Not just corals and fishes: distribution modelling and management of dark diversity on coral reefs

Human pressures are increasingly reshaping the biosphere with dire consequences for biodiversity and ecosystem functioning (IPBES, 2019). Collective global action to reverse declines in biodiversity and limit environmental damage have been hindered by a lack of robust indicators of ecological change that can help target vulnerable ecosystems and evaluate the effectiveness of policy decisions. However, next-generation biomonitoring approaches using DNA sequencing now provide the opportunity to create a powerful and rapid indicator of ecological change (Bohan et al., 2017; Dornelas et al., 2019).



DNA sequencing enables rapid estimates of the biological composition and functional attributes of whole ecosystems. It consists of the bulk extraction of DNA from environmental samples, followed by the mass amplification and identification of a multitude of taxa, and functional genes based on universal markers (Leray and Knowlton, 2015; Ransome et al., 2017). These approaches produce enormous quantities of data but remain limited by the lack of standardised analytical pipelines that can generate metrics for use in policy frameworks.



Coral reefs provide an ideal system in which to continue development of bulk environmental DNA analysis for ecosystem monitoring, and its application to evidence-based policy. Coral reefs are exceptionally vulnerable to many of the accelerating global drivers of change which are impacting all ecosystems - so providing an early indicator of the magnitude of future change possible (Hoegh et al., 2017). They are globally threatened and prioritised (Wear et al., 2016) - so ensuring strong public and government attention, and they harbour the greatest diversity of marine species on the planet, including vast cryptic diversity (Pandolf et al., 2003; Jackson et al., 2014; Hughes et al., 2017) - so providing a challenging system for traditional biomonitoring.



This project will use sequencing data from bulk samples of cryptic reef taxa to develop cutting-edge species distribution models across global reefs in collaboration with the Smithsonian Institute Global ARMS Program (https://naturalhistory.si.edu/research/global-arms-program) the project will:



develop tools to better quantify diversity from the cytochrome c oxidase subunit I (COI) gene region, and other taxonomic marker genes, which play pivotal roles in the global effort to document biodiversity;

quantify the inflation of diversity using available methods and tackle current limitations, such as the influence of pseudogenes on species delimitation (Tay et al., 2017; Brandt et al., 2019)

develop joint distribution models of cryptic reef taxa to elucidate key species interactions, using an existing dataset that spans more than 100 reef sites across the Pacific;

use models to explore the role of possible drivers of functional and compositional ecological attributes (e.g. threats and conservation actions) using benthic community data and satellite-derived datasets; and

develop metrics to inform policy recommendations for the monitoring, management and conservation of ecosystems.