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11 pages, 5 figures, 3 tables, supplementary data https://doi.org/10.1016/j.ympev.2023.107729, Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirroteuthidae, Grimpoteuthidae, Opisthoteuthidae and Stauroteuthidae) and six families of Incirrata (Amphitretidae, Argonautidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, and Megaleledonidae) which were assembled using genome skimming. Phylogenetic trees were built using Maximum Likelihood and Bayesian Inference with several alignment matrices. All mitochondrial genomes had the ‘typical’ genome composition and gene order previously reported for octopodiforms, except Bathypolypus ergasticus, which appears to lack ND5, two tRNA genes that flank ND5 and two other tRNA genes. Argonautoidea was revealed as sister to Octopodidae by the mitochondrial protein-coding gene dataset, however, it was recovered as sister to all other incirrate octopods with strong support in an analysis using nuclear rRNA genes. Within Cirrata, our study supports two existing classifications suggesting neither is likely in conflict with the true evolutionary history of the suborder. Genome skimming is useful in the analysis of phylogenetic relationships within Octopoda; inclusion of both mitochondrial and nuclear data may be key, This work was funded by a Tony Ryan Fellowship and an Irish Research Council postgraduate scholarship (GOIPG/2017/1740) to MT. FÁF-Á was supported by an Irish Research Council–Government of Ireland Postdoctoral Fellowship Award (ref. GOIPD/2019/460) and a JdC-I Postdoctoral Fellowship Grant (ref. IJC2020-043170-I) awarded by MCIN/AEI /10.13039/501100011033 and the European Union NextGenerationEU/PRTR. This research was supported by the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). We are grateful to two anonymous referees for their thoughtful contributions

FAMILY BATOTEUTHIDAE YOUNG & ROPER, 1968 (ONE SPECIES) Diagnosis: Medium adult-sized Chiroteuthoidea with arm suckers in two series and tentacle suckers in six series, spanning 80% of tentacle length; photophores in aboral surface of ventral arm tips (large in males, small in females); distinctly curved funnel–mantle locking apparatus; long, unadorned tail supported by secondary conus of gladius. Remarks: Not included in our phylogenetic analyses, but its position within the superfamily is supported provisionally by its morphology (Young & Roper, 1968; Young & Vecchione, 2019c) and the phylogenetic results of Lindgren (2010) and Lindgren et al. (2012)., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1226, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115, {"references":["Young RE, Roper CFE. 1968. The Batoteuthidae, a new family of squid (Cephalopoda; Oegopsida) from Antarctic waters. Antarctic Research Series 2: 185 - 202.","Vecchione M, Young RE. 2019 c. Neoteuthis thielei Naef, 1921. Version 26 March 2019 (under construction). Available at: http: // tolweb. org / Neoteuthis _ thielei / 19926 / 2019.03.26","Lindgren AR. 2010. Molecular inference of phylogenetic relationships among Decapodiformes (Mollusca: Cephalopoda) with special focus on the squid Order Oegopsida. Molecular Phylogenetics and Evolution 56: 77 - 90.","Lindgren AR, Pankey MS, Hochberg FG, Oakley TH. 2012. A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment. BMC Evolutionary Biology 12: 129."]}

SUPERFAMILY OCTOPOTEUTHOIDEA BERRY, 1912 (NINE SPECIES) Diagnosis: Medium or large adult-sized weakly or strongly muscled ammoniacal Oegopsida with buccal connectives attached to the ventral borders of ventral arms; with two series of arm suckers, some or all of which may be modified into hooks; adults without tentacles; the funnel–mantle locking apparatus straight, reaching the anterior margin of the mantle in some species; with secondary conus in the gladius; paralarval tentacle club characteristic, with small compact clubs with a few small and large suckers arranged in two series; with a characteristic mitogenome lacking the oegopsid duplicated genes cox1, cox2, atp6, atp8 and trnD from the duplicated gene block after nad3, with nad2 associated with rrnL as follows: ‘ −rrnL −trnY −trnW −trnG −trnE NC_0 cox3_1 trnK trnR trnS1 nad2 ’; and with rrnS associated with nad3 as follows: ‘ −rrnS −trnM −trnC −trnQ NC_1 cox3_0 trnA trnN trnI nad3 ’., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1229, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115, {"references":["Berry SS. 1912. A catalogue of Japanese Cephalopoda. Proceedings of the Academy of Natural Sciences of Philadelphia 64: 380 - 444."]}

