Cephalopod Species Research Articles

Paucispecific invertebrate associations in the Coniacian (Upper Cretaceous) Essen Formation (Tébessa Mountains, northeast Algeria)

The Coniacian strata of the Tébessa Mountains in northern Algeria are predominantly marly facies that have received few studies. The present study is the first one to be carried out at Djebel Essen (west of Tébessa) to reveal the paleoenvironmental setting. The macrofossil taxa identified herein include fifteen bivalve species, three gastropods, and one cephalopod species, in addition to four irregular echinoid species. Quantitative analysis of these macrofossils indicates the occurrence of three benthic Coniacian macrofaunal associations, which include: 1) Agelasina plenodonta, 2) Cucullaea, and 3) Oscillopha-Plicatula. Both Agelasina plenodonta and Cucullaea associations are dominated by infauna. However, Cucullaea Association contains only suspension-feeders, where deposit-feeders are completely absent, suggesting oligotrophic conditions, that might have resulted in the lowest diversity level. In contrast, epifaunal taxa dominated the Oscillopha-Plicatula association. All the three associations are paucispecific. This low diversity of the Coniacian associations at study area and in other North African countries, can be attributed to the retreat of the sea and the shrinking of shallower habitats’ area. Probably, these associations lived within restricted marginal marine environments. The absence of any potential indicator of the middle-upper Coniacian anoxic event (OAE-3) agrees with the case in nearby sections and confirms a restricted extent of this event. The occurrence of many taxa of either regional or cosmopolitan affinity suggests episodic connection with the Tethyan Ocean.

Unveiling Encrypted Antimicrobial Peptides from Cephalopods' Salivary Glands: A Proteolysis-Driven Virtual Approach.

Antimicrobial peptides (AMPs) have potential against antimicrobial resistance and serve as templates for novel therapeutic agents. While most AMP databases focus on terrestrial eukaryotes, marine cephalopods represent a promising yet underexplored source. This study reveals the putative reservoir of AMPs encrypted within the proteomes of cephalopod salivary glands via in silico proteolysis. A composite protein database comprising 5,412,039 canonical and noncanonical proteins from salivary apparatus of 14 cephalopod species was subjected to digestion by 5 proteases under three protocols, yielding over 9 million of nonredundant peptides. These peptides were effectively screened by a selection of 8 prediction and sequence comparative tools, including machine learning, deep learning, multiquery similarity-based models, and complex networks. The screening prioritized the antimicrobial activity while ensuring the absence of hemolytic and toxic properties, and structural uniqueness compared to known AMPs. Five relevant AMP datasets were released, ranging from a comprehensive collection of 542,485 AMPs to a refined dataset of 68,694 nonhemolytic and nontoxic AMPs. Further comparative analyses and application of network science principles helped identify 5466 unique and 808 representative nonhemolytic and nontoxic AMPs. These datasets, along with the selected mining tools, provide valuable resources for peptide drug developers.

Nutritional properties of commercially important cephalopods from the south-west coast of India

