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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

Dataset: Photosynthesis and Respiration, This dataset includes photosynthesis and respiration data recorded during experiments conducted to examine two coral species' responses to thermal stress. Species examined were Acropora hemprichii and Porites lobata. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858180, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Photosynthesis and Respiration, This dataset includes photosynthesis and respiration data recorded during experiments conducted to examine two coral species' responses to thermal stress. Species examined were Acropora hemprichii and Porites lobata. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858180, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Temperature, This dataset includes temperature data (in degrees Celsius) measured during two experiments: an 18 h acute thermal stress assay using the Coral Bleaching Automated Stress System (CBASS) and a 14 day chronic heat stress experiment using the Red Sea Simulator (RSS). Experiments were performed in Eilat, Israel in January-February 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858081, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Fv/Fm, This dataset contains values of Fv/Fm (maximum potential quantum efficiency of Photosystem II) for two coral species, Acropora hemprichii and Porites lobata, in response to thermal stress. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858112, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Final Physiology, This dataset includes physiological response metrics recorded at the end of experiments conducted to examine two coral species' responses to thermal stress. Species examined were Acropora hemprichii and Porites lobata. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858150, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Physiological Response Metrics, This dataset describes physiological responses of the coral host and associated endosymbionts measured at the end of the heating hold period and after a recovery period during experiments conducted to test the effects of acute (18 h) and chronic (14 d) thermal stress on the scleractinian coral, Stylophora pistillata. Experiments were conducted in Eilat, Israel in January-February 2019. Methods and results are published in Evensen et al., 2021 (doi: 10.1002/lno.11715). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858036, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Final Physiology, This dataset includes physiological response metrics recorded at the end of experiments conducted to examine two coral species' responses to thermal stress. Species examined were Acropora hemprichii and Porites lobata. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858150, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Physiological Response Metrics, This dataset describes physiological responses of the coral host and associated endosymbionts measured at the end of the heating hold period and after a recovery period during experiments conducted to test the effects of acute (18 h) and chronic (14 d) thermal stress on the scleractinian coral, Stylophora pistillata. Experiments were conducted in Eilat, Israel in January-February 2019. Methods and results are published in Evensen et al., 2021 (doi: 10.1002/lno.11715). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858036, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Temperature, This dataset includes temperature data (in degrees Celsius) measured during two experiments: an 18 h acute thermal stress assay using the Coral Bleaching Automated Stress System (CBASS) and a 14 day chronic heat stress experiment using the Red Sea Simulator (RSS). Experiments were performed in Eilat, Israel in January-February 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858081, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Fv/Fm, This dataset contains values of Fv/Fm (maximum potential quantum efficiency of Photosystem II) for two coral species, Acropora hemprichii and Porites lobata, in response to thermal stress. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858112, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Physiological Response Metrics, This dataset describes physiological responses of the coral host and associated endosymbionts measured at the end of the heating hold period and after a recovery period during experiments conducted to test the effects of acute (18 h) and chronic (14 d) thermal stress on the scleractinian coral, Stylophora pistillata. Experiments were conducted in Eilat, Israel in January-February 2019. Methods and results are published in Evensen et al., 2021 (doi: 10.1002/lno.11715). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858036, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Photosynthesis and Respiration, This dataset includes photosynthesis and respiration data recorded during experiments conducted to examine two coral species' responses to thermal stress. Species examined were Acropora hemprichii and Porites lobata. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858180, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Temperature, This dataset includes temperature data (in degrees Celsius) measured during two experiments: an 18 h acute thermal stress assay using the Coral Bleaching Automated Stress System (CBASS) and a 14 day chronic heat stress experiment using the Red Sea Simulator (RSS). Experiments were performed in Eilat, Israel in January-February 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858081, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Final Physiology, This dataset includes physiological response metrics recorded at the end of experiments conducted to examine two coral species' responses to thermal stress. Species examined were Acropora hemprichii and Porites lobata. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858150, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Fv/Fm, This dataset contains values of Fv/Fm (maximum potential quantum efficiency of Photosystem II) for two coral species, Acropora hemprichii and Porites lobata, in response to thermal stress. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858112, NSF Division of Ocean Sciences (NSF OCE) OCE-1833215, NSF Division of Ocean Sciences (NSF OCE) OCE-1833201

