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    Authors: Diego Robledo; Juan A. Rubiolo; Santiago Cabaleiro; Paulino Martínez; +1 Authors

    Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates This work was funded by Spanish Ministry of Economy and Competitiveness and European Regional Development Funds (AGL2012-35904), Ministry of Science and Innovation (Consolider Ingenio, Aquagenomics, CSD2007-00002), and Local Government. Xunta de Galicia (GRC2014/010). DR was supported by a FPU fellowship funded by Spanish Ministry of Education, Culture and Sport (AP2012-0254) and a postdoctoral contract funded by the Biotechnology and Biological Science Research Council (BBSRC) grant BB/N024044/1 SI

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    Scientific Reports
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    Scientific Reports
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    Authors: Caroline Vernette; Julien Lecubin; Pablo Sánchez; Silvia G Acinas; +31 Authors

    11 pages, 8 figures, 2 tables.-- Data availability: Ocean Gene Atlas 2.0 is freely available and can be accessed via the following link: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/. Source code is available at GitLab repository: https://gitlab.osupytheas.fr/ocean_atlas/oga. Shotgun sequences are available at the European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) under accession number PRJEB7988 (OM-RGCv1 and v2), PRJEB6609 (MATOU), PRJEB41575 (Tara Arctic metagenome co-assemblies) and PRJEB402 (EUK_SMAGs) (see Table 1). The predicted genes from the OM-RGC are available at ENA under the accession numbers ERZ094224 and ERZ096909 to ERZ097151, and the protein sequences are available at: ftp://ftp.genome.jp/pub/db/mgenes/Environmental/Tara.pep.gz. For OM-RGCv2, all data files can be found through BioStudies with the accession S-BSST297 and for the 530 Tara Arctic metagenome co-assemblies with S-BSST451. All MATOU, EUK_SMAGs, MGT and BAC_ARC_MAGs resources are available at http://www.genoscope.cns.fr/tara/. Registry of all the samples from the Tara Oceans Expedition (2009–2013) with environmental metadata are available at PANGAEA: https://doi.org/10.1594/PANGAEA.875582. For the Global Malaspina 2010 Expedition, all raw sequences are publicly available at both DOE's JGI Integrated Microbial Genomes and Microbiomes (IMG/MER) and the European Nucleotide Archive (ENA). Individual metagenome assemblies, annotation files, and alignment files can be accessed at IMG/MER. All accession numbers are listed at https://www.nature.com/articles/s42003-021-02112–2#MOESM4 in Supplementary Data 1. The metagenomic data can be found through ENA with accession number PRJEB44456 and the co-assembly for the MAG dataset construction with accession number PRJEB40454, the nucleotide sequence for each MAG and their annotation files can be found through BioStudies with accession S-BSST457 and also in the companion publication website at: https://malaspina-public.gitlab.io/malaspina-deep-ocean-microbiome/. The user manual is available at https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/build/pdf/Ocean-Gene-Atlas_User_Manual.pd Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/ French Government ‘Investissements d'Avenir’ programmes OCEANOMICS [ANR-11-BTBR-0008]; FRANCE GENOMIQUE [ANR-10-INBS-09-08]; Institut Français de Bioinformatique (IFB) [ANR-11-INBS-0013]; SeqDigger [ANR-19-CE45-0008]; AO-EMBRC [ANR-21-ESRE-0038]. Funding for open access charge: ANR [ANR-19-CE45-0008] With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S) Peer reviewed

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    Research Collection
    Article . 2022
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    Nucleic Acids Research
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      Nucleic Acids Research
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    Authors: Rute R. da Fonseca; Alvarina Couto; André M. Machado; Brona Brejova; +40 Authors

    Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments. Rede Nacional de Espectrometria de Massa | Ref. LISBOA-01-0145-FEDER-022125 Biotechnology and Biological Sciences Research Council | Ref. BB/M009122/1 COMPETE and North Portugal Regional Operational Programme | Ref. Norte2020 Biotechnology and Biological Sciences Research Council | Ref. BB/N020146/1 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. SFRH/BD/126560/2016 Netherlands Organization for Scientific Research | Ref. 825.09.016 Rede Nacional de Espectrometria de Massa | Ref. ROTEIRO/0028/2013 European Regional Development Fund | Ref. UID/Multi/04423/2019 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. 1/0458/18 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. 1/0684/16 Portuguese Science Foundation | Ref. PTDC/MAR/115347/2009 Portuguese Science Foundation | Ref. COMPETE-FCOMP-01-012 Portuguese Science Foundation | Ref. FP7-PEOPLE-2010-IEF Deutsche Forschungsgemeinschaft | Ref. HO 5569/2-1 Portuguese Science Foundation | Ref. FEDER-015453 Danish National Research Foundation | Ref. DNRF94 Danish National Research Foundation | Ref. DNRF96 Novo Nordisk Foundation | Ref. NNF14CC0001 DeiC National Life Science Supercomputer European Molecular Biology Laboratory Wellcome Trust | Ref. WT108749/Z/15/Z Lundbeck Foundation | Ref. R52-A4895 Lundbeck Foundation | Ref. R52–5062 David and Lucile Packard Foundation Villum Fonden | Ref. VKR023446 National Science Foundation

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    NTNU Open
    Article . 2020
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    Investigo
    Article . 2020
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    Authors: Ingo Braasch; Andrew R. Gehrke; J. Joshua Smith; Kazuhiko Kawasaki; +57 Authors

    Funding: We thank the Broad Institute Genomics Platform for constructing and sequencing gar DNA and RNA libraries and J. Turner-Maier for the gar transcriptome assembly. We thank the teams of the Bayousphere Research Laboratory (Nicholls State University) and the University of Oregon Fish Facility for gar work and husbandry. We thank J. Westlund for the design of the species illustrations. The generation of gar sequences and assemblies by the Broad Institute of MIT and Harvard University was supported by US National Institutes of Health (NIH)/National Human Genome Research Institute grant U54 HG03067. This work was further supported by US NIH grants R01 OD011116 (alias R01 RR020833) and R24 OD01119004 (J.H.P.); a Feodor Lynen Fellowship from the Alexander von Humboldt Foundation and the Volkswagen Foundation Initiative Evolutionary Biology, grant I/84 815 (I.B.); US NIH grant T32 HD055164 and National Science Foundation (NSF) Doctoral Dissertation Improvement Grant 1311436 (A.R.G.); Uehara Memorial Foundation Research Fellowship 2013, Japan Society for the Promotion of Science Postdoctoral Research Fellowship 2012-127 and Marine Biological Laboratory Research Award 2014 (T.N.); Brazilian National Council for Scientific and Technological Development (CNPq) grants 402754/2012-3 and 477658/2012-1 (I.S.); the Brinson Foundation and the University of Chicago Biological Sciences Division (N.H.S.); NSF grant BCS0725227 (K.K.); call 'ARISTEIA I' of the National Strategic Reference Framework 2007-2013 (SPARCOMP, 36), Ministry of Education and Religious Affairs of Greece (T.M.); Agence Nationale de la Recherche (ANR) grant ANR-10-GENM-017 (PhyloFish; J.B.); the Wellcome Trust (grants WT095908 and WT098051) and the European Molecular Biology Laboratory (D.B., S.M.J.S. and B.A.); the Biomedical Research Council of the Agency for Science, Technology and Research (A*STAR), Singapore (B.V.); European Research Council grant 268513 (P.W.H.H. and K.J.M.); the Ministerio de Ciencia e Innovacion (BFU2010-14875 and BFU2015-71340) and the Generalitat de Catalunya, AGAUR (SGR2014-290) (C. C.); US NIH grant R01 AI057559 (G.W.L. and J.A.Y.); US NIH grants R24 OD010922 and R01 GM079492 (C. T. A.); and the National Basic Research Program of China (973 Program) (2012CB947600) and the National Natural Science Foundation of China (NSFC) (31030062) (H.W.). To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

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    Oxford University Research Archive
    Article . 2016
    License: CC BY NC SA
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    Nature Genetics
    Article . 2016 . Peer-reviewed
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    Nature Genetics
    Article . 2016 . Peer-reviewed
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    Authors: Mikkel-Holger S. Sinding; Shyam Gopalakrishnan; Jazmín Ramos-Madrigal; Marc de Manuel; +31 Authors

