Genome skimming elucidates the evolutionary history of Octopoda

11 pages, 5 figures, 3 tables, supplementary data https://doi.org/10.1016/j.ympev.2023.107729Phylogenies 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 keyThis 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 contributionsPeer reviewe

Updated taxonomy of the genus Ommastrephes d’Orbigny, 1834 (Oegopsida: Ommastrephidae)

Cephalopod International Advisory Council Conference (CIAC 2018) : Cephalopod Research Across Scales: From Molecules to Ecosystems, 12-16 November 2018, St. Petersburg, Florida, USA.-- 1 pageCryptic 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 believedPeer Reviewe

A mitochondrial phylogeny of the family Onychoteuthidae Gray, 1847 (Cephalopoda: Oegopsida)

10 pages, 3 figures, 2 tablesThe 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 (Barcode Index Number) 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 the Onychoteuthidae can be achievedThis work was supported by the New Zealand government under “Coasts & Oceans” core funding from the Ministry of Business, Innovation and Employment (project: Food-web dynamics of New Zealand marine ecosystems)Peer reviewe

A Mitochondrial Phylogeny of the Family Onychoteuthidae Gray, 1847 (Cephalopoda: Oegopsida)

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 (Barcode Index Number) 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 the Onychoteuthidae can be achieved

Molecular phylogenetic analysis of the squid family Histioteuthidae (Mollusca, Cephalopoda)

Cephalopod International Advisory Council Conference (CIAC 2018) : Cephalopod Research Across Scales: From Molecules to Ecosystems, 12-16 November 2018, St. Petersburg, Florida, USA.-- 1 pageHistioteuthid squids are an important part of marine food webs, being abundant in the diets of many predators. Although they represent a substantial biomass in the deep sea, their systematics are not fully understood; damaged (especially ex-gut-content) and paralarval specimens are difficult to identify morphologically, since most morphological characters presently used to distinguish species involve external photophore patterns. The purpose of this study was to test a morphological hypothesis for the division of the family Histioteuthidae into species groups using two mitochondrial genes (cytochrome c oxidase subunit I [COI] and 16S rRNA). Both the Bayesian and maximum-likelihood analyses supported the division of this family into six genera (formalising previously hypothesised species groups): Calliteuthis, Fragariateuthisgen. nov. Histioteuthis, Histiothauma, Naviagen. nov., andStigmatoteuthis. Barcode Index Numbers based on COI and 16S rRNA were used to distinguish 17 currently accepted species, and revealed up to nine additional species, including potentially new, unnamed species. A DNA barcode reference library of sequences generated in this study is available on the Barcode of Life Data Systems (BOLD), which can be used to confirm identifications or identify damaged specimens, such as those from gut contents. This study is the largest, most complete phylogenetic analysis of this family to datePeer Reviewe

Cryptic biodiversity in the commercial diamondback squid Thysanoteuthis rhombus Troschel 1857

21 pages, 4 figures, 3 tables, supplementary information https://doi.org/10.1007/s11160-023-09813-3.-- Data availability: Alignments and raw data generated can be found in FigShare (https://doi.org/10.6084/m9.figshare.22559374). All the new sequences generated here are in the National Center for Biotechnology Information (NCBI) database under the GenBank accession numbers OP970836-OP970872 (cytochrome oxidase c subunit I.), OP970877-OP970912 (16S ribosomal RNA), and OP971221-OP971257 (12S ribosomal RNA)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 the Late Oligocene and Early Miocene. Our work identifies three different putative species within Thysanoteuthis and has potential use for improving fishery management and conserving the diversity in these speciesD.D. was supported by The Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) fellowship. G.S. wants to thank the support of the 22K15085 Grant-in-Aid for Early-Career Scientists (KAKENHI). F.Á.F.-Á. was supported by a JdC-I Postdoctoral Fellowship Grant (ref. IJC2020-043170-I) awarded by MCIN/AEI https://doi.org/10.13039/501100011033, by a Beatriu de Pinós fellowship from Secretaria d'Universitats i Recerca del Departament de Recerca i Universitats of the Generalitat de Catalunya (Ref. BP 2021 00035), the project ECOPHYN (Ref. PID2021-126824NB-C32, Ministerio de Ciencia e Innovación, Gobierno de España) and the European Union and the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). A.E was supported by a Margarita Salas Postdoctoral Fellowship Grant awarded by Ministry of Universities of Spanish government and is thankful to the support of project DEEPCOM (Ref. CTM2017-88686-P, Ministerio de Ciencia e Innovación, Gobierno de España). We are thankful to the Director of ICAR-CMFRI, Kochi, India for facilities and support. CH. S. is thankful to the support of the JSPS KAKENHI Grant-in-Aid for Early-Career Scientists, Grant Number 19K15901Peer reviewe