Dataset: Host-Symbiont respiration relationship, Host-symbiont respiration related to symbiont density; anemones from Key Largo from (AnemoneOA project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/649708, NSF Emerging Frontiers Division (NSF EF) EF-1316055

Dataset: Host-symbiont reinfections, Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/649728, NSF Emerging Frontiers Division (NSF EF) EF-1316055

Dataset: Host-Symbiont respiration relationship, Host-symbiont respiration related to symbiont density; anemones from Key Largo from (AnemoneOA project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/649708, NSF Emerging Frontiers Division (NSF EF) EF-1316055

Dataset: Host-symbiont reinfections, Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/649728, NSF Emerging Frontiers Division (NSF EF) EF-1316055

Dataset: Host-symbiont reinfections, Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/649728, NSF Emerging Frontiers Division (NSF EF) EF-1316055

Dataset: Host-Symbiont respiration relationship, Host-symbiont respiration related to symbiont density; anemones from Key Largo from (AnemoneOA project) For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/649708, NSF Emerging Frontiers Division (NSF EF) EF-1316055

High sea surface temperatures often lead to coral bleaching wherein reef-building corals lose significant numbers of their endosymbiotic dinoflagellates (Symbiodiniaceae). These increasingly frequent bleaching events often result in large scale coral mortality, thereby devasting reef systems throughout the world. The reef habitats surrounding Palau are ideal for investigating coral responses to climate perturbation, where many inshore bays are subject to higher water temperature as compared with offshore barrier reefs. We examined fourteen physiological traits in response to high temperature across various symbiotic dinoflagellates in four common Pacific coral species, Acropora muricata, Coelastrea aspera, Cyphastrea chalcidicum and Pachyseris rugosa found in both offshore and inshore habitats. Inshore corals were dominated by a single homogenous population of the stress tolerant symbiont Durusdinium trenchii, yet symbiont thermal response and physiology differed significantly across coral species. In contrast, offshore corals harbored specific species of Cladocopium spp. (ITS2 rDNA type-C) yet all experienced similar patterns of photoinactivation and symbiont loss when heated. Additionally, cell volume and light absorption properties increased in heated Cladocopium spp., leading to a greater loss in photo-regulation. While inshore coral temperature response was consistently muted relative to their offshore counterparts, high physiological variability in D. trenchii across inshore corals suggests that bleaching resilience among even the most stress tolerant symbionts is still heavily influenced by their host environment.

High sea surface temperatures often lead to coral bleaching wherein reef-building corals lose significant numbers of their endosymbiotic dinoflagellates (Symbiodiniaceae). These increasingly frequent bleaching events often result in large scale coral mortality, thereby devasting reef systems throughout the world. The reef habitats surrounding Palau are ideal for investigating coral responses to climate perturbation, where many inshore bays are subject to higher water temperature as compared with offshore barrier reefs. We examined fourteen physiological traits in response to high temperature across various symbiotic dinoflagellates in four common Pacific coral species, Acropora muricata, Coelastrea aspera, Cyphastrea chalcidicum and Pachyseris rugosa found in both offshore and inshore habitats. Inshore corals were dominated by a single homogenous population of the stress tolerant symbiont Durusdinium trenchii, yet symbiont thermal response and physiology differed significantly across coral species. In contrast, offshore corals harbored specific species of Cladocopium spp. (ITS2 rDNA type-C) yet all experienced similar patterns of photoinactivation and symbiont loss when heated. Additionally, cell volume and light absorption properties increased in heated Cladocopium spp., leading to a greater loss in photo-regulation. While inshore coral temperature response was consistently muted relative to their offshore counterparts, high physiological variability in D. trenchii across inshore corals suggests that bleaching resilience among even the most stress tolerant symbionts is still heavily influenced by their host environment.

