High-resolution monitoring of marine vertebrates in changing polar oceans with eDNA

Climate change is particularly pronounced in the polar regions, precipitating widespread range shifts, invasions of new species and losses of others. These changes present significant challenges for conservation of marine vertebrates; thus a suite of biomonitoring strategies is required to help manage marine resources and monitor biodiversity. Furthermore, polar regions provide extreme and expensive field conditions for researchers with many understudied species and a dearth of knowledge on ecosystem functioning.

Monitoring methods such as visual survey, bioacoustics, and biologging are spatially limited and expensive, often requiring extensive ship time and expert knowledge. In many cases, they also do not provide high-resolution taxonomic classification and are not effective in evaluating taxonomically cryptic, elusive or undescribed species. Environmental DNA (eDNA) monitoring is one strategy that could provide a rapid, non-invasive tool to characterise polar vertebrate biodiversity.

Routinely used in, for example, freshwater ecology, eDNA is currently an underdeveloped method for monitoring marine animals. Current eDNA-based methods focus on cataloguing taxa, but rarely generate information on intraspecific community diversity or resilience, nor are they developed for systematic monitoring.

Recent expeditions by Greenpeace, in collaboration with SPYGEN (www.spygen.com) and the University of Montpellier (France), collected 100+ samples from polar regions generating mitochondrial 12S sequence datasets for mammals, teleosts and elasmobranchs. The student will analyse these samples and generate bioinformatic pipelines and protocols that will help to provide the next step in eDNA monitoring for marine ecosystem characterisation and conservation.

Project Aims and Methods

The student will use bioinformatic procedures based on sequence-level classification to maximise the utility of eDNA datasets for biomonitoring to inform the future implementation of eDNA biomonitoring in relation to marine biodiversity management (Figure 1). The PhD student will:

1. Further develop a bioinformatics pipeline to classify eDNA sequence datasets to examine polar communities at the population level (instead of basic cataloguing at the species, genus and family levels) and use the recovered phylogenetic signal to measure intra- and intercommunity diversity as captured by eDNA sampling.

2. Take advantage of available molecular sequence databases, e.g. Genbank (www.ncbi.nlm.nih.gov/genbank) and generated by Tara Ocean Expeditions (www.oceans.taraexpeditions.org) to investigate trophic links between vertebrates and phyto- and zooplankton community diversity.

3. Feedforward results to web-based platforms to visually represent the geographical and temporal distribution of such diversity for better interfacing with end-user management needs.

4. Use existing portable DNA sequencing equipment to trial field protocols that integrate real-time eDNA sequencing and bioinformatic web-based frameworks