Conclusion
Human-related disturbances affect all marine ecosystems by disrupting major interdependent abiotic and biotic factors (Goudie 2018) and these unprecedented threats are likely to increase in the near future, stressing the need to understand and document ecosystems responses (Duarte et al. 2020). Preserving marine biodiversity via protection of species richness has been an explicit aim of management and conservation policies (Qureshi 2017). The functional and phylogenetic associations between species, however, have been gradually incorporated to conserve multiple dimensions of ecosystem diversity. We show that functional and phylogenetic diversity metrics can be derived from eDNA compositional data rapidly sampled from the field. Once the pipeline linking raw eDNA to traits and phylogeny can be automatized, the direct computation of indices will allow a fast translation into indicators that are useful for management, which can serve the monitoring of reef biodiversity over time. Our study provides the foundation for the generation of ecological indices for the long-term monitoring of marine ecosystems. Further analyses at a larger scale covering a wider range of habitats and reef types will enable these diversity patterns to be tested more broadly. Importantly, findings from this study provide further directions for the conservation of coral reefs backed by evolutionary history and trait data.