Application of Omics Tools in Designing and Monitoring Marine Protected Areas For a Sustainable Blue Economy

Abstract

A key component of the global blue economy strategy is the sustainable extraction of marine resources and conservation of marine environments through networks of marine protected areas (MPAs). Connectivity and representativity are essential factors that underlie successful implementation of MPA networks, which can safeguard biological diversity and ecosystem function, and ultimately support the blue economy strategy by balancing ocean use with conservation. New “big data” omics approaches, including genomics and transcriptomics, are becoming essential tools for the development and maintenance of MPA networks. Current molecular omics techniques, including population-scale genome sequencing, have direct applications for assessing population connectivity and for evaluating how genetic variation is represented within and among MPAs. Effective baseline characterization and long-term, scalable, and comprehensive monitoring are essential for successful MPA management, and omics approaches hold great promise to characterize the full range of marine life, spanning the microbiome to megafauna across a range of environmental conditions (shallow sea to the deep ocean). Omics tools, such as eDNA metabarcoding can provide a cost-effective basis for biodiversity monitoring in large and remote conservation areas. Here we provide an overview of current omics applications for conservation planning and monitoring, with a focus on metabarcoding, metagenomics, and population genomics. Emerging approaches, including whole-genome sequencing, characterization of genomic architecture, epigenomics, and genomic vulnerability to climate change are also reviewed. We demonstrate that the operationalization of omics tools can enhance the design, monitoring, and management of MPAs and thus will play an important role in a modern and comprehensive blue economy strategy.

Leveraging the genetic diversity of trout in the rivers of the British Isles and northern France to understand the movements of sea trout (Salmo truttaL.) around the English Channel

“…Nevertheless, to determine the efficacy of MPAs, to regulate fisheries and contribute to policy we require knowledge of where and when individuals are at sea (O’Sullivan et al, 2022). Genetic assignment studies, such as that presented here can help identify both fish movements and fisheries pressure on species, thereby providing evidence crucial to the designation and meaningful placement of MPAs (Jeffery et al, 2022).…”

Genomic vulnerability of a freshwater salmonid under climate change

“…Assessing the vulnerability of populations and species to climate change is pivotal for management and conservation. This information can be used to inform the creation of protected areas, guide habitat restoration, prioritize research and monitoring resources, and design assisted migration strategies (Chen et al., 2022; Jeffery et al., 2022). In kokanee, stocking for recreational fishing is a common practice in many parts of its range and represents a potentially viable tool to mitigate the effects of climate change on vulnerable populations.…”

Reference genome for the California ribbed mussel,Mytilus californianus, an ecosystem engineer

“…Despite growing larger in length and producing twice as much meat as M. edulis in exploratory aquaculture studies ( Yamada and Dunham 1989 ), there is a gap in the literature when it comes to aquaculture studies for M. californianus compared with its sister taxa, which this genome may help redress. Second, with biodiversity conservation as a motivator of the CCGP project, the M. californianus genome can act as a foundation for future work understanding the genetic diversity and population connectivity for planning marine protected areas (MPAs) and MPA networks ( Jeffery et al 2022 ). This reference genome, coupled with future population genomics study, will deepen our understanding of the evolutionary history of this species and give us a better understanding of how the population is structured, providing a foundation for future genomic studies on ecosystem engineers across the west coast of North America.…”