SUPERFAMILY CRANCHIOIDEA PROSCH, 1847 (63 SPECIES) Diagnosis: Small to massive adult-sized Oegopsida with modifications of the funnel–mantle locking apparatus; funnel–mantle locking apparatus reaching the anterior margin of the mantle; with two series of suckers in the arms; tentacle manus suckers usually in four series; mitochondrial gene trnM between rrnL and trnY in the following sequence: −rrnL −trnM − trnY −trnW −trnG −trnE. Synonyms: The superfamilies Ommastrephoidea Steenstrup, 1857b and Thysanoteuthoidea Keferstein, 1866 were described in a different sense than in the present work: the superfamily Ommastrephoidea included Brachioteuthidae, Ommastrephidae and Thysanoteuthidae according to Berry (1920). However, owing to our criteria the families Ommastrephidae and Thysanoteuthidae are included within the superfamily Cranchioidea. We therefore consider the names Ommastrephoidea and Thysanoteuthoidea as junior synonyms of Cranchioidea., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1224, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115, {"references":["Prosch V. 1847. Nogle nye cephalopoder, beskrevne og anatomisk undersogte. Kongelige Danske Videnskabernes Selskabs Skrifter, Naturvidenskabelig og Mathematisk 1: 53 - 72.","Steenstrup J. 1857 b. Oplysning om en ny Art af Blaeksprutter, Dosidicus Eschrichtii. Oversigt over det Kongelige Danske Videnskabernes Selskabs Forhandlinger 1857: 11 - 14.","Keferstein W. 1866. Kopffusser: Cephalopoda Cuvier. In: Bronn HG, ed. Die Klassen und Ordnungen des Thierreiches: Weichthiere (Malacozoa). Leipzig: C. F. Winter, 1307 - 1464.","Berry SS. 1920. Light production in cephalopods, I. An introductory survey. Biological Bulletin 38: 141 - 169."]}

SUPERFAMILY CHIROTEUTHOIDEA GRAY, 1849 (41 SPECIES) Diagnosis: Ammoniacal and weakly muscled Oegopsida with a secondary adult tentacular club but with primary tentacle club in early stages, with protective membranes on clubs symmetrical or subsymmetrical, without carpal locking apparatus, without keel, without terminal pad; buccal connectives attach ventrally to ventral arms; funnel–mantle locking apparatus usually oval, although sometimes modified by projections (tragus and/or antitragus), reaching the anterior margin of the mantle; fins usually terminal; often with a long tail supported by the secondary conus of the gladius during some stages of development. Remarks: Tragus and antitragus refer to two protruding knobs found in the funnel–mantle locking apparatus of some Chiroteuthoidea; see Young & Vecchione (2019c) for more information. Adults of the paedomorphic genus Planctoteuthis Pfeffer, 1912 retain the primary club; hence, the morphological characters related to the tentacle morphology in this diagnosis do not apply to this genus. The funnel–mantle locking apparatus of Grimalditeuthis bonplandi (Vérany, 1839) is fused., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1226, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115, {"references":["Gray JE. 1849. Catalogue of the Mollusca in the collection of the British Museum. Part I. Cephalopoda Artepedia. London: Trustees of the British Museum.","Vecchione M, Young RE. 2019 c. Neoteuthis thielei Naef, 1921. Version 26 March 2019 (under construction). Available at: http: // tolweb. org / Neoteuthis _ thielei / 19926 / 2019.03.26","Pfeffer G. 1912. Die Cephalopoden der Plankton-Expedition. Zugleich eine monographische ubersicht der Oegopsiden Cephalopoden. Ergebnisse der Plankton-Expedition der Humboldt-stiftung 2: 1 - 815.","Verany JB. 1839. Memoire sur six nouvelles especes de Cephalopodes trouves dans la Mediterranee a Nice. Memorie della Reale Accademia delle Scienze di Torino 1: 91 - 98."]}

FAMILY BRACHIOTEUTHIDAE PFEFFER, 1908 B (SEVEN SPECIES IN TWO GENERA) Diagnosis: Small adult-sized, weakly muscled Cycloteuthoidea with many series of small irregular suckers on proximal manus and four series of larger suckers on distal manus; terminal pad present, with central space lacking suckers; funnel–mantle locking apparatus straight, reaching the anterior margin of the mantle; digestive gland located far posterior to the cephalic cartilage; gladius with a secondary conus; paralarvae with long retractile neck connected with a fluid-filled chamber inside the mantle., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1227, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115