High sea surface temperatures often lead to coral bleaching wherein reef-building corals lose significant numbers of their endosymbiotic dinoflagellates (Symbiodiniaceae). These increasingly frequent bleaching events often result in large scale coral mortality, thereby devasting reef systems throughout the world. The reef habitats surrounding Palau are ideal for investigating coral responses to climate perturbation, where many inshore bays are subject to higher water temperature as compared with offshore barrier reefs. We examined fourteen physiological traits in response to high temperature across various symbiotic dinoflagellates in four common Pacific coral species, Acropora muricata, Coelastrea aspera, Cyphastrea chalcidicum and Pachyseris rugosa found in both offshore and inshore habitats. Inshore corals were dominated by a single homogenous population of the stress tolerant symbiont Durusdinium trenchii, yet symbiont thermal response and physiology differed significantly across coral species. In contrast, offshore corals harbored specific species of Cladocopium spp. (ITS2 rDNA type-C) yet all experienced similar patterns of photoinactivation and symbiont loss when heated. Additionally, cell volume and light absorption properties increased in heated Cladocopium spp., leading to a greater loss in photo-regulation. While inshore coral temperature response was consistently muted relative to their offshore counterparts, high physiological variability in D. trenchii across inshore corals suggests that bleaching resilience among even the most stress tolerant symbionts is still heavily influenced by their host environment.

Increased sea-surface temperatures linked to warming climate threaten coral reef ecosystems globally. To better understand how corals and their endosymbiotic dinoflagellates (Symbiodinium spp.) respond to environmental change, tissue biomass and Symbiodinium density of seven coral species were measured on various reefs approximately every four months for up to thirteen years in the Upper Florida Keys, United States (1994-2007), eleven years in the Exuma Cays, Bahamas (1995-2006), and four years in Puerto Morelos, Mexico (2003-2007). For six out of seven coral species, tissue biomass correlated with Symbiodinium density. Within a particular coral species, tissue biomasses and Symbiodinium densities varied regionally according to the following trends: Mexico≥Florida Keys≥Bahamas. Average tissue biomasses and symbiont cell densities were generally higher in shallow habitats (1-4 m) compared to deeper-dwelling conspecifics (12-15 m). Most colonies that were sampled displayed seasonal fluctuations in biomass and endosymbiont density related to annual temperature variations. During the bleaching episodes of 1998 and 2005, five out of seven species that were exposed to unusually high temperatures exhibited significant decreases in symbiotic algae that, in certain cases, preceded further decreases in tissue biomass. Following bleaching, Montastraea spp. colonies with low relative biomass levels died, whereas colonies with higher biomass levels survived. Bleaching- or disease-associated mortality was also observed in Acropora cervicornis colonies; compared to A. palmata, all A. cervicornis colonies experienced low biomass values. Such patterns suggest that Montastraea spp. and possibly other coral species with relatively low biomass experience increased susceptibility to death following bleaching or other stressors than do conspecifics with higher tissue biomass levels.

Increased sea-surface temperatures linked to warming climate threaten coral reef ecosystems globally. To better understand how corals and their endosymbiotic dinoflagellates (Symbiodinium spp.) respond to environmental change, tissue biomass and Symbiodinium density of seven coral species were measured on various reefs approximately every four months for up to thirteen years in the Upper Florida Keys, United States (1994-2007), eleven years in the Exuma Cays, Bahamas (1995-2006), and four years in Puerto Morelos, Mexico (2003-2007). For six out of seven coral species, tissue biomass correlated with Symbiodinium density. Within a particular coral species, tissue biomasses and Symbiodinium densities varied regionally according to the following trends: Mexico≥Florida Keys≥Bahamas. Average tissue biomasses and symbiont cell densities were generally higher in shallow habitats (1-4 m) compared to deeper-dwelling conspecifics (12-15 m). Most colonies that were sampled displayed seasonal fluctuations in biomass and endosymbiont density related to annual temperature variations. During the bleaching episodes of 1998 and 2005, five out of seven species that were exposed to unusually high temperatures exhibited significant decreases in symbiotic algae that, in certain cases, preceded further decreases in tissue biomass. Following bleaching, Montastraea spp. colonies with low relative biomass levels died, whereas colonies with higher biomass levels survived. Bleaching- or disease-associated mortality was also observed in Acropora cervicornis colonies; compared to A. palmata, all A. cervicornis colonies experienced low biomass values. Such patterns suggest that Montastraea spp. and possibly other coral species with relatively low biomass experience increased susceptibility to death following bleaching or other stressors than do conspecifics with higher tissue biomass levels.