Abstract
Environmental DNA (eDNA) holds great promise for conservation applications like the monitoring of invasive or imperiled species, yet this emerging technique requires ongoing testing in order to determine the contexts over which it is effective. For example, little research to date has evaluated how seasonality of organism behavior or activity may influence detection probability of eDNA. We applied eDNA to survey for two highly imperiled species endemic to the upper Black Warrior River basin in Alabama, US: the Black Warrior Waterdog (Necturus alabamensis) and the Flattened Musk Turtle (Sternotherus depressus). Importantly, these species have contrasting patterns of seasonal activity, with N. alabamensis more active in the cool season (October-April) and S. depressus more active in the warm season (May-September). We surveyed sites historically occupied by these species across cool and warm seasons over two years with replicated eDNA water samples, which were analyzed in the laboratory using species-specific quantitative PCR (qPCR) assays. We then used occupancy estimation with detection probability modeling to evaluate both the effects of landscape attributes on organism presence and season of sampling on detection probability of eDNA. Importantly, we found that season strongly affected eDNA detection probability for both species, with N. alabamensis having higher eDNA detection probabilities during the cool season and S. depressus have higher eDNA detection probabilities during the warm season. These results illustrate the influence of organismal behavior or activity on eDNA detection in the environment and identify an important role for basic natural history in designing eDNA monitoring programs.
Highlights
The fields of conservation science and natural resource management are being transformed by a number of molecular approaches that facilitate the measurement and monitoring of PLOS ONE | DOI:10.1371/journal.pone.0165273 October 24, 2016Environmental DNA and Seasonal Activity biodiversity [1,2]
We found that presence of both N. alabamensis and S. depressus was negatively related to area of impervious surface at the watershed scale, and that both species were more likely to occur in the high-gradient headwater streams of smaller watersheds
We found that environmental DNA (eDNA) detection probability for both species was strongly affected by season of sampling, with eDNA detection probability highest for N. alabamensis in the cool season and S. depressus in the warm season, consistent with the known natural history of both species
Summary
The fields of conservation science and natural resource management are being transformed by a number of molecular approaches that facilitate the measurement and monitoring of PLOS ONE | DOI:10.1371/journal.pone.0165273 October 24, 2016Environmental DNA and Seasonal Activity biodiversity [1,2]. Modeling approaches with explicit corrections for detection probabilities (i.e., the rate and causes of false negatives) and the inverse issue of false positives (e.g., sample contamination) have only recently been applied to eDNA and are still not in wide use [10,19,26]. To this list of needs in refining eDNA methodologies for conservation and management, we propose as well that incorporating information on seasonal activity or behavior of focal organisms into evaluations of eDNA performance has to date been largely neglected
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