of natural mortality rates. The approach is applicable if fish predation is a major cause for fish natural mortality and all fish species which significantly interact among themselves through predation are taken into account. It is additionally assumed that these fish species do not leave the area under consideration. Compliance with these conditions allows the prediction, on the basis of ecological theory and required field and laboratory data, of a major component of natural mortality, predation mortality, within extended cohort analysis. The paper describes the proposed procedure (extended cohort analysis) and outlines possible ways of collecting the required input data.Key words: assessment, fish population abundance, age-structure, multispecies approach, natural and fishing mortality

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