Article
Biodiversity Conservation
Eva Decru, Jos Snoeks, Albert Walanga, Emmanuel J. W. M. N. Vreven
Summary: A morphological and molecular study of the Labeobarbus species in the Epulu River identified five different species, including four rubberlips and one chiselmouth. The study also found possible hybrid specimens, distinguishing it from similar cases found in other regions.
Article
Ecology
Matthew J. Burnett, Gordon C. O'Brien, Graham Jewitt, Colleen T. Downs
Summary: This study evaluated how the yellowfish population in the uMngeni River in South Africa has adapted to anthropogenic stressors, finding that water temperature, seasonal activities, and habitat availability play important roles. Recommendations were made to maintain adequate flows, improve fish passage, and reduce the impacts of anthropogenic stressors on important river ecosystems.
ENVIRONMENTAL BIOLOGY OF FISHES
(2021)
Article
Marine & Freshwater Biology
Arnold Roger Bitja-Nyom, Jean-Francois Agnese, Antoine Pariselle, Charles Felix Bilong-Bilong, Andre Gilles, Jos Snoeks
Summary: The study revises the group of large five-spotted Hemichromis species from West Africa and Lower Guinea using a combination of morphometry and genetics. The results suggest potential synonymy of species and admixture of populations from different regions. Additionally, a new species, Hemichromis camerounensis sp. nov., was described in the study.
Article
Biology
Keltoum Ouassal, Ignacio Doadrio, Silvia Perea, Miriam Casal-Lopez, Ahmed Yahyaoui, Hassane Jaziri
Summary: This study aims to provide genetic and biogeographic information of nine Luciobarbus species in Morocco. Sequencing of the cytochrome b gene revealed two evolutionary lineages in Morocco and different levels of genetic diversity within Luciobarbus populations.
Article
Environmental Sciences
Eleni Kalogianni, Nicholas Koutsikos, Ioannis Karaouzas, Evangelia Smeti, Yiannis Kapakos, Sofia Laschou, Elias Dimitriou, Leonidas Vardakas
Summary: This study developed a reliable tool for assessing the feasibility of freshwater fish translocations in Mediterranean-type riverine ecosystems. The tool integrates quantitative and semi-quantitative data, incorporates uncertainty, and consists of two main components: evaluating the suitability of potential release water bodies and evaluating the genetic compatibility and propagule provision of potential source water bodies. A trial application in a Mediterranean basin demonstrated the robustness of the tool.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Fisheries
Mateusz Sikora, Joanna Nowosad, Dariusz Kucharczyk
Summary: This study examined the daily fluctuations of ammonium and nitrite concentrations under different biofilter and feeding protocols in a Recirculation Aquaculture System. Results indicate that the choice of feeding protocol and biofilter can impact the concentrations of ammonium and nitrite in the RAS system.
Article
Environmental Sciences
Tamara Leite, Paulo Branco, Maria Teresa Ferreira, Jose Maria Santos
Summary: The study found that increasing salinity has sub-lethal effects on freshwater fish behavior, including reduced swimming activity and shoal cohesion, as well as an increase in bolder individuals. Changes in fish behavior can reflect shifts in ecological condition.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Melanie Nolden, Mark J. Paine, Ralf Nauen
Summary: Cytochrome P450 monooxygenases play a crucial role in the oxidative metabolism of xenobiotics in insects and their duplication and upregulation can lead to insecticide resistance. The interaction between P450s and other enzymes like NADPH cytochrome P450 oxidoreductase and cytochrome b5 is complex and can impact metabolic capacity. Recombinant expression of P450s in insect cells with cytochrome b5 can significantly enhance their ability to metabolize certain substrates, but not necessarily insecticides like deltamethrin.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xueping Lu, Marilou Vandenhole, Dimitra Tsakireli, Spiros A. Pergantis, John Vontas, Wim Jonckheere, Thomas Van Leeuwen
Summary: Acequinocyl and bifenazate, as powerful acaricides, have been found to induce resistance development in spider mites. Target-site resistance resulting from mutations in the Qo pocket of cytochrome b has been identified as the main resistance mechanism. A new mutation, L258F, has been discovered in field populations of Tetranychus urticae, and its role in resistance has been confirmed. However, the resistance in this strain is likely due to a combination of target-site resistance and increased detoxification through P450 enzymes.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2023)
Article
Fisheries
Martin Hubalek, Vojtech Kaspar, Tomas Tichopad, Marek Rodina, Martin Flajshans
Summary: This study compares the performance of polyploid sturgeon with diploid sturgeon under unfavorable temperature conditions. The findings show that triploid sturgeon have similar survival, growth, and development abilities compared to diploid sturgeon, while tetraploid sturgeon have significantly reduced survival rates. Additionally, the hexaploid genome state is likely lethal in sturgeon.
