Coral reef decline persists as a global issue with ties to climate change and human footprint. The SeaFlower Biosphere reserve includes some of the most isolated oceanic coral reefs in the Southwestern Caribbean, which provide natural experiments to test global and/or basin-wide factors affecting coral reefs. In this study, we compared coral and other substrate cover (algae, cyanobacteria, and octocorals), along population densities of keystone urchin species from two atolls (Serrana and Roncador Banks), during 1995, 2003, and 2015/2016. We also surveyed benthic foraminifera as a water quality proxy for coral growth in the last period. A steady reduction in coral cover was clearly observed at Roncador's lagoon, but not at Serrana's reefs, with significant differences between 1995 and 2015/2016. Percent cover of fleshy algae decreased significantly also at Roncador between 1995 and 2003 but did not change notably from 1995 to 2016 at Serrana. However, both Banks exhibited a loss in crustose coralline algae from 2003 to 2015/2016. Likewise, a reduction in bottom complexity, measured as bottom rugosity, was evident between 1995 and 2003. Roncador Bank had unprecedented high octocoral densities, which increased almost threefold from 2003 to 2015. In contrast, urchin densities were low in Roncador; only Diadema antillarum increased from 2003 to 2016 in Serrana Bank. The Foraminifera in Reef Assessment and Monitoring (FORAM) Index (FI) in the two Banks was below the range expected for healthy coral reefs. Although both Banks follow a reduction in CCA and CA cover, Roncador Bank also faces an alarming decline in coral cover, urchins and bottom complexity (rugosity) in contrast to increases in octocoral densities and potential loss of resilience and eutrophication suggested by the FI index. These unexpected findings led us to consider and discuss potential outcomes, where these reefs deteriorate (i.e., erode and drown) providing ideal conditions for octocoral growth. Hence, it is of utmost urgency to start monitoring reef budgets, octocorals and nutrient sources.

Coral cover is decreasing worldwide largely as a result of a rise in seawater temperatures that triggers coral bleaching and induces coral mortality. How coral reefs will respond to climate change will be a function of genetic variation and how it is partitioned within and among species. A critical initial step is to accurately delineate species and quantify their physiological potential to cope with heat stress. Cryptic species are morphologically similar but genetically distinct and may respond physiologically differently to climate change. A dominant Caribbean reef builder severely affected by climate change is the mountainous star coral, Orbicella faveolata. Recently in this journal, Dziedzic et al. reported quantitative genetic variation in the physiological response to thermal stress in a single population of this species, suggesting that variation within populations will allow these corals to adapt to rising ocean temperatures. We reanalysed their data and found multiple cryptic lineages rather than a single panmictic population, with one of the lineages being heat‐intolerant. While different cryptic lineages co‐occur in certain locations, there is at least one lineage that occurs only in a single location. Our finding of hidden lineages within a threatened species highlights the varying extinction risks faced by these independently evolving groups, especially when the prospects of survival under warmer oceans seem favourable for only some of them.

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Confronting a sustained coral reef conservation crisis, we need new opportunities to rethink how to protect areas successfully and efficiently in the face of a changing world. We studied the benthic community, including foraminifera, fish community, and genetic connectivity (SSRs and SNPs) of main reef-building corals, Orbicella faveolata and Agaricia undata, along a Non-Protected Area (NPA) reef tract in Barú peninsula, including some isolated banks, near Cartagena and the National Natural Park Corales del Rosario y San Bernando (NNP CRySB), Colombia. The fringing reef track is homogeneous in benthic components, including algae, sponges, and foraminifera between all the studied sites, while corals exhibited differences between sites and depth ranges. Many reef sites sustain between 42.8 and 53% coral cover, which are among the highest recorded in this region, even higher than the nearby NNP. A total of 82 fish species were found, and the Foram Index-FI varies between 2 and 2.5, showing environmental conditions marginal for reef growth. The Barú NPA reef system can be considered spatial refugia under climate change and Anthropocene conditions, including resilient reefs at the mouth of Cartagena Bay (Magdalena River), a place of increased stressing factors. The admixture between NPA and NNP populations, the high coral cover in the NPA, the fish density and composition, the uniqueness of the diapiric banks, and the disturbance resistance are major arguments to protect this reef tract. We suggest designing a co-management scheme to ensure species connectivity, avoid further degradation, and involve different stakeholders.