Phylogenomics and species delimitation of Primnoidae (class: Octocorallia) utilising ultra-conserved elements sequencing for evolutionary analysis

Previous studies of the deep-sea coral family Primnoidae have relied on mitochondrial and a small number of nuclear genetic markers to reconstruct phylogenies. Here we apply a phylogenomic approach using ultra-conserved element (UCE) loci sequenced from more than 100 Primnoid specimens, with the dual goals of reconstructing a robust phylogeny and testing species boundaries through Bayesian species delimitation. The UCE-based phylogeny produced highly supported topologies, resolving deep divergences and clarifying relationships across the family. Several genera, including Primnoa and Narella, were recovered as strongly monophyletic, while others, such as Plumarella and Primnoella, were shown to be polyphyletic, indicating that some diagnostic morphological characters do not reflect evolutionary history. Previously unsampled genera, including Microprimnoa and Narelloides, were sequenced for the first time and placed into well-supported clades, filling key gaps in Primnoid systematics. To evaluate species boundaries, we conducted coalescent-based species delimitation in BPP on multiple subsets of taxa. In the genus Thouarella, distinct genetic lineages were recovered corresponding to several morphospecies, including T. aureolabyrinthea sp. nov., T. koellikeri, T. viridis, T. brucei, and T. crenelata. By contrast, T. pendulina, T. variabilis, T. diadema, and T. andeep clustered as a single lineage, suggesting these nominal taxa represent morphological variants within one species. Within the Primnoella clade, P. antarctica and O. kuekenthali were genetically indistinguishable, although they are not proposed as synonyms given their distinct morphological traits. A broader BPP analysis across Primnoidae genera supported all tested morphospecies as independent lineages, underscoring general agreement between morphology and genome-scale data. These findings demonstrate the capacity of UCEs to resolve both deep and shallow evolutionary relationships in a family where traditional markers have failed, and they highlight the importance of integrating molecular and morphological evidence when delineating species. This work provides the most comprehensive phylogenomic framework yet produced for Primnoidae, expands molecular sampling to include underrepresented genera, and emphasizes the value of genome-scale data for accurate taxonomy and evolutionary inference in cold-water corals.