A fecal sequel: Testing the limits of a genetic assay for bat species identification
Autoři:
Faith M. Walker aff001; Abby Tobin aff001; Nancy B. Simmons aff003; Colin J. Sobek aff001; Daniel E. Sanchez aff001; Carol L. Chambers aff001; Viacheslav Y. Fofanov aff004
Působiště autorů:
Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
aff001; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
aff002; Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
aff003; School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
aff004
Vyšlo v časopise:
PLoS ONE 14(11)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0224969
Souhrn
DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is developing rapidly, which makes it especially important that predictability and reproducibility of DNA metabarcoding assays are explored together with the post-depositional ecology of the target taxon’s fecal DNA. Here, we defined the constraints of an assay called ‘Species from Feces’ used by government agencies, research groups, and non-governmental organizations to identify bat species from guano. We tested assay sensitivity by examining how time and humidity affect the ability to recover and successfully sequence DNA in guano, assessing whether a fecal pellet from a rare bat species could be detected in a background of feces from other bat species, and evaluating the efficacy of Species from Feces as a survey tool for bat roosts in temperate and tropical areas. We found that the assay performs well with feces over two years old in dry, cool environments, and fails by 12 months at 100% relative humidity. We also found that it reliably identifies rare DNA, has great utility for surveying roosts in temperate and tropical regions, and detects more bat species than do visual surveys. We attribute the success of Species from Feces to characteristics of the assay paired with application in taxa that are particularly well-suited for fecal DNA survival. In a time of rapid evolution of DNA metabarcoding approaches and their use with feces, this study illustrates the strengths and limitations of applied assays.
Klíčová slova:
Archaeology – Bats – DNA – DNA extraction – DNA sequencing – Humidity – Sequence assembly tools – Taxonomy
Zdroje
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