Article
Engineering, Marine
Zhier Chen, Wenkang Jiao, Kai Ren, Jiancheng Yu, Yu Tian, Kuo Chen, Xingjian Zhang
Summary: This paper discusses the current status and future development directions of adaptability in marine robots. It provides an overview of how marine robots adapt to pressure and buoyancy at different depths, and analyzes the limitations and potential solutions of pressure and buoyancy adaptation technologies. Improvement measures for active buoyancy control are proposed, and promising areas for future development are identified. The challenges and prospects for adaptive technologies in marine robots are also outlined.
Article
Biochemistry & Molecular Biology
Gianni M. Castiglione, Frances E. Hauser, Alexander Van Nynatten, Belinda S. W. Chang
Summary: Antarctic icefishes have adapted to the cold environment through mutations in their visual pigment, rhodopsin, which red-shift the spectral absorbance, lower the activation energy, and accelerate the return to the dark state. These adaptations allow them to thrive in the cold dark seas of the Antarctic.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Nik Lupse, Fabio Cortesi, Marko Freese, Lasse Marohn, Jan-Dag Pohlmann, Klaus Wysujack, Reinhold Hanel, Zuzana Musilova
Summary: The study revealed a developmental switch from cone to rod cells in deep-sea fish, with adults relying on rod opsins for vision in dim light and larvae mainly expressing middle-wavelength-sensitive cone opsins. The findings also showed a limited opsin gene repertoire in deep-sea fishes, following a conserved vertebrate pattern of cone photoreceptors developing first, with rod photoreceptors added later in development.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Virginie Ricci, Fabrizia Ronco, Nicolas Boileau, Walter Salzburger
Summary: Through studying the retinal transcriptomes of cichlid fishes from Lake Tanganyika, we found that adaptive changes in gene expression at the macro-evolutionary and ecosystem level primarily occur through variation in the expression of a subset of cone opsin genes.
Article
Environmental Sciences
Fella Moualek, Dominic Belanger, Mathieu Babin, Genevieve J. Parent, Dominic E. Ponton, Marc Amyot, Caroline Senay, Dominique Robert, Zhe Lu
Summary: Mercury pollution, particularly in the form of methylmercury, poses a significant threat to the environment. This study investigated the distribution of methylmercury and total mercury in the muscle of deep-sea redfish and assessed the associated health risks for humans consuming redfish. The study found that factors such as fish length, muscle moisture, and nitrogen levels influenced the concentrations of methylmercury in redfish muscle. However, the average fish consumption rate by the general population is not expected to have adverse effects.
ENVIRONMENTAL POLLUTION
(2023)
Article
Multidisciplinary Sciences
Diego Deville, Kentaro Kawai, Hiroki Fujita, Tetsuya Umino
Summary: The Sebastes inermis complex consists of three sympatric species with ecomorphological differences. Genetic analyses confirm the presence of genetic divergence and hybridization within the complex. The findings suggest the potential role of hybridization in generating novelties within the species complex.
Article
Oceanography
Chenguang Feng, Ruoyu Liu, Wenjie Xu, Yang Zhou, Chenglong Zhu, Jun Liu, Baosheng Wu, Yongxin Li, Qiang Qiu, Shunping He, Wen Wang, Haibin Zhang, Kun Wang
Summary: The high-quality genome assembly of a new deep-sea anemone species living at a depth of 3230 m in the Xisha Trough revealed molecular signatures of adaptation to the deep-sea environment. The genomic analyses showed rapid evolution of genes and amino acid substitutions to cope with high hydrostatic pressure or low temperature, while demographic events of the deep-sea anemone coincided with post-Pliocene climate transformations, suggesting the impact of global climate changes on deep-sea creatures.
DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
(2021)
Article
Plant Sciences
Zane K. J. Hartley, Andrew P. French
Summary: This paper explores the impact of using synthetic data for wheat head detection on the global wheat head challenge dataset, demonstrating the challenges of domain augmentation and proposing a novel approach to improve scores.
