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Inference of genetic marker concentrations from field surveys to detect environmental DNA using Bayesian updating.

ABSTRACT: Field studies to detect environmental DNA (eDNA) can be undertaken to infer the presence of a rare or cryptic species in a water body. These studies are implemented by collecting water samples from the water body, processing those samples to isolate genetic material contained in the water sample, and using a laboratory assay to find a species-specific genetic marker within a sample of the genetic material. To date, conventional polymerase chain reaction (PCR) has been one of the most widely used assays in field studies to detect eDNA. This assay is strictly a test for the presence of the genetic marker. It provides no estimate of the concentration of the target genetic marker in the sample or in the environment. Understanding the concentration of a target marker in the environment is a critical first step toward using the results of eDNA field surveys to support inferences about the location and strength of eDNA sources. In this study, the results of eDNA field surveys are combined with a model of the sensitivity of the field survey methods to estimate target marker concentrations using Bayesian updating. The method is demonstrated for Asian carp in the Chicago Area Waterway System (CAWS) using the results of field surveys for eDNA carried out during the period 2009 through 2012, a four-year period during which more than 5,800 two-liter water samples were collected and analyzed using PCR. Concentrations of bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix) eDNA are estimated for twenty hydrologic reaches of the CAWS. This study also assesses the sensitivity of these concentration estimates to evidentiary criteria that limit what evidence is used in Bayesian updating based on requirements for sampling intensity and frequency.

SUBMITTER: Schultz MT

PROVIDER: S-EPMC5790220 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Inference of genetic marker concentrations from field surveys to detect environmental DNA using Bayesian updating.

Schultz Martin T MT

PloS one 20180130 1

Field studies to detect environmental DNA (eDNA) can be undertaken to infer the presence of a rare or cryptic species in a water body. These studies are implemented by collecting water samples from the water body, processing those samples to isolate genetic material contained in the water sample, and using a laboratory assay to find a species-specific genetic marker within a sample of the genetic material. To date, conventional polymerase chain reaction (PCR) has been one of the most widely used ...[more]

PMID: 29381694

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Project description:The environmental DNA (eDNA) method is the practice of collecting environmental samples and analyzing them for the presence of a genetic marker specific to a target species. Little is known about the sensitivity of the eDNA method. Sensitivity is the probability that the target marker will be detected if it is present in the water body. Methods and tools are needed to assess the sensitivity of sampling protocols, design eDNA surveys, and interpret survey results. In this study, the sensitivity of the eDNA method is modeled as a function of ambient target marker concentration. The model accounts for five steps of sample collection and analysis, including: 1) collection of a filtered water sample from the source; 2) extraction of DNA from the filter and isolation in a purified elution; 3) removal of aliquots from the elution for use in the polymerase chain reaction (PCR) assay; 4) PCR; and 5) genetic sequencing. The model is applicable to any target species. For demonstration purposes, the model is parameterized for bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) assuming sampling protocols used in the Chicago Area Waterway System (CAWS). Simulation results show that eDNA surveys have a high false negative rate at low concentrations of the genetic marker. This is attributed to processing of water samples and division of the extraction elution in preparation for the PCR assay. Increases in field survey sensitivity can be achieved by increasing sample volume, sample number, and PCR replicates. Increasing sample volume yields the greatest increase in sensitivity. It is recommended that investigators estimate and communicate the sensitivity of eDNA surveys to help facilitate interpretation of eDNA survey results. In the absence of such information, it is difficult to evaluate the results of surveys in which no water samples test positive for the target marker. It is also recommended that invasive species managers articulate concentration-based sensitivity objectives for eDNA surveys. In the absence of such information, it is difficult to design appropriate sampling protocols. The model provides insights into how sampling protocols can be designed or modified to achieve these sensitivity objectives.

Dataset Information

Inference of genetic marker concentrations from field surveys to detect environmental DNA using Bayesian updating.

Publications

Inference of genetic marker concentrations from field surveys to detect environmental DNA using Bayesian updating.

Similar Datasets

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