Beyond Tubipora musica: Phylogenomics unveils the overlooked diversity and endemism of the hermatypic octocoral genus Tubipora

• Ultra-Conserved Elements help delimit species boundaries in the genus Tubipora. • At least 15 species-level lineages of Tubipora occur in the Indo-Pacific region • All recovered lineages appear to be endemic to the locality they were sampled from. • Broader sampling across the Indo-Pacific region is needed. Although scleractinians are typically considered the main reef-building corals, a few octocoral taxa also contribute to coral reef framework formation. The genus Tubipora deposits hard calcareous skeletons organised in tubes connected by horizontal stolonic platforms constituted of fused sclerites. The genus is broadly distributed across the tropical Indo-Pacific, but its diversity and evolutionary history remain poorly understood. Most recent treatments have recognized only the type species Tubipora musica , albeit historically ten species have been named. Here, using an integrative approach combining morphological and phylogenomic (based on Ultra-Conserved Element and exon loci) analyses of 136 Tubipora colonies collected across six marine provinces in the Indo-Pacific, we delimited 15 morphologically distinct and genetically strongly supported lineages. All lineages retrieved in our results exhibited restricted geographic distributions, limited to single areas, highlighting potential regional endemism. Endemic diversification is suggested by sister species restricted to the Red Sea, Madagascar, and Eastern Australia, as well as regional diversification in Arabia, the Western Indian Ocean, and the Western Pacific. Our results reveal deep diversification within the Western Pacific and are consistent with colonization of the Western Indian Ocean by a single clade that subsequently diversified there. Accordingly, these findings underscore the need for broader sampling across the Indo-Pacific to assess Tubipora diversity and diversification and highlight the power of genomics in clarifying species boundaries and evolutionary relationships, providing a foundation towards the taxonomic revision of Tubipora . Accurate species definition is essential for biodiversity assessment and conservation planning, particularly for reef-building taxa that may include geographically restricted lineages vulnerable to environmental change, ultimately enhancing our ability to monitor and mitigate such impacts on these organisms.