Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
KAUST Repository Item: Exported on 2023-05-23
Acknowledgements: Funding for the virtual workshop during which the content of this manuscript was developed was provided by the National Science Foundation Division of Biological Oceanography (OCE 2127506; 2127514; and 2127508 to Sarah W. Davies, Adrienne M. S. Correa, and John Everett Parkinson, respectively). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We would like to thank Dan Thornhill, Allison Lewis, and Joanna Shisler at NSF for attending and facilitating the workshop, and Andrea Grottoli, Jody Harwood, Krista Liguori, Amy Pruden, and Rebecca Vega Thurber for advice on running workshops. We thank Julia Baum, David Baker, Ramkumar Balakrishnan, Arthur Grossman, Sridhar Jayavel, Thomas Krueger, Mikhail Matz, Rajesh Kannan Murugesan, Ramakritinan Chockalingam Muthiah, Sivakumar Natesan, and Michael Sweet for feedback throughout the development of this work. We appreciate reviewer feedback we received on the manuscript from Tom Oliver, an anonymous reviewer, and Rob Toonen (handling editor at PeerJ). Finally, we thank all Symbiodiniaceae researchers, past and present, whose research has helped shape our understanding of Symbiodiniaceae diversity and biology.
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