Article
Biochemistry & Molecular Biology
Maeva Perez, Oluchi Aroh, Yanan Sun, Yi Lan, Stanley Kim Juniper, Curtis Robert Young, Bernard Angers, Pei-Yuan Qian
Summary: We conducted the first genome-wide survey of DNA methylation in polychaetes dominant in deep-sea vents and seeps, and found that these animals possess a mosaic methylome similar to other invertebrates. The transcriptomic data supported the hypotheses that gene body methylation strengthens gene expression and promoter methylation acts as a silencing mechanism, but not the hypothesis that DNA methylation suppresses transposable element activity. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest an important adaptive role of DNA methylation in these worms.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biodiversity Conservation
Junyuan Li, Tong Zhou, Yang Li, Kuidong Xu
Summary: This study analyzed the mitochondrial genome and transcriptome of deep-sea solitary coral Polymyces wellsi living in the oxygen minimum zone (OMZ) and showed the genetic mechanisms underlying its adaptation to low pH, low oxygen content, and extreme food limitation. The findings revealed positive selection and expansion of genes related to biomineralization, mitochondrial components, and ciliary motion, indicating their significance in facilitating the coral's adaptation to the stressors in the OMZ. Moreover, the study identified a novel bio-indicator, the increased isoelectric points of skeleton organic matrix proteins, which may reflect the adaptive capacity of the coral to external acidified seawater. Overall, this study provides insights into the adaptive mechanisms of deep-sea solitary corals and offers strategies for addressing global climate change.
ECOLOGICAL INDICATORS
(2023)
Article
Biochemistry & Molecular Biology
Kai Zhang, Jin Sun, Ting Xu, Jian-Wen Qiu, Pei-Yuan Qian
Summary: This study utilized mitogenomes to analyze the phylogeny and environmental adaptation of deep-sea mussels, revealing a unique gene order rearrangement in bathymodioline species. Deep-sea mussels have experienced relaxed purifying selection compared to shallow-water mussels, with certain genes showing signs of positive selection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Optics
Tianyu Wang, Mandar M. Sohoni, Logan G. Wright, Martin M. Stein, Shi-Yuan Ma, Tatsuhiro Onodera, Maxwell G. Anderson, Peter L. McMahon
Summary: A nonlinear optical neural network image sensor based on an image intensifier enables efficient all-optical image encoding for various machine-vision tasks. The nonlinear ONN encoder outperforms linear optical encoders in machine-vision benchmarks, flow-cytometry image classification, and object identification in a 3D printed real scene. This concept allows for a significant reduction in camera resolution and electronic post-processing complexity, and enables image-sensing applications with fewer pixels, photons, higher throughput, and lower latency.
Article
Chemistry, Multidisciplinary
Xinyi Liu, Baofeng Zhang, Na Liu
Summary: Both transformer and one-stage detectors have not widely used effective domain adaptive techniques. In this paper, we propose a novel improved YOLO model called CAST-YOLO, which implements cross-domain object detection through knowledge distillation. Extensive experiments show that our method outperforms existing methods in foggy weather adaptive detection, significantly improving the detection results.
APPLIED SCIENCES-BASEL
(2023)
Article
Food Science & Technology
Yu Xu, Jinmei Kou, Qian Zhang, Shudan Tan, Lichun Zhu, Zhihua Geng, Xuhai Yang
Summary: To classify sea buckthorn fruits with different water content ranges, a convolutional neural network (CNN) detection model was constructed. 900 images of sea buckthorn fruits with different water contents were collected from 720 fruits, and eight classic deep learning network models were used for feature extraction and transfer learning. 180 images were randomly selected for testing, and the network model achieved an identification accuracy of 98.69% for the water content range of sea buckthorn fruit, with a test set accuracy of 99.4%. The program in this study can quickly identify the moisture content range of sea buckthorn fruit by collecting images during the drying process, and it can be applied to detect the moisture content range of other agricultural products.
