Phylogenomics of Palythoa (Hexacorallia: Zoantharia): probing species boundaries in a globally distributed genus

• Published in: Coral reefs Vol. 41; no. 3; pp. 655 - 672
• Main Authors: Dudoit, ‘Ale‘alani, Santos, Maria E. A., Reimer, James D., Toonen, Robert J.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.06.2022; Springer Nature B.V
• Subjects: Bayesian analysis; Biological evolution; Biomedical and Life Sciences; Boundaries; Datasets; Discordance; Freshwater & Marine Ecology; Gene mapping; Genomes; Geographical distribution; Hexacorallia; Life Sciences; Marine invertebrates; Markers; Mitochondria; Oceanography; Oceans; Palythoa; Phylogeny; Probability theory; Resolution; Single-nucleotide polymorphism; Species; Surveying; Taxonomy; Transcriptomes; Tropical climate; Systematics; Next-generation sequencing; Mitochondrial; Holobiont; Transcriptome
• ISSN: 0722-4028; 1432-0975
• DOI: 10.1007/s00338-021-02128-4

Zoantharians (Cnidaria: Hexacorallia: Zoantharia) of the genus Palythoa are ubiquitous species that occupy reef habitats in every tropical ocean. Disagreements among classifications based on morphology, reproductive traits, and molecular techniques have generated taxonomic challenges within this group. Molecular studies provide limited phylogenetic resolution between species, and discordance is frequently attributed to slow mitochondrial rates and lack of resolution among molecular markers. Here we conducted the first phylogenomic survey of Palythoa , using a reduced representation genomic approach (ezRAD) to resolve relationships among eight described and four putative Palythoa species ( N  = 22 plus two outgroups) across the Pacific and Atlantic Oceans. We constructed nearly complete mitochondrial genomes and assembled transcriptome loci datasets by reference mapping. A de novo assembly was performed for the holobiont dataset, and we compared a range of filtering strategies from unfiltered data down to 136 unlinked high-quality biallelic SNPs shared by all samples to resolve evolutionary lineages within Palythoa . Across all these datasets, the resulting Bayesian and ML trees revealed six highly concordant and well-supported clades, however, the phylogenomic data were inconclusive in resolving species relationships within the clades. We detected putative species complexes within two well sampled Palythoa clades (clades I and II), but species delimitation results were inconsistent in whether these clades contain multiple nominal species or represent a single variable species. Polyphyly in the broadly distributed species Palythoa tuberculosa and P. mutuki highlight the need for additional study. Consistency among nuclear and mitogenomic datasets points to a lack of biological understanding of species boundaries among these zoantharians rather than limitations of the molecular markers. More complete taxonomic sampling of nominal species across the geographic ranges of distribution is necessary to resolve species boundaries and evolutionary histories among members of this genus.