Mr John Kronenberger1,2, Prof Conrad Hoskin1, Prof Damien Burrows1,2, Dr Cecilia Villacorta-Rath1,2
1James Cook University, Townsville, Australia, 2Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), Townsville, Australia
Biography:
John Kronenberger has specialized in eDNA research for over eight years and is passionate about helping the field maximize its potential. He has developed dozens of targeted assays and innovative methods for assay specificity prediction, high-throughput qPCR, and metabarcoding of novel environmental substrates. Formerly of the National Genomics Center for Wildlife and Fish Conservation—a premier eDNA institution in the United States—John has recently moved to Australia to pursue his PhD at James Cook University. His thesis focuses on sequencing multiple eDNA and eRNA barcodes in parallel to expand inference beyond species detection.
Abstract:
Environmental DNA and RNA (eNA) analyses usually target one barcode per taxon. This may be sufficient for species-level identification, but provides limited data on intraspecific variation and the “ecology” of eNA. Such information is vital for resolving population structure, abundance, and gene expression in environmental samples. In this talk, I will discuss the premise of mitochondrial eNA “profiling,” or simultaneous targeting of multiple barcodes and/or their transcripts to expand inference beyond detection. We have begun trialing this approach using three species endemic to tropical North Queensland—Bloomfield River cod (Guyu wujalwujalensis), Kuranda treefrog (Spicicalyx myola), and Irwin’s turtle (Elseya irwini). Our aim is to haplotype and quantify eNA for each species at four D-loop markers, both rRNA genes (12S and 16S), and several mRNA genes (e.g., CO1, ND4, and CYTB) in parallel. Resulting eNA profiles can be compared across sample replicates to evaluate site consistency. Profiles can be compared across sites to evaluate spatial patterns in (1) eDNA haplotype distribution to infer population structure and relative abundance, (2) eDNA and eRNA quantity to infer relative abundance and distance from occupied habitat, and (3) eRNA quantity by gene to infer relationships with putative drivers of organismal stress. Mitochondrial barcodes are appealing because they have high copy numbers, can be readily confirmed as species-specific, and encode proteins with pivotal physiological functions; simultaneously targeting several may improve estimates and provide novel insights.