Phylogenomic Insights into Cryptic Diversity and Lineage Complexity within the Acropora Genus

Scleractinian corals, particularly the speciose genus Acropora, are the main engineers of coral reefs which is a major contributor to coastal biodiversity and the marine Blue Economy. As climate-driven reef degradation accelerates, active restoration programs relying on the propagation of resilient coral fragments have become critical management strategies. However, the success of these interventions is entirely reliant on on accurate species identification and an understanding of standing genetic diversity. Traditional Acropora taxonomy relies heavily on skeletal morphology, which is often confounded by phenotypic plasticity, morphological convergence, and introgressive hybridization. To investigate these ambiguities, this study used a phylogenomic framework, integrating low-coverage Whole Genome Sequencing (lcWGS) and targeted Ultraconserved Elements (UCEs) across a broad sampling of regional Western Indian Ocean (WIO) and local (Shimoni, Kenya) scleractinian taxa.

Preliminary phylogenetic reconstructions reveal substantial discrepancies between traditional morphospecies assignments and genomic topologies. Initial analyses suggest widespread paraphyly and cryptic diversity within widespread taxa. Notably, the classic "staghorn" morphotype appears to mask distinct evolutionary trajectories; samples morphologically identified as Acropora muricata (reference genome) and Acropora formosa (local lcWGS samples) resolve into deeply divergent clades. In addition, topological mixing was observed among locally sampled lineages, such as the Acropora tenuis and Acropora verweyi complexes, highlighting potential zones of introgression or unresolved species boundaries that single-locus markers fail to capture.

While maximum-likelihood bootstrapping is ongoing to confirm these fine-scale clade structures, the overarching genomic patterns challenge the utility of visual identification alone. These findings suggest that highly generalized coral “species” in the region may actively mask distinct evolutionary, and potentially locally adapted, lineages. Recognizing this hidden diversity is critical as using unresolved species complexes in restoration nurseries risks outbreeding depression and the loss of resilient genotypes. This research advocates for the integration of genomic tools to establish precise evolutionary baselines, ensuring the long-term ecological viability of coral reef restoration initiatives in Kenya, the WIO region and beyond.