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Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications
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Assessing environmental DNA detection in controlled lentic systems.

Gregory R Moyer1, Edgardo Díaz-Ferguson2, Jeffrey E Hill3

  • 1United States Fish and Wildlife Service, Conservation Genetics Laboratory, Warm Springs, Georgia, United States of America.

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Summary

Environmental DNA (eDNA) sampling for rare species requires careful strategy. Detecting African jewelfish eDNA is more likely at the surface, with higher fish density increasing detection probability.

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Area of Science:

  • Environmental DNA (eDNA) analysis
  • Aquatic ecology
  • Conservation genetics

Background:

  • Environmental DNA (eDNA) sampling strategies for rare species are underexplored.
  • Accurate species detection hinges on understanding false positive and negative error rates.

Purpose of the Study:

  • To assess African jewelfish eDNA detection at varying densities using artificial ponds.
  • To identify optimal water strata for eDNA sampling.
  • To estimate eDNA detection rates and determine necessary sample volumes for reliable detection.

Main Methods:

  • Utilized artificial ponds with controlled African jewelfish densities (0-5.25 fish/m³).
  • Collected 324 1-L water samples across different water strata.
  • Applied logistic regression models to analyze eDNA detection probability in relation to fish density and water temperature.

Main Results:

  • eDNA detection probability increased with fish density and decreased with water temperature.
  • Surface and bottom water strata yielded the highest eDNA detection rates.
  • At high densities, 3-5 L of water ensured >95% detection probability; low densities required >100 L.

Conclusions:

  • Effective eDNA sampling for rare species necessitates optimizing water stratum and volume based on estimated species density.
  • Achieving high certainty of detection at low densities may require filtering hundreds of liters of water.
  • Occupancy modeling frameworks can help mitigate biases from incomplete eDNA detection.