Cephalopods are widely regarded as healthy and nutritionally rich seafood resources. This study focuses on analysing the nutritional composition of six commercially important edible cephalopod species viz., Cistopus indicus, Amphioctopus marginatus, Amphioctopus aegina, Sepia pharaonis, Sepia elliptica and Sepia aculeata, from the Malabar coast of the Indian peninsula. The selected cephalopods were determined to be a rich source of protein ranging from 12.41 to 19.02 g 100 g-1. The amino acid profile demonstrated a balanced ratio of essential to non-essential amino acids (0.93-1.63) with a higher concentration of essential amino acids, attributing enhanced biological value of proteins in these cephalopods. S. pharaonis recorded the highest arginine-to-lysine ratio (~1.77), indicating excellent cholesterolemic index. Notably, octopus species had the lowest total cholesterol content (~100 mg 100 g-1) compared to cuttlefish species which recorded higher cholesterol levels (~160 mg 100 g-1). A. marginatus recorded more significant quantities of polyunsaturated fatty acids (PUFA) (36.85% total fatty acids) among all the species studied. Octopus species exhibited significantly greater Σn-3/Σn-6 ratio than cuttlefish species. The ideal atherogenicity/thrombogenicity indices (<1.0) in the edible tissues of the studied cephalopods qualify these species as potentially healthy food. A. aegina was found to exhibit greater vitamin E (α-tocopherol) contents (17.84 IU), whereas ascorbic acid was pronounced more in A. marginatus (47.06 μg 100 g-1). The higher vitamin D3 content in A. aegina (96.23 μg 100 g-1) among the species studied, highlights its potential role in preventing osteoporosis in adults. Among microelements such as iron and zinc were found in significant quantities in the cephalopod species studied. The findings from the current study provide valuable insights into the nutritional benefits of these species, positioning them as promising candidates for the seafood industry as possible healthy dietary options. Keywords: Amino acid composition, Atherogenicity index, Cephalopods, Fatty acid composition, Thrombogenicity index

Potential impacts of climate change on cephalopods in a highly productive region (Northwest Pacific): Habitat suitability and management

Cephalopods occupy a mid-trophic level in marine ecosystems and are vital both ecologically and as fishery resources. However, under the pressure of climate change and fishing, the sustainability of cephalopod resources requires reasonable management. This study aims to study climate change and fishing impacts on the common economic cephalopod species habitats using species distribution models. We take the northwest Pacific Ocean region as an example, which stands out as a significant region for cephalopod production around the world. Results found that the habitats of cephalopods are moving to higher latitudes or deeper waters (Bohai Sea, mid-bottom Yellow Sea, and the Okinawa Trough waters) under climate change. Additionally, these regions are currently under lower fishing pressure, which suggests that species migration might mitigate the effects of warming and fishing. This study provides the large-scale assessment of the distribution range of cephalopods affected by climate change coping with fishing pressure in the northwest Pacific Ocean. By identifying climate refuges and key fishing grounds, we underscore the importance of this information for managing cephalopod resources in the context of climate adaptation and sustainable fishing practices.

Prevalence of environmental microplastics in Taiwan and its impact on the seafood safety: An integrative review

AbstractHuman activity has led to microplastic contamination throughout the marine environment. As a result of widespread contamination, microplastics are ingested by many species of wildlife, including fish, cephalopods, and shellfish. Taiwan is surrounded by oceans that offer a rich range of seafood. Taiwanese residents can easily acquire seafood as a source of dietary protein. A recent research project by Greenpeace shows that the Taiwanese eat 16,000 microplastic particles per year. There is concern regarding microplastic physical and chemical toxicity, which poses potential health risks to the local community via food chains. Thus, monitoring microplastic contamination in seafood is imperative to provide helpful information for the government and local communities. Efforts should be taken to reduce microplastic pollution at the source to minimize potential effects on ecological and health safety. This review article emphasizes the urgent need for further research on microplastic pollution in Taiwan, highlights the potential challenges to mitigate this emerging environmental threat, and analyzes food safety hazards as well as microplastic contamination in seafood.

A Pilot Study on the Diel Vertical Migration Pattern of Mesopelagic Fishes in the Southern and Central South China Sea

