Dr Shaun Wilkinson1, Miss Amy Gault1, Dr Andy Hicks2, Mr Daniel Fake2, Dr Bruno David3, Mr Josh Smith3, Dr Alastair Suren4, Dr Nicholas Ling5, Dr Bobby Lust1, Dr Megan Shaffer1, Professor Michael Bunce6
1Wilderlab NZ Ltd., Miramar, Aotearoa New Zealand, 2Hawke’s Bay Regional Council, Napier, Aotearoa New Zealand, 3Waikato Regional Council, Hamilton, Aotearoa New Zealand, 4Bay of Plenty Regional Council, Whakatāne, Aotearoa New Zealand, 5University of Waikato, Hamilton, Aotearoa New Zealand, 6New Zealand Environmental Protection Authority, Wellington, Aotearoa New Zealand
Intense land use and urban development have left much of Aotearoa’s fresh waters in a degraded state. Recent policy reforms including the revised National Policy Statement for Freshwater Management (2020) aim to improve environmental outcomes through integrated, whole-ecosystem monitoring. However, there is a shortage of cost-effective and scientifically-robust tools for measuring ecological condition. For example, Aotearoa’s primary bioassessment tool, the Macroinvertebrate Community Index (MCI), does not consider ecologically important groups such as fish, birds, macrophytes, microeukaryotes and bacteria. Standard assessment methods are further hindered by prohibitive costs, inconsistencies, and a shortage of skilled taxonomists. eDNA analysis offers a powerful and scalable tool with the potential to circumvent this problem, but the accuracy and resolution of taxonomic assignments limit the development of eDNA-based ecological health indices such as a molecular MCI.
Here we show that a taxon-independent community index (TICI) – that objectively assigns indicator values to amplicon sequence variants (ASV) rather than taxa – can significantly improve the statistical power of eDNA-based bioassessments. In collaboration with 14 of Aotearoa’s Regional Councils and Territorial Authorities, we carried out high-replication (n = 16) eDNA sampling at 54 riverine monitoring sites, and used a panel of 11 short-amplicon metabarcoding assays targeting multiple groups including bacteria, microeukaryotes, fungi, plants, inverts and vertebrates. Site-specific TICI values were strongly correlated with MCI (R2 = 0.82), and TICI variation between replicates was minimal (CV = 0.01). This demonstrates the potential for taxon-free eDNA analysis to provide a reliable and low-cost assessment of ecological health in riverine environments.
Biography:
Shaun Wilkinson is the founder and CEO of Wilderlab, Aotearoa New Zealand’s only exclusive eDNA testing laboratory. As a graduate of the University of Wellington, Shaun completed a PhD in genetics and a Rutherford Foundation Postdoctoral Research Fellowship in bioinformatics, where he developed statistical software packages for sequence alignment and classification. Since starting Wilderlab in 2019, Shaun has grown the company to a team of 10 scientists and technicians who oversee the majority of freshwater eDNA work across Aotearoa. Shaun’s research interests include community-based science, molecular assay and bioinformatic software development, integrated ecological monitoring, and taxon-free approaches to eDNA analysis.