Environmental DNA (eDNA) Detection Probability Is Influenced by Seasonal Activity of Organisms

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.

环境DNA（eDNA）在入侵物种或濒危物种监测等保护应用领域展现出巨大潜力，但这一新兴技术仍需开展持续测试，以明确其发挥最佳效果的适用场景。例如，截至目前鲜有研究探讨生物行为或活动的季节性如何影响eDNA的检出概率。我们利用eDNA技术对美国阿拉巴马州黑沃里克河上游流域特有的两种极度濒危物种开展调查：黑沃里克泥螈（Necturus alabamensis）与平背麝香龟（Sternotherus depressus）。值得注意的是，这两个物种的季节性活动模式截然相反：阿拉巴马泥螈在凉季（10月至次年4月）更为活跃，而平背麝香龟则在暖季（5月至9月）活动更为频繁。我们在两年时间内，于凉季与暖季对这两个物种的历史栖息点开展调查，采集多组重复的水样eDNA样本，并在实验室中通过物种特异性定量聚合酶链式反应（qPCR）检测对样本进行分析。随后，我们结合检出概率模型开展占用度估算，以此评估景观属性对物种存在情况的影响，以及采样季节对eDNA检出概率的影响。值得注意的是，我们发现季节对两个物种的eDNA检出概率均有显著影响：阿拉巴马泥螈在凉季的eDNA检出概率更高，而平背麝香龟则在暖季的检出概率更优。本研究结果阐明了生物行为或活动对环境中eDNA检出的影响，并证实了基础自然史知识在设计eDNA监测方案中的重要作用。