FAMILY LEPIDOTEUTHIDAE PFEFFER, 1912 (ONE SPECIES) Diagnosis: Large adult-sized Octopoteuthoidea with overlapping dermal scales on mantle; without photophores; males with hooks near the bases of dorsolateral arms; paralarva with brachial pillar and eyes slightly tubular., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1229, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115, {"references":["Pfeffer G. 1912. Die Cephalopoden der Plankton-Expedition. Zugleich eine monographische ubersicht der Oegopsiden Cephalopoden. Ergebnisse der Plankton-Expedition der Humboldt-stiftung 2: 1 - 815."]}

SUBFAMILY TODARODINAE ADAM, 1960 (NINE SPECIES IN FOUR GENERA) Diagnosis: Medium to large adult-sized Ommastrephidae without photophores; funnel groove with foveola, without lateral pockets; tentacles without carpal locking apparatus; tentacle club with horny rings of manus suckers with homogeneous dentition; four series of suckers on dactylus; diameter of the lateral suckers of the paralarva proboscis larger than or equal to the central ones; paralarvae with skin sculpture; adult female with multiple seminal receptacles in the buccal membrane., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1225, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115, {"references":["Adam W. 1960. Notes sur les Cephalopodes XXIV: contribution a la connaissance de l'hectocotyle chez les Ommastrephidae. Bulletin de l'Institut Royal des Sciences Naturelles de Belgique 36: 1 - 10."]}

FAMILY CYCLOTEUTHIDAE NAEF, 1923 (FOUR SPECIES IN TWO GENERA) Diagnosis: Medium adult-sized ammoniacal Cycloteuthoidea with four series of suckers on the tentacle clubs; with subtriangular funnel–mantle locking apparatus not reaching the anterior margin of the mantle; gladius with secondary conus or without conus., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1227, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115

SUPERFAMILY ENOPLOTEUTHOIDEA PFEFFER, 1900 (57 SPECIES) Diagnosis: Oegopsida with eight or the remnants of eight buccal supports, the ventral supports attached to the dorsal margins of ventral arms; with photophores; two series of arms suckers usually with hooks; four series of tentacle suckers in young stages, sometimes reduced in adults; spermatangia usually attached to specialized tissue in the nuchal region. Remarks: According to Berry (1920), this superfamily included the families Benthoteuthidae Pfeffer, 1900 (= Bathyteuthidae), Enoploteuthidae, Gonatidae, Histioteuthidae, Lampadioteuthidae Berry, 1916, Lycoteuthidae, Octopoteuthidae and Onychoteuthidae. This taxonomic composition does not agree with our phylogenetic results (Fig. 3)., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1227, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115, {"references":["Pfeffer G. 1900. Synopsis der oegopsiden Cephalopoden. Mitteilungen aus dem Naturhistorischen Museum Hamburg 17: 147 - 198.","Berry SS. 1920. Light production in cephalopods, I. An introductory survey. Biological Bulletin 38: 141 - 169.","Berry SS. 1916. Cephalopoda of the Kermadec Islands. Proceedings of the Academy of Natural Sciences of Philadelphia 68: 45 - 66."]}

SUBFAMILY ILLICINAE POSSELT, 1891 (FOUR SPECIES IN ONE GENUS) Diagnosis: Medium adult-sized Ommastrephidae without photophores; funnel groove without foveola or lateral pockets; tentacles without carpal locking apparatus; tentacle club with manus horny sucker rings smooth or with rounded teeth; eight series of suckers on dactylus; lateral suckers of the paralarva proboscis equal in diameter to the central ones; paralarvae without skin sculpture; adult female without seminal receptacles in the buccal membrane., Published as part of Fernández-Álvarez, Fernando Á, Taite, Morag, Vecchione, Michael, Villanueva, Roger & Allcock, A Louise, 2022, A phylogenomic look into the systematics of oceanic squids (order Oegopsida), pp. 1212-1235 in Zoological Journal of the Linnean Society 194 (4) on page 1225, DOI: 10.1093/zoolinnean/zlab069, http://zenodo.org/record/6457115, {"references":["Posselt HI. 1891. Todarodes sagittatus (Lmk.) Stp., En anatomiskstudiemedBemaerkingeromSlaegtskabsforholdet mellem Ommatostrephfamiliens Genera. Videnskabelige Meddelelser fra den Naturhistoriske Forening I Kjobenhavn 1890: 301 - 359."]}