Dr Emma Carroll1, Dr Richard O'Rorke
1University Of Auckland
Biography:
Emma Carroll is a molecular ecologist and statistical modeller whose lab uses genomics, isotopes, telemetry data, life history and novel statistical models to investigate and monitor natural populations.
Abstract:
Marine mammals are considered ecosystem sentinels as their populations integrate information across the food chain and respond to environmental change or disturbance. They are also often species of importance for conservation or cultural reasons. However, many eDNA studies use genetic markers that do not fully resolve species identity. A commonly used DNA barcoding marker for cetaceans is the mitochondrial control region, but current methods use non-specific primers and target a region too long for Illumina platforms. Here we present a phylogenetic clustering approach to design minimally degenerate primers that amplify four short (~200bp) contiguous regions of taxonomically informative DNA for whales, dolphins and porpoises. Each sequenced region contains its neighbour’s primer binding site and therefore enables detection of sequence diversity that was not available during primer design due to biased databases. We apply this panel, dubbed CetSet, to eDNA, bone and varying quality tissue samples and report on efforts to develop a curated reference dataset.