Article
Computer Science, Artificial Intelligence
Fang Peng, Zheng Miao, Fei Li, Zhenbo Li
Summary: The study proposed an automatic detection method of underwater sea cucumber based on deep learning, which improves the multi-scale feature fusion strategy through shortcut connection. The results demonstrate that this method achieves higher detection accuracy in complex underwater environments.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Review
Evolutionary Biology
Christophe Pampoulie, Paul Ragnar Berg, Sissel Jentoft
Summary: Stock structure is crucial for sustainable management of exploited resources, and genetic markers have been used for decades to understand spatial structure and stock dynamics. This review focuses on genetic studies of Atlantic cod in Icelandic waters, highlighting the importance of genomic data and behavioral monitoring in understanding population structure and diversity.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Fisheries
Linda Albonetti, Giulia Maiello, Alessia Cariani, Paolo Carpentieri, Alice Ferrari, Alice Sbrana, Peter Shum, Lorenzo Talarico, Tommaso Russo, Stefano Mariani
Summary: Conservation and management of chondrichthyans are important due to their vulnerability to fishing activities, and using eDNA metabarcoding can accurately assess bycatch composition and detect rare species. Chondrichthyan diversity is influenced by environmental variables and fishing effort. As DNA metabarcoding becomes a staple tool for biodiversity monitoring, it can provide additional insights into threatened and elusive megafauna.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Fisheries
L. McGill, A. D. McDevitt, B. Hellemans, F. Neat, H. Knutsen, S. Mariani, H. Christiansen, T. Johansen, F. A. M. Volckaert, I Coscia
Summary: This study focuses on two commercially important gadoid species, the common ling and the blue ling, which have overlapping geographical distribution but different depth habitats. Genotyping-by-sequencing analysis revealed genetic differentiation in both species, with two major groups identified for each species. Fine-scale genetic structure was found along the coast of Norway for the common ling, while the blue ling showed stronger signals of differentiation related to adaptation to different depth habitats and cold temperatures.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Environmental Sciences
Giorgio Aglieri, Federico Quattrocchi, Stefano Mariani, Charles Baillie, Davide Spatafora, Antonio Di Franco, Gabriele Turco, Marco Tolone, Rosalia Di Gerlando, Marco Milazzo
Summary: By combining eDNA surveys, public registers, and Automatic Identification Systems data, we found significant positive relationships between fishing fleet activities and the taxonomic fish assemblage composition in eleven Mediterranean fishing ports. We identified 160 fish and 123 invertebrate OTUs, including non-indigenous species, suggesting that eDNA assessments of fishing harbours' waters can rapidly monitor marine biodiversity and reconstruct underreported fishing catches.
MARINE POLLUTION BULLETIN
(2023)
Article
Multidisciplinary Sciences
Eeva Jansson, Ellika Faust, Dorte Bekkevold, Maria Quintela, Caroline Durif, Kim Tallaksen Halvorsen, Geir Dahle, Christophe Pampoulie, James Kennedy, Benjamin Whittaker, Laila A. Unneland, Soren Post, Carl Andre, Kevin A. Glover
Summary: Using two approaches, researchers investigated the population genetic structure of the lumpfish in the North Atlantic and found extensive population structuring, including a major split between the East and West Atlantic and a distinct Baltic Sea population. The study suggests that despite its potential for dispersal and gene-flow, the lumpfish exhibits natal homing behavior and local populations with adaptive differences.
Article
Biology
Sara Gonzalez-Delgado, Owen S. Wangensteen, Carlos Sangil, Celso A. Hernandez, Beatriz Alfonso, Ana Z. Soto, Rocio Perez-Portela, Stefano Mariani, Jose Carlos Hernandez
Summary: Metabarcoding techniques have revolutionized ecological research by revealing hidden biodiversity. This study used DNA metabarcoding to assess the effects of ocean acidification on marine benthic communities. The results show that subtropical communities are expected to maintain high biodiversity levels under future ocean acidification.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Marine & Freshwater Biology
Thomas I. Gibson, Gary Carvalho, Amy Ellison, Enrica Gargiulo, Tristan Hatton-Ellis, Lori Lawson-Handley, Stefano Mariani, Rupert A. Collins, Graham Sellers, Marco Antonio Distaso, Carlo Zampieri, Simon Creer
Summary: Fishes are important components of estuarine ecosystems, and assessing their biodiversity is crucial for understanding the health of these ecosystems. This study used environmental DNA (eDNA) metabarcoding to investigate fish assemblage composition in the River Dee estuary in Wales. The results showed that eDNA metabarcoding could enhance existing fish sampling methods by providing more comprehensive information on fish biodiversity.
