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Natacha Nikolic Gilles Morandeau Ludovic Hoarau Wendy West Haritz Arrizabalaga Simon Hoyle Simon J. Nicol Jérôme Bourjea Alexis Puech Jessica H. Farley Ashley J. Williams Alain Fonteneau 《Reviews in Fish Biology and Fisheries》2017,27(4):775-810
Albacore is one of the most important commercially harvested species in the world’s oceans. Despite a long history of scientific research, there is no global review or synthesis of knowledge about the species across all oceanic regions. We analysed 613 published studies that report on albacore and summarize the current state of knowledge on biology, stock structure, fisheries and management. To describe the trends in albacore fisheries, we examined the catch and effort databases of Regional Fisheries Management Organisations. The stocks of albacore are generally largest in the Pacific Ocean and smallest in the Mediterranean Sea. The biology of Atlantic and Pacific Ocean stocks are well documented, while the Indian Ocean and the Mediterranean Sea stocks are more data deficient. These two latter areas should be considered as priorities for future research and data collection in order to better understand the state of global stocks of albacore tuna. Improved information would also assist with delineating stock boundaries needed for sustainable management of this species. 相似文献
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Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past
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Clio Der Sarkissian Vianney Pichereau Catherine Dupont Peter C. Ilsøe Mickael Perrigault Paul Butler Laurent Chauvaud Jón Eiríksson James Scourse Christine Paillard Ludovic Orlando 《Molecular ecology resources》2017,17(5):835-853
Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo‐) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro‐) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high‐throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome‐scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management. 相似文献
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Diana I. Cruz‐Dávalos Bastien Llamas Charleen Gaunitz Antoine Fages Cristina Gamba Julien Soubrier Pablo Librado Andaine Seguin‐Orlando Mélanie Pruvost Ahmed H. Alfarhan Saleh A. Alquraishi Khaled A. S. Al‐Rasheid Amelie Scheu Norbert Beneke Arne Ludwig Alan Cooper Eske Willerslev Ludovic Orlando 《Molecular ecology resources》2017,17(3):508-522
High‐throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best‐suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture‐enrichment methods represent cost‐effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in‐solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self‐annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains. 相似文献
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The mutualistic relationships that occur between myrmecophilous aphids and ants are based on the rich food supply that honeydew represents for ants and on the protection they provide against aphid natural enemies. While aphid predators and parasitoids actively forage for oviposition sites by using aphid semiochemicals, scouts of aphid-tending ant species would also benefit from locating honeydew resources by orienting toward aphid pheromone sources. The present study aims to provide additional information on the use of Aphis fabae alarm pheromone, i.e. (E)-β-farnesene (EβF), by ant scouts. The perception and behavioral impact of EβF on Lasius niger were investigated using electroantennography and two bio-assays measuring their attraction and orientation towards aphid semiochemicals. Pronounced electrical depolarizations were observed from L. niger scout antennae to stimulations of A. fabae alarm pheromone, while other sesquiterpenes elicited weak or no responses. L. niger scouts were significantly attracted toward EβF in a four-arm olfactometer, as well as in an two-choice bioassay. These laboratory results suggest for the first time that low amounts of aphid alarm pheromone can be used by L. niger scouts as a cue indicating the presence of aphid colonies and could therefore mediate the aphid-ant partnership in the field. 相似文献
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Costes B Fournier G Michel B Delforge C Raj VS Dewals B Gillet L Drion P Body A Schynts F Lieffrig F Vanderplasschen A 《Journal of virology》2008,82(10):4955-4964
Koi herpesvirus (KHV) is the causative agent of a lethal disease in koi and common carp. In the present study, we describe the cloning of the KHV genome as a stable and infectious bacterial artificial chromosome (BAC) clone that can be used to produce KHV recombinant strains. This goal was achieved by the insertion of a loxP-flanked BAC cassette into the thymidine kinase (TK) locus. This insertion led to a BAC plasmid that was stably maintained in bacteria and was able to regenerate virions when permissive cells were transfected with the plasmid. Reconstituted virions free of the BAC cassette but carrying a disrupted TK locus (the FL BAC-excised strain) were produced by the transfection of Cre recombinase-expressing cells with the BAC. Similarly, virions with a wild-type revertant TK sequence (the FL BAC revertant strain) were produced by the cotransfection of cells with the BAC and a DNA fragment encoding the wild-type TK sequence. Reconstituted recombinant viruses were compared to the wild-type parental virus in vitro and in vivo. The FL BAC revertant strain and the FL BAC-excised strain replicated comparably to the parental FL strain. The FL BAC revertant strain induced KHV infection in koi carp that was indistinguishable from that induced by the parental strain, while the FL BAC-excised strain exhibited a partially attenuated phenotype. Finally, the usefulness of the KHV BAC for recombination studies was demonstrated by the production of an ORF16-deleted strain by using prokaryotic recombination technology. The availability of the KHV BAC is an important advance that will allow the study of viral genes involved in KHV pathogenesis, as well as the production of attenuated recombinant candidate vaccines. 相似文献
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Miquel De Cáceres Milan Chytrý Emiliano Agrillo Fabio Attorre Zoltán Botta‐Dukát Jorge Capelo Bálint Czúcz Jürgen Dengler Jörg Ewald Don Faber‐Langendoen Enrico Feoli Scott B. Franklin Rosario Gavilán François Gillet Florian Jansen Borja Jiménez‐Alfaro Pavel Krestov Flavia Landucci Attila Lengyel Javier Loidi Ladislav Mucina Robert K. Peet David W. Roberts Jan Roleček Joop H.J. Schaminée Sebastian Schmidtlein Jean‐Paul Theurillat Lubomír Tichý Donald A. Walker Otto Wildi Wolfgang Willner Susan K. Wiser 《应用植被学》2015,18(4):543-560