The diel vertical migration of mesopelagic fishes in the southern (S-May station and S-Nov station) and central (C-Jun station and C-Dec station) South China Sea was investigated through a series of continuous field surveys conducted in May, June, November, and December 2017. These surveys employed a combination of mid-water trawl and acoustics techniques. The diel migration process, vertical distribution, acoustic migration proportion, and migration pattern of mesopelagic fishes were analyzed. The results revealed that mesopelagic fishes initiated an upward migration before sunset, with the process concluding within 30–120 min after dark. Subsequently, they commenced a downward migration before dawn, which terminated within 10–50 min after sunrise. The mesopelagic deep-sea layers of mesopelagic fishes at the S-May, S-Nov, C-Jun, and C-Dec stations ranged from 360 to 700 m, 350 to 680 m, 350 to 520 m, and 300 to 700 m, respectively. The acoustic migration proportions of mesopelagic fishes at the corresponding stations were found to be approximately 44.5%, 25.7%, 29.8%, and 58.0%, respectively. There were seasonal and regional differences in the vertical migration and distribution patterns of mesopelagic fishes in the South China Sea. A total of 228 species were identified, including 203 fish species, 23 cephalopod species, and 2 shark species. Among these, a subset of 43 fish and cephalopod species exhibited extensive diel vertical migrating behavior. Specifically, this subset comprised 23 lanternfish species, 8 cephalopod species, and 12 other fish species. Lanternfishes were the predominant diel vertical migratory species, while cephalopods also played a significant role in diel vertical migration. The diel migration behavior was found to be slight for Diaphus lucidus, Melamphaes microps, Argyropelecus affinis, and six other fish species. Non-migratory behavior was observed in Sternoptyx obscura, Argyropelecus sladeni, Sternoptyx diaphana, and 13 other fish species. The diel migration habits of 178 additional species of fish, cephalopods, and sharks could not be definitively determined.

Long-term annual trawl data show shifts in cephalopod community in the western Barents sea during 18 years

Climate change is threatening marine ecosystems on a global scale but particularly so in the Arctic. As a result of warming, species are shifting their distributions, altering marine communities and predator-prey interactions. This is known as the Atlantification of the Arctic. Warming may favor short-lived, opportunistic species such as cephalopods, marine mollusks that previously have been hypothesized to be winners in an ocean of change. To detect temporal regional trends in biodiversity, long-term annual surveys in hotspots of climate change are an unparalleled source of data. Here, we use 18 years of annual bottom trawl data (2005–2022) to analyse cephalopods in the western Barents Sea. More specifically, our research goals are to assess temporal trends in cephalopod fauna composition, abundance and biomass, and to relate these trends to climate change in the western Barents Sea. Main changes in cephalopod diversity and distribution occurred in mid-2000s and early 2010s, which corresponds with a period of warming in the Arctic since the late 1990s/early 2000s. Repeated increased occurrence of the boreal-subtropical cephalopods was recorded from 2005–2013 to 2014–2022. Moreover, the abundance of cephalopods in the area (in general and for most taxa) increased from 2005–2013 to 2014–2022. These observations suggest that the cephalopod community of the Barents Sea is subjected to Atlantification since the 2005–2013 period. This corresponds with previously reported evidence of the Atlantification in fishes and benthic invertebrates in the Barents Sea and benthic invertebrates. ‘Typical’ Arctic cephalopod species such as Bathypolypus spp., Gonatus fabricii and Rossia spp., however, are still much more abundant in the western Barents Sea compared to the deep-sea and the boreal-subtropical species. We also found indirect indications for body-size reduction in Bathypolypus spp. from 2005–2013 to 2014–2022. Overall, the temporal trends in the Barents Sea cephalopod fauna provide evidence for changing marine communities in the Arctic.

A comparative analysis of the puncturing abilities of cephalopod beak rostra using engineering tools

Cephalopods, a diverse class of carnivorous marine predators, exhibit a wide range of feeding behaviours and foraging strategies related to their lifestyle, habitat and morphological adaptations. Their beaks play a crucial role in capturing and processing prey. This study investigates the link between the shape of the rostrum of cephalopod beaks and their function through a mix of experimental and computational approaches. Fourteen upper beak rostrum models from a range of cephalopod species, representing their morphological and ecological diversity, were 3D-printed, and subjected to uniaxial puncture tests. Force and displacement were recorded to estimate puncture ability. Finite Element Analysis (FEA) was used to explore the form–function relationship under loading conditions mimicking biting and pulling, analysing stress patterns across different rostrum morphologies. The results show that rostrum size significantly influenced puncture performance, with smaller rostra requiring less force and displacement for puncturing. However, larger rostra exhibited higher structural stiffness, suggesting increased vulnerability to stress during biting. Morphology-driven tests demonstrated species-specific differences in puncture abilities, with rostrum sharpness playing a crucial role. FEA results further indicated that longer and sharper rostra were more susceptible to stress, potentially impacting their overall structural integrity. The findings highlight the trade-off between rostrum size and sharpness in cephalopod beaks, with implications for prey selection and feeding efficiency. The study contributes to understanding the morpho-functional aspects of cephalopod beaks and their role in prey capture and consumption, shedding light on the evolutionary pressures shaping these remarkable marine predators.

