Atlantic and Indo-Pacific separation in Palythoa sister species: a phylogenomic analysis using ultraconserved elements across Brazil, the Red Sea, Okinawa, and New Caledonia

Zoantharian systematics has been constrained by pronounced morphological plasticity and slow mitochondrial evolution obscuring species limits. This thesis applies ultraconserved elements (UCEs) recovered via genome skimming to evaluate whether the sister pair Palythoa tuberculosa (Indo–West Pacific) and Palythoa caribaeorum (western Atlantic) represent reciprocally exclusive species or a species complex. Specimens from Brazil, the Red Sea, Okinawa, and New Caledonia were processed with a PHYLUCE bioinformatic pipeline. Sequencing data were quality-filtered, assembled, matched to Hexacorallia UCE targets and compiled into concatenated supermatrices under multiple occupancy thresholds. Maximum-likelihood phylogenies were inferred in IQ-TREE with per-locus partitioning and UFBoot2; topology sensitivity was assessed with Robinson–Foulds distances; regional clustering with a parsimony tip-shuffle; and genetic depth with pairwise patristic distances. Primary results focus on the 45% and 55% supermatrices. Trees are genetically shallow (total tree length ≈ 0.25–0.28 substitutions/site) with modest tip-proximal support. P. caribaeorum tips are non-monophyletic in all matrices; a faint Brazil adjacency at 45% disappears under stricter occupancy. Robinson-Foulds comparisons show stronger topological sensitivity at 55% than at 65–70%. Patristic medians are low (~2–2.4% substitutions/site) and between-basin values do not exceed within-basin values. Parsimony scores indicate no more regional clustering than expected by chance. These patterns are consistent with short internodes and incomplete lineage sorting at UCE depths rather than reciprocal exclusivity. On present evidence, P. tuberculosa and P. caribaeorum either represent a single widespread species or a species complex whose boundaries remain unresolved. Limitations include sparse Brazil specimens, concatenation without explicit species-tree or introgression tests, and absence of matched morphology. Nonetheless, this appears to be the first UCE-based assessment of the sister pair, providing a conservative UCE framework for future integrative work.