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.

The order Zoantharia (= Zoanthiniaria, Zoanthidea) remains one of the most taxonomically neglected anthozoan groups, primarily owing to the difficulty of examining the internal morphology of sand-encrusted zoanthids, upon which classification has been largely based until very recently. Additionally, relatively few zoanthid species (all belonging to the genus Epizoanthus) have been properly described from the deep-sea. Numerous individuals of an unidentified sediment-encrusting zoanthid-like species were observed and sampled during a Shinkai 6500 deep-sea submersible dive at a methane cold seep (depth 3259 m) off Muroto at the Nankai Trough, Japan. Unlike previously described deep-sea zoanthids, Abyssoanthus nankaiensis, gen. et sp. nov. (Abyssoanthidae fam. nov.) was found to be non-colonial, free-living (non-commensal), and, uniquely, on mudstone in the vicinity of a methane cold seep. Morphologically, A. nankaiensis, gen. et sp. nov. is characterised by its relatively uniform polyp diameter from oral to aboral end with 19–22 mesenteries. Additionally, DNA (mitochondrial 16S rDNA and mitochondrial cytochrome oxidase c subunit I DNA) sequences obtained from these samples also unambiguously place this specimen in a previously undescribed and new family within the order Zoantharia. This is the first reported zoanthid species from a methane cold seep or other so-called ‘extreme’ environment, and the first molecular characterisation of any such deep-sea zoanthid.

Okinawa, Japan is known for its high marine biodiversity, yet little work has been performed on examining impacts of numerous large-scale coastal development projects on its marine ecosystems. Here, we examine apparent impacts of the construction of the Kaichu-Doro causeway, which was built over 40 years ago. The causeway is a 4.75 km long embankment that divides a large tidal flat and has only two points of water exchange along its entire length. We employed quadrats, transects, sampling, visual surveys, and microbial community analyses combined with environmental, water quality data, and 1m cores, at five stations of two paired sites each (one on each side of Kaichu-Doro) to investigate how the environment and biota have changed since the Kaichu-Doro was built. Results indicate reduction in water flow, and site S1 was particularly heavily impacted by poor water quality, with low diversity and disturbed biotic communities.