Monitoring terrestrial wildlife by combining hybridization capture and metabarcoding data from waterhole environmental DNA

Abstract

In conservation science, observation-based methods are generally applied to wildlife monitoring. While useful, such approaches are often restricted to well-characterized and conspicuous species. Environmental DNA (eDNA) can complement observation-dependent surveys, as sample collection is generally less labor-intensive. Furthermore, eDNA can be used to simultaneously detect multiple taxa in various habitats. Most eDNA applications rely on short PCR product-based meta-barcoding approaches. However, such approaches may be less robust when applied to genetically uncharacterized species. Hybridization capture techniques while less sensitive than metabarcoding, can identifying divergent sequences, especially those obtained from highly degraded DNA. To assess eDNA based methods for surveillance in a conservation context, we collected samples during the dry season from randomly selected waterholes from a protected area in eastern Cambodia. We applied both hybridization capture enrichment and metabarcoding targeting mammal mitogenomes to water (N = 46) and sediment (N = 10) samples. Seventeen species were detected, including 11 mammals, three amphibians, two reptiles, and one bird. Six species overlapped between the two applied methods. Seven species were hybridization capture-specific detections, and four were metabarcoding-specific. Metabarcoding was more sensitive to abundant or large body-size species while hybridization capture provided more mitogenomic information. While both methods have some advantages over observational approaches, combining them may improve the sensitivity, number of species detected and amount of genetic information obtained from eDNA. We demonstrate that eDNA from tropical forest waterholes can be used to determine the presence of wildlife that may be difficult to detect using other observational approaches.