Seasonal and Spatial Distribution Characteristics of Sepia esculenta in the East China Sea Region: Transfer of the Central Distribution from 29° N to 28° N.

The golden cuttlefish (Sepia esculenta) is an important cephalopod species with a lifespan of approximately one year. The species plays a crucial role in marine ecological support services and is commercially valuable in fisheries. In the seas around China, this species has emerged as the main target for cuttlefish fisheries, replacing Sepiella maindroni since the 1990s. Variations in oceanographic conditions associated with global warming could significantly impact the temporal-spatial distribution of the species. In this study, we performed bottom trawling surveys with four cruises during 2018-2019 in the East China Sea region to determine the current resource status and seasonal-spatial variations in S. esculenta. We found that the average individual weight (AIW) values were 4.87 and 519.00 g/ind at stations located at 30.50° N, 124.00° E and 30.50° N, 124.50° E, respectively, with the aggregation of larvae and parent groups in spring. The species was not distributed north of 32.00° N in summer. The catch per unit effort by weight (CPUEw) value decreased in the order of 2772.50→2575.20→503.29→124.36 g/h, corresponding to latitudes of 34.50° N→34.00° N→33.50° N→32.50° N 121.50° E in autumn. The most suitable fishing areas were the south of the East China Sea region in spring; the south of the East China Sea region extending to the center and outer parts of the East China Sea region in summer; the south of the Yellow Sea close to the Haizhou Bay fishing ground and the forbidden fishing line region of the Lusi and Dasha fishing grounds in autumn; and the south and center of the East China Sea region in winter. The most suitable sea bottom temperature (SBT) values from spring to winter were 14.76-20.53 °C, 19.54-22.98 °C, 11.79-17.64 °C, and 16.94-20.36 °C, respectively. The most suitable sea bottom salinity (SBS) values were 31.53-34.80‱ in spring, 32.95-34.68‱ in summer, 31.51-34.77‱ in autumn, and 33.82-34.51‱ in winter. We concluded the following: (1) the southern and northern areas of the East China Sea region are spawning and nursery grounds, respectively, in spring; (2) the central distribution is located at a latitude of 28.00° N in autumn and winter; and (3) the southern area of the Yangtze River to the north is a spawning ground in spring, and the areas located at 29.00-34.50° N, 124.00-124.50° E, and 28.00-30.50° N, 125.50-126.50° E are nursery grounds. The results of this study provide useful guidance for appropriate fisheries management, thereby avoiding a collapse in the S. esculenta population, which has been experienced in other species in this area.

The EU Interreg Project "ADRINET": Assessment of Well-Known and Emerging Pollutants in Seafood and Their Potential Effects for Food Safety.

Anthropogenic activities lead to the spread of chemicals and biological materials, including plastic waste, toxic metals, and pharmaceuticals, of which the impact on the Mediterranean Sea is of high concern. In this context, the EU Interreg Italy-Albania-Montenegro Project "ADRINET (Adriatic Network for Marine Ecosystem) _244" (2018-2020) arises. It aims to carry out biomonitoring campaigns in the main commercial interest of fish and cephalopod species, such as Sparus aurata, Dicentrarchus labrax, Sepia spp., and Loligo spp. sampled in three different subregions of the Mediterranean Sea. The presence of the main environmental contaminants, such as cadmium, microplastics, and antibiotics was investigated in these seafood samples. Contamination by cadmium and antibiotics in the seafood investigated in our study was negligible. However, a high value of microplastics was detected in the stomach and gut of Sparus aurata and Dicentrarchus labrax. Overall, even though the presence of microplastics needs to be investigated by further studies, the results confirmed that the environmental conditions of the three bays investigated by the ADRINET project partners (Italy, Albania, Montenegro) are positive and not affected by intensive anthropogenic activity.