JOURNAL OF FISH BIOLOGY
(2022)
Article
Ecology
Emily A. Wright, Rachael C. Wiedmeier, Emma K. Roberts, David R. Pipkin, Froylan Hernandez, Joseph P. Bayouth, Warren C. Conway, Robert D. Bradley
Summary: Translocation records indicate that aoudad populations in the United States are a product of multiple human-mediated introductions. Genetic analysis shows high genetic diversity among US populations and suggests the presence of two subspecies, supporting the hypothesis of multiple introductions from multiple sources.
ECOLOGY AND EVOLUTION
(2022)
Article
Fisheries
Andrea Simkova, Kristina Civanova, Lukas Vetesnik
Summary: The F1 generation of hybrids demonstrates heterosis in vigour-related traits, showing a superior expression compared to the parents. However, post-F1 generations may exhibit disadvantageous traits. The susceptibility of hybrids to viral infection may be influenced by cyto-nuclear incompatibility and the direction of cross-breeding.
Review
Biochemistry & Molecular Biology
Carlos Gutierrez-Merino, Oscar H. Martinez-Costa, Maria Monsalve, Alejandro K. Samhan-Arias
Summary: Membrane cytochrome b(5) reductase is an oxidoreductase that reduces multiple acceptors localized in cellular membranes using NADH as an electron donor. The understanding of the electron transfer process of the reductase towards potential acceptors is still only partially understood. Computational analysis of protein structures provides a potential method to further investigate the roles of different domains within the reductase structure.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Fisheries
Belay Abdissa, Abebe Getahun, Eshete Dejen
Summary: The cryopreservation of Lake Tana Labeobarbus semen was studied for the first time. DMSO 10% showed the best performance in the cryo-diluent, and a suitable preservation protocol was proposed for L. brevicephalus sperm. Further research is needed to evaluate the viability and development of larvae produced from cryopreserved sperm, as well as the sustainability and feasibility of cryogenic gene banking for sperm use.
Article
Plant Sciences
Jianhui Ma, Meng Yuan, Bo Sun, Daijing Zhang, Jie Zhang, Chunxi Li, Yun Shao, Wei Liu, Lina Jiang
Summary: The study identified the evolutionary stages and expansion of NAC transcription factors in green plants, particularly in hexaploid wheat. The results showed that tandem replications during polyploidization play a significant role in increasing the number of NAC transcription factors in wheat. Additionally, the analysis of TaNACs in wheat revealed distinct groups and clusters, indicating the presence of neofunctionalization and subfunctionalization genes which are important in responding to various stresses.
Article
Multidisciplinary Sciences
Alexandros A. Karamanlidis, Tomaz Skrbinsek, George Amato, Panagiotis Dendrinos, Stephen Gaughran, Panagiotis Kasapidis, Alexander Kopatz, Astrid Vik Stronen
Summary: The Mediterranean monk seal is a flagship species for marine conservation, but it still faces challenges such as population decline, high levels of inbreeding, and loss of genetic diversity. Research has shown that males exhibit philopatry over short distances, possibly due to their unique breeding behavior. Immediate action is necessary to improve the long-term prospects of survival for this species.
SCIENTIFIC REPORTS
(2021)
Review
Biology
Haris Zafeiropoulos, Anastasia Gioti, Stelios Ninidakis, Antonis Potirakis, Savvas Paragkamian, Nelina Angelova, Aglaia Antoniou, Theodoros Danis, Eliza Kaitetzidou, Panagiotis Kasapidis, Jon Bent Kristoffersen, Vasileios Papadogiannis, Christina Pavloudi, Quoc Viet Ha, Jacques Lagnel, Nikos Pattakos, Giorgos Perantinos, Dimitris Sidirokastritis, Panagiotis Vavilis, Georgios Kotoulas, Tereza Manousaki, Elena Sarropoulou, Costas S. Tsigenopoulos, Christos Arvanitidis, Antonios Magoulas, Evangelos Pafilis
Summary: This article introduces a Tier 2 HPC facility at the Hellenic Centre for Marine Research, which has been running for over a decade. The facility aims to balance the depth of high-memory nodes with the breadth of slimmer nodes to meet the computational needs of various marine research fields. Analysis of hardware and software architectures, usage statistics, policy, and user management aspects have led to lessons learned that will guide future directions of the facility.
