From jaguars to pathogens: simultaneous genetic detection of diverse taxa across biodiversity hotspots in the U.S. arid southwest

The management of biodiversity on arid landscapes can be challenging: Arid landscapes are often highly vulnerable to environmental and land-use changes. Moreover, these landscapes are home to rare and endemic species which are difficult to monitor. Environmental DNA sampling—the inference of species presence from genetic material in the environment—using high-throughput quantitative PCR (HT-qPCR) panels may be an efficient, cost-effective monitoring tool when multiple, taxonomically diverse taxa are of conservation concern. We validated and applied a HT-qPCR panel to detect ten native, invasive, and pathogenic taxa of relevance to conservation in the arid southwestern United States. We found that the sensitivity and specificity of our HT-qPCR platform was similar to that of single-taxon qPCR (ST-qPCR) (concordance on environmental samples 0.900–1.000, n = 315 samples) and that landscape patterns of detection were largely concordant with previous, conventional sampling. For example, our data reconstructed previously documented ecological patterns: Amphibian pathogens Batrachochytrium dendrobatidis (Bd) and Ranavirus were rare in samples without detection of invasive American bullfrog (Rana catesbeianus; 1.9% and 1.2% respectively), but common where bullfrogs were detected (29.1% and 21.8% of samples). Data generation with HT-qPCR required substantially less time and reagents than would be required using ST-qPCR alone.