Untangling the cephalopod market: Authentication of seafood products in Greece with DNA-barcoding

Cephalopod products are very popular in Greece and are considered a delicacy. However, heavy processing and marketing practices interfere with visual inspection and impede morphological identification, allowing species substitution. Mislabeling of seafood products remains a worldwide issue despite existing labeling regulations at local and European level. For the detection of fraudulent products, a variety of identification methods have been developed, however DNA barcoding remains the most favored. This study aims to investigate the cephalopod species sold in the country's seafood market and assess their mislabeling rates. Two mitochondrial genes, the cytochrome c oxidase subunit I (COI) and the 16S ribosomal RNA (16S), were selected for the analyses. A total of 156 samples were collected from fishmongers, markets, and restaurants across four cities. Identification was successful in 93.58% of the samples and 59 discrepancies (40.41%) between the label and the identified species were recorded. However, in some cases, substitution might have been unintentional, caused by negligence, lack of detailed information on the label, and the overall low awareness of the legislation by retailers. High mislabeling rates were estimated, especially when compared against the average global substitution rate in seafood products but align with those reported by studies on cephalopod products. This study is the first to investigate mislabeling rates in cephalopod commodities in Greece. With the aim of a transparent seafood trade, our results highlight the need for monitoring of all seafood products available in the country's market.

Changing Humboldt Squid Abundance and Distribution at Different Stages of Oceanic Mesoscale Eddies

Humboldt squid, Dosidicus gigas, is one of the main economic cephalopod species off Peruvian waters, and their abundance and distribution are regulated by localized oceanic mesoscale dynamical processes. To this end, the present study employs normalization and frequency distribution methods, combining mesoscale eddy, oceanic environment, and D. gigas fishery data. This is the first exploration into the different stages of mesoscale eddies during their evolution off Peruvian waters and their influence on the regional marine environment, as well as the abundance and distribution of D. gigas resources. The results indicate that across the four stages of eddies, namely formation, intensification, mature, and aged, their kinetic energy and structure follow a pattern of “growth–equilibration–decay”. The abundance of D. gigas within the eddy’s covered zone undergoes an initial increase, followed by a decrease during the evolution of the four stages, peaking during the eddy’s mature stage. The abundance of D. gigas was higher in the anticyclonic eddies than that in the cyclonic eddies under different stages. The environmental factors conducive to D. gigas in eddies exhibited similar changes to D. gigas abundance throughout the eddy’s different stages. Our research emphasizes that anticyclonic eddies, during their evolution, exerted a more significant impact on the abundance and distribution of D. gigas in the Peruvian waters compared with cyclonic eddies. The eddy-induced changes in water temperature and productivity caused by the eddies may be the primary drivers of this impact.

Geometric morphometrics casts light on phylogenetic relevance of cephalopod beak morphological.

The feeding organ of cephalopod species, the beak, can be used to reveal important ecological information. In this study, geometric morphometric approaches were employed to investigate the phylogenetic relevance and classification effect of beak lateral profile shape. The two-dimensional beak morphologies of 1164 pairs of 24 species from 13 genera and five families were constructed, and their evolutionary relationships and taxonomic status were confirmed using geometric morphometrics and molecular biology approaches. We also assessed the phylogenetic signals of beak shape. The analysis results show shape variation in the beak mainly in the rostrum, hood, and lateral wall. The overall shape parameters (all PCs) of the upper and lower beak are more useful for species identification. The shapes of the upper and lower beak show a strong phylogenetic signal, and the phenogram based on the beak shape basically reflected the families' taxonomic positions. We also hypothesized that the shape variation in the beaks of cephalopods may be ascribed to genetic and environmental differences. In summary, beaks are a reliable material for the classification of cephalopod species. Geometric morphometric approaches are a powerful tool to reveal the identification, phylogenetic relevance and phenotypic diversity of beak shape in cephalopods.