Article
Fisheries
Maria Papapetrou, Zoi Kazlari, Kantham Papanna, Leonidas Papaharisis, Stavroula Oikonomou, Tereza Manousaki, Dimitrios Loukovitis, Lefteris Kottaras, Arkadios Dimitroglou, Evgenia Gourzioti, Charalampos Pagonis, Andreas Kostandis, Costas S. Tsigenopoulos, Dimitrios Chatziplis
Summary: The European seabass is a major commercial fish in Mediterranean aquaculture, but its production is negatively affected by outbreaks of parasitic, bacterial, and viral diseases. Genetic improvement for disease resistance is an important strategy for controlling infectious diseases in farmed fish. Research into genetic variations for resistance to gill parasites through cohabitation trials provides promising results for potential genetic improvement and further analysis using molecular markers.
AQUACULTURE REPORTS
(2021)
Article
Genetics & Heredity
Theodoros Danis, Vasileios Papadogiannis, Alexandros Tsakogiannis, Jon B. Kristoffersen, Daniel Golani, Dimitris Tsaparis, Aspasia Sterioti, Panagiotis Kasapidis, Georgios Kotoulas, Antonios Magoulas, Costas S. Tsigenopoulos, Tereza Manousaki
Summary: This study presents the first near-chromosome level genome assembly of L. sceleratus and explores its evolutionary landscape, positioning it closer to T. nigroviridis through phylogenomic analysis. Gene family evolution analysis reveals rapid expansion of genes associated with immune response, providing insights into the genetic basis of successful colonization by L. sceleratus. Additionally, mutations in voltage-gated sodium channel (NaV 1.4) linked to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, indicating a complex evolution of this trait.
FRONTIERS IN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Stavroula Oikonomou, Athanasios Samaras, Maria Tekeoglou, Dimitrios Loukovitis, Arkadios Dimitroglou, Lefteris Kottaras, Kantham Papanna, Leonidas Papaharisis, Costas S. Tsigenopoulos, Michail Pavlidis, Dimitrios Chatziplis
Summary: This study investigates the genetic structure of stress response, body weight, and disease resistance in European seabass. The findings identify genomic regions affecting these traits and estimate their heritability. These results have important implications for genetic improvement in aquaculture breeding programs.
Article
Biodiversity Conservation
Catalina A. Garcia-Escudero, Costas S. Tsigenopoulos, Vasilis Gerakaris, Alexandros Tsakogiannis, Eugenia T. Apostolaki
Summary: Non-indigenous species pose a major threat to the native marine ecosystems of the Mediterranean Sea. A reassessment of a reported exotic seagrass species in Salamina Island, Greece, using DNA barcoding revealed that it is likely a morphologically variant of Halophila stipulacea. This study highlights the importance of applying an integrated taxonomic approach to effectively monitor the introductions of non-indigenous species.
Article
Multidisciplinary Sciences
O. Nousias, S. Oikonomou, T. Manousaki, V Papadogiannis, N. Angelova, D. Tsaparis, A. Tsakogiannis, N. Duncan, A. Estevez, K. Tzokas, M. Pavlidis, D. Chatziplis, C. S. Tsigenopoulos
Summary: This study constructed a high-density genetic map of meagre using ddRAD sequencing and provided genomic appreciation for weight traits. Comparative genomics analysis with other teleost species revealed the evolutionary history of meagre's genome and highlighted its potential as a valuable resource for research and production.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Sergio Vela-Avitua, Ingunn Thorland, Vasileios Bakopoulos, Kantham Papanna, Arkadios Dimitroglou, Eleftherios Kottaras, Papaharisis Leonidas, Bruno Guinand, Costas S. Tsigenopoulos, Muhammad L. Aslam
Summary: Viral nervous necrosis (VNN) is an infectious disease caused by the red-spotted grouper nervous necrosis virus (RGNNV) in European sea bass. A genome-wide association analysis revealed a strong signal of quantitative trait loci (QTL) at LG12, which explained around 33% of the genetic variance. The genes HSPA4L and/or REEP1 were found to be highly relevant in managing disease-associated symptoms.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Dimitrios Tsaparis, Thomas Lecocq, Dimitrios Kyriakis, Katerina Oikonomaki, Pascal Fontaine, Costas S. Tsigenopoulos
Summary: The genetic background of pikeperch populations was assessed using genetic markers, revealing that current broodstocks have similar genetic diversity to wild populations. Genetic differentiation analysis showed that European pikeperch populations can be divided into two groups, with one predominantly found in Northern Europe and around the Baltic Sea, and the other primarily in Central Europe. Aquaculture broodstocks were found to have fish of a single origin with a few exceptions. The study provides valuable information on the genetic diversity of pikeperch and offers a genetic tool for fish stock management and improvement.
