Testing The Effectiveness of eDNA Metagenomics To Detect Endemic Wetland Bird Species

Anastasia Rahlin, Matthew L. Niemiller, Mark A. Davis

Research output: Chapter in Book/Report/Conference proceedingConference contribution


In 2017 we collected environmental DNA (eDNA) samples from 18 locations at 4 sites to determine if we could detect migratory bird DNA in samples in order to improve cryptic wetland bird occupancy estimates. Using degenerate bird and vertebrate primers, we successfully detected Sora Rail (Porzana carolina) eDNA in samples. Here we present a reanalysis of our metagenomics data to probe the robustness of our method. Specifically, we sought to assess its ability to detect both rare and common Illinois bird species, and confirm it fails to detect common and rare non-endemic bird species. To test our method, we created custom databases pooling GenBank data for common Illinois wetland bird species: American Coot (Fulica americana) and Great Blue Heron (Ardea herodias); closely-related common wetland bird species not endemic to Illinois: Red-knobbed Coot (Fulica cristata), Hawaiian Coot(Fulica alai), Grey Heron (Ardea cinerea); rare and cryptic Illinois wetland bird species: Sora Rail (Porzana carolina), King Rail (Rallus elegans), and Virginia Rail (Rallus limicola); and rare and cryptic wetland bird species not endemic to Illinois: Spotted Crake (Porzana porzana), Ridgway's Rail (Rallus obsoletus), and the Fasciated Tiger-heron (Tigrisoma fasciatum - sister to Ardea). We used blastn megablast program in Blast2Go software to compare each sequence in our custom database to each sample sequence, using an E-value threshold of 1.0E-10 for positive bird species detections. Our metagenomics approach was able to detect and distinguish between all three local rail species. More unique sequences of common species were detected than of rare or cryptic species. We did not detect non-endemic species other than common Grey Herons and Red-knobbed Coots; rare non-endemic species were never detected. Our method appears robust for detecting rare and cryptic rails in Illinois, however, using eDNA sampling to detect Illinois herons may require creating species-specific primers.
Original languageEnglish (US)
Title of host publicationMidwest Fish and Wildlife Conference 2020
StatePublished - 2020


  • INHS

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