Capsule Summary An integrated, high resolution, data-driven regional modeling system has been recently developed for the Red Sea region and is being used for research and various environmental applications.

The southern Red Sea is genetically distinct from the rest of the basin; yet the reasons responsible for this genetic separation remain unclear. Connectivity is a vital process for the exchange of individuals and genes among geographically separated populations, and is necessary for maintaining biodiversity and resilience in coral reef ecosystems. Here, using long-term, high-resolution, 3-D backward particle tracking simulations, we investigate the physical connectivity of coral reefs in the southern Red Sea with neighbouring regions. Overall, the simulation results reveal that the southern Red Sea coral reefs are more physically connected with regions in the Indian Ocean (e.g., the Gulf of Aden) than with the northern part of the basin. The identified connectivity exhibits a distinct monsoon-related seasonality. Though beyond the country boundaries, relatively remote regions of the Indian Ocean may have a substantial impact on the southern Red Sea coral reef regions, and this should be taken into consideration when establishing conservation strategies for these vulnerable biodiversity hot-spots.

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The Red Sea is an extremely warm tropical sea that hosts diverse ecosystems; thus, it is important to understand its ecology in the context of global warming. Using a coupled physical–biogeochemical model validated against in situ data, we provide the first report on the diel cycle (i.e., diel variability) in the Red Sea chlorophyll (CHL) concentration, revealing near-sunset CHL maxima at 17h ± 1h local time over the entire basin. This CHL peak time is considerably later than those reported in most other oceans, suggesting low grazing rates in this high-irradiance tropical sea. Model-based analyses reveal that CHL diel cycle is predominantly controlled by irradiance, whereas longer-timescale (e.g., seasonal) CHL variability is regulated by nutrient availability, suggesting a light-limited biological production at diel timescale. The identified CHL diel cycle comprises a fundamental component of the Red Sea ecology and has implications for CHL remote sensing and in situ measurements.