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Cephalopod fisheries are increasing, but little is known about the cryptic diversity of some key commercial species. Recent studies have shown that cryptic speciation is common in cephalopods, including several oceanic squids formerly considered ‘cosmopolitan species.’ Further efforts are needed to investigate the cryptic diversity of commercial species, to inform management and support sustainable fisheries practices. Thysanoteuthis rhombus is an oceanic squid, currently recognized as the single species of the family Thysanoteuthidae. Thysanoteuthis. rhombus has a global distribution in tropical and subtropical waters and is an economically important species, with the highest catches occurring off Okinawa in Japan and of potential fishery resource for other countries due to its high abundance and large size. Here, we used sequences from 12S rRNA, 16S rRNA, and cytochrome c oxidase I to characterize its cryptic diversity using samples collected throughout most of its known geographic range. We identified three different putative species whose distributions are concordant with main ocean basins: Thysanoteuthis major, the most abundant species, is widely distributed in the North Pacific Ocean, North Indian Ocean, and limits of the South Atlantic Ocean; Thysanoteuthis rhombus is distributed in the North and South Atlantic Ocean and Mediterranean Sea; and Thysanoteuthis cf. filiferum, likely the least sampled to date, is found in the southwestern Pacific Ocean. A sister relationship was observed between T. rhombus and T. major, and T. cf. filiferum was found to be the most divergent species. Based on our divergence estimation, we hypothesize that the closure of the Isthmus of Panama during the early Pliocene played a significant role in the split of T. rhombus and T. major, while the split of their ancestor from T. cf. filiferum coincided with an increase in the Pacific Walker Circulation and the longitudinal gradient of surface temperatures in the Pacific Ocean during

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

Cryptic speciation among morphologically homogeneous species is a phenomenon increasingly reported in cosmopolitan marine invertebrates. This situation usually leads to the discovery of new species, each of which occupies a smaller fraction of the original distributional range. The resolution of the taxonomic status of species complexes is essential because species are used as the unit of action for conservation and natural resource management politics. Before the present study, Ommastrephes bartramii was considered a monotypic cosmopolitan species with a discontinuous distribution. Here, individuals from nearly its entire distributional range were evaluated with mitochondrial DNA (cytochrome c oxidase subunit I and 16S rRNA). Four distinct species were consistently identified using four molecular species delimitation methods. These results, in combination with morphological and metabolic information from the literature, were used to resurrect three formerly synonymized names (Ommastrephes brevimanus, Ommastrephes caroli and Ommastrephes cylindraceus) and to propose revised distributional ranges for each species. In addition, diagnostic characters from the molecular sequences were incorporated in the species description. At present, only one of the four newly recognized species (Ommastrephes bartramii) is commercially exploited by fisheries in the North Pacific, but it now appears that the distributional range of this species is far smaller than previously believed, which is an essential consideration for effective fisheries management

Cryptic speciation, where distinct species sharemorphological features, has been increasingly reported among marineinvertebrates. In general, the recognition of these distinct species leads to ascenario in which the distribution of each newly discovered species representsa smallfraction of the original distribution range. Because conservation andnatural resourcemanagement politics rely on recognition at the species level, resolvingthe taxonomic status of species-complexes is a crucial task. Until the presentstudy, Ommastrephes bartramii(Lesueur, 1821) was considered a monotypic species of flying squid with acosmopolitan and discontinuous distribution range. However, some morphologicaland metabolic difference between individuals from different regions raised someuncertainties about its taxonomic status. In the present study, molecular dataof cytochrome c oxidase subunit 1 (COI)and 16S rRNA revealed that O. bartramiiactually represents four species. Three previously synonymized names from theliterature were resurrected for the additional species recognized in this genus:Ommastrephes brevimanus(Gould, 1852)comb. nov., Ommastrephes caroli(Furtado, 1887), and Ommastrephes cylindraceusD'Orbigny, 1835 In 1834-1847. Thedistribution range of each species was tentatively drawn based on the availablemolecular data and putative oceanographic features that are acting asreproductive barriers. Only one of thefour newly recognized species is currentlyexploited by commercial fisheries; therefore, understanding the truedistribution range of this species important for fisheries management becauseit is much more restricted than previously believed

The oegopsid squid family Onychoteuthidae was recently revised based on morphology, but sufficient material for a complementary molecular analysis has not been available until now. In the present study, over 250 sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA for 222 individuals were analysed to create a combined phylogeny for the family. Results support monophyly for the family and all seven onychoteuthid genera (including Moroteuthopsis, established herein as the senior genus name for species formerly attributed to Kondakovia); 29 genetically distinct species were recovered, with the BIN analysis for COI showing good congruence overall with morphological species groupings. No sequences were available for five additional known species, making the total family diversity likely to exceed 34 species. Seven of the BINs formed in this study appear to represent undescribed taxa, suggesting that even in this relatively well-studied family, much additional work remains before a comprehensive understanding of the diversity and evolutionary relationships for Onychoteuthidae can be achieved