Conserved Gene Order and Adaptive Evolution in Mitochondrial Genomes of Calappa Crabs: Insights Into Ecological Specialization and Phylogenetic Utility

Due to their maternal uniparental inheritance, structural conservation, and heterogeneous substitution rates, mitochondrial genomes are critical molecular markers for elucidating lineage diversification and reconstructing high‐resolution phylogenetic trees in marine invertebrates. Before this study, only one complete mitochondrial genome was available for the family Calappidae. We present the first complete mitochondrial genome sequences for five Calappa crab species. These mitogenomes exhibit characteristic features including 37 genes, a high AT nucleotide bias, and structural variation such as incomplete stop codons in certain taxa. Phylogenomic analyses confirmed the monophyly of Calappa . Positive selection analysis identified significant adaptive signals in energy metabolism genes ( ATP6 , ND2 , ND5 ). Specifically, these adaptive mutations likely enhance proton transport efficiency and ATP synthesis during hypoxic burial, reflecting molecular adaptation to high‐energy‐demand environments. Notably, all examined species retain the conserved ancestral gene order of Brachyura, exhibiting remarkable stability in mitochondrial genome organization despite their ecological specialization. This conserved gene arrangement can serve as a reliable phylogenetic marker, although the molecular mechanisms underlying this stability require further investigation across additional brachyuran taxa. This study provides essential molecular resources for Calappidae systematics and Brachyuran evolutionary history, while underscoring the need to integrate future nuclear genomic data to refine higher‐level phylogenies.