Multi-tool Monitoring: eDNA Sample Collection and Processing Protocol: Water, Tree roller, Soil and Scat sampling v1

This protocol describes the collection, extraction, and initial processing of environmental DNA (eDNA) samples used in a multi-tool vertebrate monitoring study in the Scottish Highlands, UK. Sampling was conducted in June 2023 with the aim to understand the comparative effectiveness of different sample-types. The methods outlined here cover: Sample collection from water, soil, tree surfaces, and scat Contamination control practices throughout sampling and filtering DNA extraction using modified Mu-DNA protocols Preparation of samples for sequencing, amplifying the 12S mitochondrial gene region to detect vertebrate DNA Bioinformatics and taxonomic assignment, including quality control This protocol is part of an integrated monitoring approach that also includes camera traps and passive acoustic recorders, with the goal of assessing vertebrate taxonomic, functional, and trophic diversity. The procedures are modular and may be adapted for other terrestrial field studies involving eDNA.