ESTUARINE COASTAL AND SHELF SCIENCE
(2023)
Article
Fisheries
Adam J. Andrews, Christophe Pampoulie, Antonio Di Natale, Piero Addis, Dario Bernal-Casasola, Veronica Aniceti, Gabriele Carenti, Veronica Gomez-Fernandez, Valerie Chosson, Alice Ughi, Matt Von Tersch, Maria Fontanals-Coll, Elisabetta Cilli, Vedat Onar, Fausto Tinti, Michelle Alexander
Summary: The health of ocean ecosystems and fish populations has been threatened by overexploitation, pollution, and climate change. Without long-term ecological data, we lack understanding of the impact on fish diet and habitat use. Recovering depleted fish populations and predicting their future dynamics requires this vital information.
FISH AND FISHERIES
(2023)
Article
Biochemistry & Molecular Biology
Anna Thomasdotter, Peter Shum, Francesco Mugnai, Marina Vingiani, Marco Abbiati, Federica Costantini
Summary: The ability to use DNA metabarcoding of bulk samples to gather genetic information directly from the environment is crucial for understanding biodiversity and population dynamics in the marine realm. In this study, we use bioinformatics tools to investigate intraspecific genetic variability for marine invertebrates in the Mediterranean Sea. By analyzing samples from Autonomous Reef Monitoring Structures (ARMS), we identify diverse haplotypes and emphasize the spatial scale of genetic variability.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Fisheries
Gert-Jan Jeunen, Miles Lamare, Jennifer Devine, Stefano Mariani, Sadie Mills, Jackson Treece, Sara Ferreira, Neil J. Gemmell
Summary: Given the challenges of monitoring the Southern Ocean through visual observations, this study explores the potential of marine sponge eDNA monitoring to assess the fish community in the region. The findings show that eDNA provides a more comprehensive view of the fish community compared to catch records, highlighting its potential for improving our understanding of this understudied ecosystem and aiding conservation efforts.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2023)
Review
Genetics & Heredity
Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul R. Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido R. Gallo, Jose A. Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsboll, Christophe Pampoulie, Maria J. Ruiz-Lopez, Simona Secomandi, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Erich D. Jarvis, Miklos Balint, Claudio Ciofi, Robert M. Waterhouse, Camila J. Mazzoni, Jacob Hoglund
Summary: The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts. Reference genomes play a key role in facilitating biodiversity research and conservation. Integrating the use of reference genomes as a best practice in conservation genomics is essential.
TRENDS IN GENETICS
(2023)
Article
Biodiversity Conservation
Andhika P. Prasetyo, Joanna M. Murray, Muh. Firdaus A. K. Kurniawan, Naiara G. Sales, Allan D. McDevitt, Stefano Mariani
Summary: Illegal fishing, unregulated bycatch, and market demand for certain products are causing a rapid decline in shark and ray populations. Controlling the trade of endangered species is challenging due to various factors, but a new genetic approach using trace DNA fragments retrieved from trade leftovers shows promise in identifying traded species, even those that are difficult to recover from tissue samples. This approach could become a powerful and cost-effective monitoring tool in wildlife trade.
CONSERVATION LETTERS
(2023)
Article
Marine & Freshwater Biology
Charalampos Dimitriadis, Erika F. Neave, Peter Shum, Stefano Mariani, Manuela D'Amen, Ernesto Azzurro
Summary: In 2021, the presence of three Lessepsian yellowstripe barracuda and eight Indo-Pacific needle-spined sea urchin specimens were observed along the coasts of Zakynthos Island, with some of them found within the Marine Protected Area.
Article
Fisheries
James Kennedy, Anna Heioa Olafsdottir, Svandis Eva Aradottir, Svanhildur Egilsdottir, Christophe Pampoulie
Summary: The black ruff is a rare species found in the Atlantic and Pacific Oceans as well as the Mediterranean Sea. It is sporadically caught south of Iceland, possibly indicating its northern distribution limit. This species primarily inhabits the surface waters and feeds on invertebrates.
JOURNAL OF FISH BIOLOGY
(2023)