Trophic niche partitioning of golden cuttlefish (Sepia esculenta) during ontogeny revealed by stable isotope analysis and DNA metabarcoding

Cephalopods are becoming more important in global fishery. Understanding the trophic ecology partitioning during their ontogeny is critical to the stock assessment and fishery management. The golden cuttlefish (Sepia esculenta), one of commercially important cephalopod species has been found at different life-history stages that co-inhibit in the coastal waters of Qingdao, China. In the present study, the trophic ecology of S. esculenta was assessed by using stable isotope analysis (SIA: based δ13C and δ15N from muscle and liver tissue) and DNA metabarcoding of the stomach contents through high-throughput sequencing (HTS). SIA uncovered the variation in isotope niche and trophic position of S. esculenta during ontogeny. DNA metabarcoding showed a higher resolution of prey identification than before. The combined analysis of SIA and DNA metabarcoding indicated that diet shifts occurred in the ontogeny of S. esculenta. Paralaval and juvenile prefer zooplankton, while sub-adult and adult prefer demersal fishes. The standard ellipse area (SEAc) indicated that low isotope niche overlaps among paralaval, juvenile and sub-adult of S. esculenta, which reflect the squid foraging strategy during ontogeny. The study confirmed that S. esculenta resources can be partitioned into different life stages, suggesting a survival strategy to maintain population dynamics.

Progenesis in dicyemids

AbstractDicyemids (Phylum Dicyemida) are the most common and characteristic endosymbiont living in the renal sac of benthic cephalopod molluscs. Precocious development of a hermaphroditic gonad occurs in the larvae and smaller juveniles of 40 dicyemid species from 17 cephalopod species so far and is the usual phenomenon in dicyemids. Based on the developmental and morphological features of precocious individuals, progenesis (a form of heterochrony) is the appropriate term for such precocious development. In general, progenetic individuals have much lower fecundity than normal ones because of their smaller body size, and therefore, it appears to be a disadvantageous reproductive trait. Nonetheless, the number of progenetic individuals consists of 30%–50% of the population, a relatively large proportion suggesting that the presence of progenetic individuals probably plays an important role in life history strategy. Precocious development significantly reduces growth time and enables early maturation. Progenetic individuals are common in short‐living cephalopod species, in which precocious development seems appropriate for dicyemids, enabling fast larval release before the end of the host's life span.

Evolutionary history influences the microbiomes of a female symbiotic reproductive organ in cephalopods.

Many female squids and cuttlefishes have a symbiotic reproductive organ called the accessory nidamental gland (ANG) that hosts a bacterial consortium involved with egg defense against pathogens and fouling organisms. While the ANG is found in multiple cephalopod families, little is known about the global microbial diversity of these ANG bacterial symbionts. We used 16S rRNA gene community analysis to characterize the ANG microbiome from different cephalopod species and assess the relationship between host and symbiont phylogenies. The ANG microbiome of 11 species of cephalopods from four families (superorder: Decapodiformes) that span seven geographic locations was characterized. Bacteria of class Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were found in all species, yet analysis of amplicon sequence variants by multiple distance metrics revealed a significant difference between ANG microbiomes of cephalopod families (weighted/unweighted UniFrac, Bray-Curtis, P = 0.001). Despite being collected from widely disparate geographic locations, members of the family Sepiolidae (bobtail squid) shared many bacterial taxa including (~50%) Opitutae (Verrucomicrobia) and Ruegeria (Alphaproteobacteria) species. Furthermore, we tested for phylosymbiosis and found a positive correlation between host phylogenetic distance and bacterial community dissimilarity (Mantel test r = 0.7). These data suggest that closely related sepiolids select for distinct symbionts from similar bacterial taxa. Overall, the ANGs of different cephalopod species harbor distinct microbiomes and thus offer a diverse symbiont community to explore antimicrobial activity and other functional roles in host fitness.IMPORTANCEMany aquatic organisms recruit microbial symbionts from the environment that provide a variety of functions, including defense from pathogens. Some female cephalopods (squids, bobtail squids, and cuttlefish) have a reproductive organ called the accessory nidamental gland (ANG) that contains a bacterial consortium that protects eggs from pathogens. Despite the wide distribution of these cephalopods, whether they share similar microbiomes is unknown. Here, we studied the microbial diversity of the ANG in 11 species of cephalopods distributed over a broad geographic range and representing 15-120 million years of host divergence. The ANG microbiomes shared some bacterial taxa, but each cephalopod species had unique symbiotic members. Additionally, analysis of host-symbiont phylogenies suggests that the evolutionary histories of the partners have been important in shaping the ANG microbiome. This study advances our knowledge of cephalopod-bacteria relationships and provides a foundation to explore defensive symbionts in other systems.

