Shifting up a gear with iDNA: from mammal detection events to standardized surveys

Abstract

1. Invertebrate-derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost-efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statistical framework that allows for robust biodiversity assessments.2. Here, we compare concurrent iDNA and camera-trap surveys. Leeches were repeatedly collected in close vicinity to 64 camera-trap stations in Sabah, Malaysian Borneo. We analyze iDNA-derived mammalian detection events in a modern occupancy model that accounts for imperfect detection and compare the results with those from occupancy models parameterized with camera-trap-derived detection events. We also combine leech-iDNA and camera-trap data in a single occupancy model.3. We found consistent estimates of occupancy probabilities produced by our camera-trap and leech datasets. This indicates that the metabarcoding of leech-iDNA method provides reasonable estimates of occupancy and can be a suitable method for studying and monitoring mammal species in tropical rainforests. However, we also show that a more extensive collection of leeches would be needed to assess mammal biodiversity with a similar robustness as with camera traps. As certain taxa were only detected in leeches, we see great potential in complementing camera-trap studies with the iDNA approach, as long as the collection of leeches follows a similar robust and standardized sampling scheme. 4. Synthesis and applications. The approach we describe here is not restricted to the processing of leech samples, but can be used for the analysis of other iDNA and environmental DNA (eDNA) data. Our study is the first step to shift the application of e/iDNA studies from opportunistic ad-hoc collections to systematic surveys required for long-term wildlife populations and biodiversity monitoring programs.

Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems

“…Comparisons of species detection by traditional survey approaches and eDNA analysis are now numerous in the literature, and mainly focus on what is and what is not detected within and across different methods (Hänfling et al, ; Leempoel et al, ). Yet, there has been growing incorporation of occupancy modelling to estimate the probability of detecting the focal species, in comparison to one other survey method, either for a single species (Lugg et al, ; Tingley et al, ) or multiple species (Abrams et al, ; Valentini et al, ). Simultaneous multi‐method comparisons for multiple species have been lacking and this study directly addresses this for the first time.…”

“…At present, we would recommend the use of eDNA metabarcoding alongside other non‐invasive surveying methods (e.g. camera traps) when monitoring invasive species or species of conservation concern to maximize monitoring efforts (Abrams et al, ; Sales, Kaizer, et al, ).…”

“…The use of eDNA sampling to generate species‐specific detection data has unsurprisingly increased in recent years, and in many cases has outperformed or at least matched conventional survey methods (Lugg, Griffiths, van Rooyen, Weeks, & Tingley, ; Tingley, Greenlees, Oertel, van Rooyen, & Weeks, ). Although comparisons between eDNA analysis and conventional surveys for multi‐species detection are numerous (see table S1 in Lugg et al, ), studies focusing on detection probability estimates for multiple species identified by metabarcoding are rare (Abrams et al, ; Valentini et al, ).…”

Shifting up a gear with iDNA: From mammal detection events to standardised surveys

“…Data and scripts supporting this manuscript are available from Dryad Digital Repository https://doi.org/10.5061/dryad.4558p38 (Abrams et al., ). We have anonymised both species and station names as it contains sensitive information about endangered and threatened species.…”

Monitoring Mammal Community Shifts Across Silvicultural Treatments Utilizing Camera Traps and the Development of Invertebrate- Derived Dna in Hardwood Forests of North America

“…Abrams et al (2018) found that the leeches' effectiveness was dependent on the species of the leech. Each leech species had specific mammals it fed off of and the preferential feeding lead to brown leeches (Haemadipsa zeylanica) having DNA from less abundant mammal species, while more abundant species within the mammalian community were detected through tiger leeches (Haemadipsa picta; Abrams et al 2018). The host preference directly affects the species found when utilizing iDNA which can limit the mammals detected.…”