DOI: 10.5061/dryad.4558p38
title: Data from: Shifting up a gear with iDNA: from mammal detection events to standardized surveys

description: 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 analyse 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 may 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 robustness similar to that of
 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 robust and standardized
 sampling scheme. 4.Synthesis and applications. Here, we describe an
 approach to analyse detection records of mammals derived from leech
 samples using an occupancy framework that accounts for leech‐specific
 factors influencing the detection probability. We further combined
 camera‐trap and leech data, which lead to increased confidence in
 occupancy estimates. Our approach is not restricted to the processing of
 leech samples, but can be used for the analysis of other invertebrate DNA
 (iDNA) and environmental DNA (eDNA) data. Our study is the first step to
 shift the application of iDNA studies from opportunistic ad‐hoc
 collections to the systematic surveys required for long‐term management of
 wildlife populations.
description: all species
 detecteddata for the detections
 of all species in camera traps and leechesall_species_detected.csvcamera trap input datainput data for single species models using only camera trap detection historiescam_trap_input.Rdetections and sizedetection data for camera traps and leeches (broken down by leech type), as well as body size information for each speciesdetections_and_size.csvmodel code combinedJAGS model code for the combined datasetmodel_combined.txtmodel code camera trapJAGS model code analysing the camera trap datasetmodel_CT.txtmodel code leechJAGS model code for analysing the leech datasetmodel_leech.txtWeather analysis datazip file containing the data and code used to analyse leech collection success dependence on Keetch-Byram Drought IndexWeather.zipleech input datainput data for single species models using only leech detection historiesleech_input.Rcombined input datainput data for single species models using the combined leech and camera trap data setscombined_input.R