Atlantic and Indo-Pacific separation in Palythoa sibling species: phylogenomic analyses using ultraconserved elements

The delineation of closely related species remains a persistent challenge in Zoantharia, where morphological plasticity and limited genetic differentiation complicate taxonomy. In this study, we investigated the phylogenetic relationship between the widely distributed sibling taxa Palythoa tuberculosa (Indo-Pacific) and Palythoa caribaeorum (Atlantic) using ultraconserved elements (UCEs) recovered from genome skimming. A dataset comprising 116 loci (35,699 bp) across 37 specimens from Brazil, the Red Sea, Okinawa, and New Caledonia was analysed using both concatenated maximum-likelihood and coalescent-based approaches. Phylogenetic reconstructions did not recover monophyletic relationships corresponding to either species or geographic origin, instead revealing intermixed lineages across the Indo-Pacific and Atlantic regions. Concordance factor analyses indicated low gene concordance and moderate site concordance, suggesting pervasive gene tree discordance rather than a lack of phylogenetic signal. These patterns are consistent with previous studies based on mitochondrial, nuclear, and reduced-representation datasets, indicating that increased marker resolution does not resolve species boundaries within this complex. The observed lack of differentiation may reflect ongoing or recent connectivity among populations, potentially facilitated by long-distance dispersal promoted by anthropogenic rafting or historical range expansion, biological invasion, or biological processes such as incomplete lineage sorting. The results support the hypothesis that P. tuberculosa and P. caribaeorum represent a species complex or a case of incipient speciation rather than fully distinct evolutionary lineages. These findings indicate that genome-scale data alone may be insufficient to resolve very recent divergences, supporting the need for integrative approaches to resolve complicated species boundaries in zoantharians.