Reefscape Genomics: Leveraging Advances in 3D Imaging to Assess Fine-Scale Patterns of Genomic Variation on Coral Reefs

Pim Bongaerts,Caroline E Dubé,Michelle Achlatis,Katharine E Prata,Johanna C Gijsbers,Alejandra Hernandez-Agreda

doi:10.3389/fmars.2021.638979

Abstract

Coral reefs across the world are undergoing rapid deterioration, and understanding the ecological and evolutionary processes that govern these ecosystems is critical to our ability to protect them. Molecular ecological studies have been instrumental in advancing such understanding, and while initially focused primarily on broad-scale patterns, they have gradually uncovered the prevalence of local genetic structuring. Genome-wide sequencing approaches have provided new opportunities to understand both neutral and adaptive contributions to this largely unexplained diversity, but fine-scale assessments have been hampered by challenges associated with aquatic environments, in terms of (geo)referencing, seafloor characterization, and in situ phenotyping. Here, we discuss the potential of “reefscape genomics,” leveraging recent advances in underwater imaging to enable spatially explicit genomic studies on coral reefs. More specifically, we consider how (close-range) photogrammetry approaches enable (1) fine-scale spatial mapping of benthic target organisms, (2) repeatable characterization of the abiotic and biotic reefscape, and (3) simultaneous in situ mass-phenotyping. The spatially explicit consideration of genomic data –combined with detailed environmental and phenotypic characterization– opens up the opportunity for fine-scale landscape genomic approaches on coral reefs (and other marine ecosystems). Such approaches enable assessment of the spatio-temporal drivers and adaptive potential of the extensive genetic structuring and cryptic diversity encountered in benthic invertebrates, such as reef-building corals. Considering the threats that coral reefs are facing worldwide, we believe that reefscape genomics represents a promising advancement of our molecular ecological toolkit to help inform how we can most effectively conserve and restore coral reef ecosystems into the future.

Highlights

Coral reefs are one of the most biodiverse and economically important ecosystems
As advances in genomics have offered the opportunity to transition from few neutral markers to genome-wide assessments, advances in underwater imaging unlock the full potential of these assessments in benthic marine ecosystems by enabling spatially explicit sampling integrated with fine-scale biotic and abiotic characterization
As discussed in this perspective, this provides the unprecedented potential to apply fine-scale landscape genomics approaches to coral reef environments, allowing us to address fundamental knowledge gaps regarding the role of neutral and adaptive processes in the structuring of coral reef biodiversity

Summary

Introduction

Coral reefs are one of the most biodiverse and economically important ecosystems. Yet, they are undergoing an unprecedented decline due to a wide range of anthropogenic stressors (e.g., increasing sea temperatures, ocean acidification, pollution, and overfishing) (Hoegh-Guldberg et al, 2007; McClenachan et al, 2017). Our understanding of reproduction and dispersal processes in benthic reef organisms is still in its infancy given that spatially explicit, individual-based attempts have been incredibly tedious, and have lacked the ability to characterize and integrate the fine-scale composition and configuration of the reefscape.

Results

Conclusion