Comparative phylomitogenomic analyses provide insights into adaptation and carcinization in Anomura

Anomura is a morphologically and ecologically diverse infraorder of decapod crustaceans, yet its evolutionary and phylogenetic patterns remain underexplored using mitochondrial genome-based approaches, particularly regarding adaptive evolution across diverse environments. Here, we present a comprehensive phylogenomic analysis of 42 anomuran mitochondrial genomes, including three newly sequenced species: two intertidal Hapalogastrinae (<i>Hapalogaster dentata</i> and <i>Oedignathus inermis</i>) and one deep-sea pagurid (<i>Pagurus rathbuni</i>). The arrangement of protein-coding genes was identical to that reported in previously studied Lithodidae and Paguridae species; however, several tRNA genes exhibited translocations. Moreover, more than half of the 22 tRNA genes were predicted to adopt atypical cloverleaf form, and all protein-coding genes were under purifying selection. In addition, analysis of the mitochondrial control region revealed a conserved repeat structure (∼47 bp motif repeated ∼3.6 times), from which depth-associated Gibbs free energy patterns were broadly inferred. These patterns suggest potential links between control-region stability, depth-dependent adaptation, and the evolutionary process of carcinization. Time-calibrated analyses suggest that <i>H. dentata</i> and <i>O. inermis</i> diverged from other lithodids approximately 37-50 million years ago, while <i>P. rathbuni</i> diverged around 32 million years ago. These divergence events coincide with the Eocene-Oligocene transition, a period characterized by global cooling, sea-level decline, and shifts in ocean circulation. This temporal correspondence suggests that such environmental changes may have been associated with the diversification and adaptive evolution of Anomura. Overall, this study advances our understanding of anomuran phylogeny and highlights the complex interplay among adaptation to the environment, carcinization, and mitochondrial genome evolution.