Comparative transcriptomic analysis of the different developmental stages of ovary in the cuttlefish Sepia pharaonis

The cuttlefish, Sepia pharaonis, is characterized by rapid growth and strong disease resistance, making it an important commercially farmed cephalopod species in the southeastern coastal regions of China. However, in the reproductive process of S. pharaonis, there are challenges such as a low output of eggs, poor quality, and low survival rates of newly hatched juveniles. Therefore, there is an urgent need to study the molecular mechanisms underlying ovarian development in this species. In this study, we conducted the first transcriptomic analysis of the ovary at four developmental stages: the undeveloped stage, developing stage, nearly-ripe stage, and ripe stage, and compared the transcriptomics among these four stages using Illumina sequencing technology. The total numbers of clean reads of the four stages ranged from 40,890,772 to 52,055,714 reads. A total of 136,829 DEGs were obtained, GC base ratios of raw data were between 38.44 and 44.59%, and the number of uniquely mapped reads spanned from 88.08 to 95.90%. The Pearson correlation coefficient demonstrated a strong correlation among different samples within the same group, PCA and Anosim analysis also revealed that the grouping of these four stages was feasible, and each stage could be distinguished from the others. GO enrichment analysis demonstrated that ovarian follicle growth, sex differentiation, and transforming growth factor beta receptor, played a foreshadowing role at the early ovarian development stage, and the terms of small molecule metabolic process, peptide metabolic process, and catalytic activity were prominent at the mature stage. Meanwhile, KEGG analysis showed that the early ovarian development of S. pharaonis was mainly associated with the cell cycle, DNA replication, and carbon metabolism, while the mid-late ovarian development was involved with the signal transduction, endocrine system, and reproduction pathway. RT-qPCR further confirmed the consistent expression patterns of genes such as 17β-HSD, GH, VGS, NFR, and NYR in the ovaries of S. pharaonis, exhibiting elevated levels of expression during the maturation stage. Conversely, ER and OM exhibited high expression levels during the early stages of ovarian development. These transcriptomic data provide insights into the molecular mechanisms of S. pharaonis ovarian development. The findings of this study will contribute to improving the reproduction and development of cuttlefish and enriching the bioinformatics knowledge of cephalopods.

Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes

Coleoid cephalopods possess numerous complex, species-specific morphological and behavioural adaptations, e.g., a uniquely structured nervous system that is the largest among the invertebrates. The Hawaiian bobtail squid (Euprymna scolopes) is one of the most established cephalopod species. With its recent publication of the chromosomal-scale genome assembly and regulatory genomic data, it also emerges as a key model for cephalopod gene regulation and evolution. However, the latest genome assembly has been lacking a native gene model set. Our manuscript describes the generation of new long-read transcriptomic data and, made using this combined with a plethora of publicly available transcriptomic and protein sequence data, a new reference annotation for E. scolopes.

