Supporting data for "Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment".

There is increasing demand for rapid biodiversity assessment tools that have broad taxonomic coverage. Traditional approaches typically rely on specialists for identification and only evaluate small subsets of biodiversity. Environmental DNA (eDNA) approaches are being promoted as a solution to these limitations, but questions remain unresolved. Here we evaluate a suite of DNA markers coupled with next generation sequencing (NGS) that span the tree of life. We compare these data to traditional biodiversity monitoring tools, including mist-netting and call counts for birds, vegetation surveys, and invertebrate collection with DNA barcoding. Our sampling regime consisted of ten 20 × 20 metre plots, each comprising sixteen 5 × 5 metre sub-plots along a 700 metre elevational gradient on a temperate island forest ecosystem.<br>Across five molecular markers (16S, 18S, ITS, COI and trnL) we collected 3,537,908 sequence reads. From six eDNA data sets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 65 NCBI taxonomy-define phyla or equivalent high-level taxa, ranging from 12 (ITS) to 34 phyla (18S) for a given eDNA marker.