Based on Mitochondrial Genomes and Gene Order Rearrangements: Phylogenetic Relationships and Terrestrial Adaptability in Paguroidea (Crustacea: Decapoda)

The complete mitochondrial genome provides pivotal information that enhances our understanding of molecular phylogenetic analysis, evolution, and gene rearrangement. Anomura, a decapod taxon with exceptional phenotypic diversity, inhabits hydrothermal vents and various aquatic and terrestrial habitats. However, debates regarding the deep-level phylogeny of Anomura persist, particularly concerning its complex evolutionary relationships. Within this context, the superfamily Paguroidea emerges as a group of significant interest due to its unique biology and potential to illuminate broader anomuran evolutionary questions. Herein, we determined the details of mitogenomes in five Paguroidea species and further investigated phylogenetic relationships and divergence times of Anomura. Our study revealed that Paguroidea is paraphyletic, with its internal relationships still requiring further discussion. Additionally, phylogenetic analyses indicated that Coenobitidae diverged from aquatic Diogenidae and subsequently adapted to terrestrial habitats. Hence, we investigated its mechanisms of genetic rearrangement and conducted a foreground branch selection pressure analysis with Coenobitidae as the focal lineage. Branch-site selection pressure analysis identified positive selection on <i>ATP6</i>, <i>ND3</i>, <i>ND2</i>, <i>ND5</i>, and <i>ND6</i>. Therefore, we hypothesized that Coenobitidae has increased its energy metabolism through the evolution of these genes, which may be advantageous for its adaptation to terrestrial environments. Our findings provide valuable insights into the evolution of Anomura species and offer a theoretical basis for the conservation and utilization of Anomura genetic resources.