Comparison of model selection and data bias on the prediction performance of purpleback flying squid (Sthenoteuthis oualaniensis) fishing ground in the Northwest Indian Ocean

Purpleback flying squid (Sthenoteuthis oualaniensis, PFS) is one of the critical economically cephalopod species in the northwest Indian Ocean, and the accurate model and dataset selection are critical parameters for predicting and managing the PFS fishing grounds. In this study, the PFS fishery data for the years 2016–2021 was analyzed using the gravity center of fishing grounds method, generalized additive model (GAM), gradient boosted trees (GBT), 3D Convolutional Neural Network (3DCNN), and 3D Convolutional Neural Networks-Convolutional LSTM Network (3DCNN-ConvLSTM) to explore the differences in annual catches, the annual gravity center of fishing ground, model performance, and importance of environmental variables in the case of datasets A (no moonlight days) and B (no moonlight days + bright moonlight days). The results are as follows: 1) Datasets A and B exhibit similar patterns of variation, with annual catches rising and then declining and the annual gravity center of fishing ground moving northeastward overall; 2) The GAM and GBT models had better model performance on dataset B (GAM (average F1-score ± standard deviation): 0.678658 ± 0.014684; GBT: 0.737422 ± 0.011748)than on dataset A (GAM: 0.676802 ± 0.013403; GBT: 0.736547 ± 0.013323), but almost negligible, and the standard deviation of the GAM model on dataset B becomes larger. 3DCNN and 3DCNN-ConvLSTM models perform in contrast, with significantly better F1-score and standard deviations on dataset A (3DCNN: 0.75048 ± 0.019763; 3DCNN-ConvLSTM: 0.740041 ± 0.023927) than on dataset B (3DCNN: 0.746378 ± 0.020337; 3DCNN-ConvLSTM: 0.736927 ± 0.04498); 3) The 3DCNN (optimal prediction of performance) or GBT (Optimal model stability) model is optimal for predicting the PFS fishing grounds; 4) GBT, 3DCNN, and 3DCNN-ConvLSTM model results all showed that the differences in the importance of environmental variables obtained from datasets A and B were significant; 5) Unlike the GBT model, the 3DCNN and 3DCNN-ConvLSTM models were more susceptible to dataset influences, with significant dependence on environmental variables that have large positive and negative sample differences. This study provides rich suggestions for constructing a predictive model for the PFS fishing grounds in the context of climate change. It also provides a new perspective on cleaning up biased data for light fisheries.

Citizen science approach for genetic species identification in a local French seafood speciality

In coastal regions of France, seafood is a key element of traditional cuisine and is valued by consumers as quality food. However, in the last decades, the mislabelling of food products has undermined consumers' confidence in their food choices. In this study, we used genetic identification of the seafood species used to prepare a traditional dish of the city of Sète, to initiate a discussion on food labelling and sustainability. The dish, named “Tielle sétoise", is a pie traditionally filled with octopus cooked in a spicy tomato sauce. The recent substitution of octopus by jumbo flying squid (Dosidicus gigas) has triggered debates among locals about how the use of non-native cephalopod species impacts the flavour of tielles. To test this hypothesis, we coordinated a tasting event involving 35 testers from the local population and used CO1-gene metabarcoding to identify the species composition in 25 different tielles. Besides locally available octopuses’ species, including common commercial species Eledone cirrhosa, E. moschata and Octopus vulgaris, we found jumbo flying squid in 17 out of 25 tielles, of which eight (35%) were mislabelled as octopus-based products. Contrary to local belief, anonymous blind-tasting evaluations showed no significant correlation between the flavour or price of a tielle and the cephalopod composition of its filling. Our results support the impact of texture, acidity, and spices on flavour, suggesting that flavour depends more on how tielles are prepared than on the cephalopod species used. The participants in our study expressed their willingness to make informed choices about purchasing tielles based on the carbon footprint and its impact on cephalopod stocks. Our results call for further research to enable citizens to make informed food choices. Our study also highlights the need for improved labelling of traded cephalopods to improve communication between the food industry and society, as well as the possibility of evaluating this with citizen science.