Comprehensive Insights into Cnidarian Phylogenetics: cox3-Based Phylogeny, Mitochondrial Genome Variability, Introns, and Gene Rearrangements

Cnidarians, an ecologically and culturally significant group, possess mitochondrial genomes that exhibit several features deviating from conventional textbook descriptions. In this study, we analyzed mitochondrial genomes across various cnidarian orders, revealing significant variation in gene rearrangement patterns. Notably, we found that Anthozoa exhibits highly variable gene arrangements despite slow evolutionary rates, while Hydrozoa demonstrates relatively high levels of gene rearrangement coupled with faster molecular evolution. Our analysis of the cytochrome c oxidase subunit III (cox3) gene provides new insights into cnidarian phylogeny, supporting the monophyly of both Anthozoa and Medusozoa, which aligns more closely with nuclear data and the currently accepted taxonomic scheme. Within Medusozoa, our cox3-based phylogenetic tree reveals strong support for monophyly at the class level. Our reconstruction also suggests a novel topology wherein Staurozoa, Hydrozoa, and Scyphozoa form a sister group to Cubozoa. This finding is particularly significant given the frequent inconsistencies observed in previous mitochondrial gene studies. The cox3 gene's predominant distribution on the heavy(+) strand and limited intron presence in most cnidarian species potentially reduces the impact of strand bias on phylogenetic signal, making it a valuable marker for phylogenetic reconstruction. However, our study also highlights the challenges inherent in using mitochondrial genes for deep phylogenetic reconstructions within Cnidaria. We observed incongruences between nuclear and mitochondrial phylogenies, as well as conflicts among different mitochondrial gene-based studies. These discrepancies underscore the complex nature of cnidarian evolution and the potential limitations of relying on a single type of genetic marker.