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Aim: The ecosystem functions and services of coral reefs are critical for coastal communities worldwide. Due to conservation resource limitation, species need to be prioritized to protect desirable properties of biodiversity, such as functional diversity (FD), which has been associated with greater ecosystem functioning but is difficult to quantify directly. Selecting species to maximize phylogenetic diversity (PD) has been shown to indirectly capture FD in certain other taxa but not corals. Here, we test this hypothesis, the "phylogenetic gambit", on corals within global marine protected areas (MPAs). Location: Global coral reefs. Methods: Based on the global distributions of reef corals, a complete species‐level phylogeny and trait data, we compared the FD of coral assemblages within MPAs when selected to maximize PD versus FD for assemblages selected randomly. The relationships between PD and FD were also tested as predictors of surrogacy. We then used coral FD and PD to perform spatial prioritization of reefs for protection and assessed the congruence between the two approaches. Results: Selecting assemblages to maximize PD captured significantly more FD than a random subset of species for 83.1% of all selection scenarios across MPAs and would protect on average 18.7% more FD than random selection. Spatial prioritization analyses showed some mismatches between PD‐ and FD‐optimized planning units, particularly in the Tropical Western Atlantic, but the high degree of overlap between the optimizations for other reef regions lends further credence to the PD‐maximizing strategy in conserving coral FD. Main Conclusions: A PD‐maximizing strategy generally protects greater FD of coral assemblages relative to random selection of species, suggesting that the "phylogenetic gambit" is valid for reef corals. There are risks, however, and the mismatches between PD‐maximized and FD‐maximized MPA networks highlight specific shortcomings of the PD‐maximization approach. Nevertheless, in data‐deficient circumstances, maximizing PD may provide a viable alternative. [ABSTRACT FROM AUTHOR]

• Understanding spatial and temporal trends of diversity is crucial for conservation. • This study analyses long-term data from 1986 to 2020 on Singapore reefs. • Taxonomic and phylogenetic diversity increased but functional diversity declined. • Reefs shifted towards dominance of stress-tolerant traits such as slow growth. • Trait-based approaches at finer taxonomic resolution will enhance reef monitoring. Coral reefs provide a multitude of ecosystem functions owing to the high levels of biodiversity they host. Coral species, as the foundation of shallow-water reefs, differ in their contributions toward the functioning of the ecosystem due in part to the disparate phylogenetic histories of scleractinian lineages. Understanding the spatial patterns and temporal trajectories of these biodiversity facets, as well as their interrelationships, is critical for more targeted conservation strategies in the face of widespread habitat degradation and climate change. Here, we analyse long-term benthic data spanning 1986 through 2020 on coral reefs in Singapore, which have been impacted by decades of urbanisation-related and thermal stressors, to test for differences between coral biodiversity facets—specifically, taxonomic, phylogenetic (evolutionary relatedness between species), and functional (occupancy of functional trait space) richness and diversity. Analyses show that taxonomic and phylogenetic richness and diversity measures increased over the 35-year period despite declines during major bleaching events. Yet, while taxonomic and phylogenetic diversity increased, functional richness and diversity declined over the same period. Community-weighted trait measures indicate a shift towards dominance of more stress-tolerant traits such as slower growth rates, smaller corallite sizes, and massive colony forms. Together, these trends highlight the effects of chronic urban stressors alongside major bleaching events impacting reef assemblages. Critically, such assemblage shifts and functional diversity declines were masked by increasing taxonomic diversity, which is most commonly assessed, and could erode ecosystem resilience. The temporal decoupling of the biodiversity facets examined here underscore the need for more comprehensive monitoring of reefs through a combination of trait-based approaches alongside traditional field surveys at finer taxonomic resolution. [ABSTRACT FROM AUTHOR]

Information about the distribution of alleles among marine populations is critical for determining patterns of genetic connectivity that are essential in modern conservation planning. To estimate population connectivity in Singapore's urbanized equatorial reef system, we analysed single nucleotide polymorphisms (SNPs) from two species of reef‐building corals with distinct life histories. For Porites sp., a broadcast‐spawning coral, we found cryptic lineages that were differentially distributed at inshore and central‐offshore sites that could be attributed to contemporary surface current regimes. Near panmixia was observed for Pocillopora acuta with differentiation of colonies at the farthest site from mainland Singapore, a possible consequence of the brooding nature and relatively long pelagic larval duration of the species. Furthermore, analysis of recent gene flow showed that 60–80% of colonies in each population were nonmigrants, underscoring self‐recruitment as an important demographic process in this reef system. Apart from helping to enhance the management of Singapore's coral reef ecosystems, findings here pave the way for better understanding of the evolution of marine populations in South‐East Asia. [ABSTRACT FROM AUTHOR]

• Bacterial communities are temporally dynamic whereas Symbiodiniaceae are stable in an equatorial reef system. • No monsoonal or environmental effect on any directional shifts in bacterial communities. • Partnerships between bacteria and Symbiodiniaceae members are associated with biogeochemical and physiological processes. • Long-term studies shed insight into holobiont community dynamics and are critical in guiding restoration efforts. Coral-associated bacteria and Symbiodiniaceae are critical for maintaining the health of their coral hosts. Factors that are known to affect the coral microbiome include biogeography, seasonality, and environmental change, but longitudinal studies are sorely lacking. Many temporal studies rarely extend beyond a year, limiting the conclusions that can be drawn. In this study, we characterised both the bacterial and Symbiodiniaceae communities in three species of corals— Merulina ampliata , Pachyseris speciosa , and Porites lutea —found in an equatorial reef over a two-year period. Furthermore, we investigated the effect of monsoon seasons on the pattern of bacterial and Symbiodiniaceae communities using metabarcoding methods. We found significant differences in bacterial communities through time and space, but no consistent patterns of diversity between seasons and environmental conditions (temperature and rainfall) were observed. Conversely, Symbiodiniaceae communities did not differ over time and space. Taken together, our results suggest that bacterial communities, even within a stable climate regime, were highly dynamic through time, but were not affected by monsoonal variations. Finally, network analyses of bacteria and Symbiodiniaceae revealed multiple potential biogeochemical processes that worked in tandem between the members of the coral holobiont to support holobiont functioning. Longitudinal studies on host-associated microbial diversity are critical for drawing relevant conclusions about the long-term effects of environmental change on the coral holobiont, and for directing conservation efforts. [ABSTRACT FROM AUTHOR]