Article
Fisheries
Beatriz Villanueva, Almudena Fernandez, Ramon Peiro-Pastor, Carolina Penaloza, Ross D. Houston, Anna K. Sonesson, Costas S. Tsigenopoulos, Luca Bargelloni, Kutsal Gamsiz, Bilge Karahan, Emel O. Gokcek, Jesus Fernandez, Maria Saura
Summary: Population structure and genetic diversity between wild and farmed populations of gilthead sea bream and European seabass in the Mediterranean Sea were assessed in this study. Results showed clear differentiation between wild and farmed populations, with farmed populations showing high heterogeneity. Some farmed populations had a genetic makeup similar to wild populations. Effective population sizes were larger in wild populations and smaller in farmed populations.
AQUACULTURE REPORTS
(2022)
Article
Biology
Nelina Angelova, Theodoros Danis, Jacques Lagnel, Costas S. Tsigenopoulos, Tereza Manousaki
Summary: This study presents SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and is suitable for use in High Performance Computing (HPC) domains. It has been optimized for performance and tested for effectiveness with various inputs, highlighting its universal applicability in the field.
BMC RESEARCH NOTES
(2022)
Article
Biodiversity Conservation
Marcos A. L. Teixeira, Torkild Bakken, Pedro E. Vieira, Joachim Langeneck, Bruno R. Sampieri, Panagiotis Kasapidis, Ascensao Ravara, Arne Nygren, Filipe O. Costa
Summary: Using a multi-locus approach, this study identified five completely sorted lineages within the Hediste diversicolor morphotype and suggested possible hybridization between two sympatric lineages in the Baltic Sea. Additionally, two new species, Hediste pontii sp. nov. and Hediste astae sp. nov., were formally described, highlighting their importance for biomonitoring and other ecological studies.
SYSTEMATICS AND BIODIVERSITY
(2022)
Article
Evolutionary Biology
Marcos A. L. Teixeira, Joachim Langeneck, Pedro E. Vieira, Jose Carlos Hernandez, Bruno R. Sampieri, Panagiotis Kasapidis, Serena Mucciolo, Torkild Bakken, Ascensao Ravara, Arne Nygren, Filipe O. Costa
Summary: Molecular techniques have proven effective in discovering hidden diversity and unique evolutionary lineages in morphologically similar species. This study identified at least 10 divergent evolutionary lineages of Platynereis dumerilii through DNA sequence analysis and observed distinctive paragnath patterns in different lineages. Two new Platynereis species were also discovered in this study, with one being widespread in the Azores and Webbnesia islands, and the other restricted to the western Mediterranean.
INVERTEBRATE SYSTEMATICS
(2022)
Article
Biochemistry & Molecular Biology
Aglaia Antoniou, Tereza Manousaki, Francisco Ramirez, Alessia Cariani, Rita Cannas, Panagiotis Kasapidis, Antonios Magoulas, Marta Albo-Puigserver, Elena Lloret-Lloret, Jose Maria Bellido, Maria Grazia Pennino, Maria Cristina Follesa, Antonio Esteban, Claire Saraux, Mario Sbrana, Maria Teresa Spedicato, Marta Coll, Costas S. Tsigenopoulos
Summary: By evaluating genetic variation across the entire genome, the study found evidence of local adaptation and population structuring in Sardina pilchardus, which is a highly exploited species. The findings highlight the importance of physical and ecological factors in maintaining population structure, and suggest the need for continuous monitoring under a seascape genomic approach. These results contribute to a deeper understanding of the species' responses to climate change and can aid in predicting future changes.
Article
Green & Sustainable Science & Technology
Giorgio Mancinelli, Thanos Dailianis, Costas Dounas, Panagiotis Kasapidis, Panayota Koulouri, Grigorios Skouradakis, Roberta Bardelli, Cristina Di Muri, Maria Teresa Guerra, Salvatrice Vizzini
Summary: This study investigated the trophic position and isotopic niche of the blue swimming crab using carbon and nitrogen stable isotopes analysis. The results showed that the crab had a higher trophic position in the Mediterranean Sea compared to other areas. There was high inter-individual variability in the isotopic values, and no significant difference in the isotopic niche between male and female specimens was found. Furthermore, there was a significant correlation between specimen size and δ15N values, suggesting an ontogenetic dietary shift.
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
