Background/Objectives: A comprehensive analysis of the mitochondrial genomes of Japetella diaphana and Amphitretus pelagicus was conducted to investigate their genomic composition, gene size, sequence characteristics, and phylogenetic positioning within the Amphitretidae family. Methods: A rigorous phylogenetic analysis was performed utilizing a dataset comprising 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs derived from 26 cephalopod mitochondrial genomes, representing 25 species across seven families, Vampyroteuthidae, Tremoctopodidae, Octopodidae, Enteroctopodidae, Bolitaenidae, Argonautidae, and Amphitretidae, along with outgroup Nautilus macromphalus. Results: Notably, both focal species demonstrated a pronounced adenine–thymine bias in their mitochondrial genomes, with A. pelagicus exhibiting gene rearrangements and two extensive non-coding regions. The analysis, employing both the maximum likelihood and Bayesian inference methodologies, revealed a monophyletic relationship between Bolitaenidae and Vitreledonellidae, as well as a sister taxon relationship between Amphitretidae and Tremoctopodidae. The majority of species were classified into the Amphitretidae and Bolitaenidae clades, with numerous species exhibiting close phylogenetic relationships. Conclusions: This study provides novel insights into the evolutionary relationships within Octopodiformes, underscoring the significance of mitochondrial genome data in resolving phylogenetic relationships among cephalopods. The findings contribute to our understanding of the evolutionary history of octopi and pose implications for their classification and conservation. Furthermore, the results underscore the necessity for continued research into the evolutionary relationships among cephalopod taxa.
Murwanashyaka et al. (Tue,) studied this question.