    This work is embedded in “The Qimmeq Project,” funded by the Velux Foundations and Aage og Johanne Louis-Hansens Fond, and supported by ArchSci2020, funded by the European Union’s EU Framework Programme for Research and Innovation Horizon 2020 under Marie Curie Actions grant no. 676154. We thank the Rock Foundation of New York for funding excavations at the Zhokhov and Yana sites in a 15-year-long effort starting in 2000. M.-H.S.S. was supported by the Independent Research Fund Denmark (8028-00005B) and NHM Oslo. S.G. was supported by Marie Skłodowska-Curie Actions (H2020 655732 - WhereWolf) and Carlsberg (CF14 - 0995). M.d.M.M. was supported by a Formació de Personal Investigador fellowship from Generalitat de Catalunya (FI_B01111). V.V.P., E.Y.P., and P.A.N. were supported by the Russian Science Foundation project no. 16-18-10265-RNF. T.M.B. was supported by BFU2017-86471-P (MINECO/FEDER, UE), Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). M.T.P.G. was supported by a European Research Council grant (ERC-2015-CoG-681396–Extinction Genomics). G.L. and L.A.F. were supported by the ERC (Grant ERC-2013-StG-337574-UNDEAD) and the Natural Environmental Research Council (Grants NE/K005243/1 and NE/K003259/1). P.S. was supported by the Francis Crick Institute (FC001595). Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.

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    Europe PubMed Central
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      Other literature type . 2020
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Julien Kincaid-Smith; Alan Tracey; Ronaldo de Carvalho Augusto; Ingo Bulla; +11 Authors

    Schistosomes cause schistosomiasis, the world’s second most important parasitic disease after malaria in terms of public health and social-economic impacts. A peculiar feature of these dioecious parasites is their ability to produce viable and fertile hybrid offspring. Originally only present in the tropics, schistosomiasis is now also endemic in southern Europe. Based on the analysis of two genetic markers the European schistosomes had previously been identified as hybrids between the livestock- and the human-infective species Schistosoma bovis and Schistosoma haematobium, respectively. Here, using PacBio long-read sequencing technology we performed genome assembly improvement and annotation of S. bovis, one of the parental species for which no satisfactory genome assembly was available. We then describe the whole genome introgression levels of the hybrid schistosomes, their morphometric parameters (eggs and adult worms) and their compatibility with two European snail strains used as vectors (Bulinus truncatus and Planorbarius metidjensis). Schistosome-snail compatibility is a key parameter for the parasites life cycle progression, and thus the capability of the parasite to establish in a given area. Our results show that this Schistosoma hybrid is strongly introgressed genetically, composed of 77% S. haematobium and 23% S. bovis origin. This genomic admixture suggests an ancient hybridization event and subsequent backcrosses with the human-specific species, S. haematobium, before its introduction in Corsica. We also show that egg morphology (commonly used as a species diagnostic) does not allow for accurate hybrid identification while genetic tests do. PLoS Neglected Tropical Diseases, 15 (12) ISSN:1935-2727 ISSN:1935-2735

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Research Collection
    Article . 2021
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    PLoS Neglected Tropical Diseases
    Article . 2021 . Peer-reviewed
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    PLoS Neglected Tropical Diseases
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    ETH Zürich Research Collection
    Article . 2021
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      PLoS Neglected Tropical Diseases
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      PLoS Neglected Tropical Diseases
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      ETH Zürich Research Collection
      Article . 2021
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    Authors: Paolo Ronza; Diego Robledo; Ana Paula Losada; Roberto Bermúdez; +3 Authors

    The thymus is a primary lymphoid organ that plays a pivotal role in the adaptive immune system. The immunobiology of the thymus in fish is considered to be similar to that of mammals, but it is actually poorly characterized in several cultured teleost species. In particular, while investigations in human and veterinary medicine have highlighted that the thymus can be affected by different pathological conditions, little is known about its response during disease in fish. To better understand the role of the thymus under physiological and pathological conditions, we conducted a study in turbot (Scophthalmus maximus), a commercially valuable flatfish species, combining transcriptomic and histopathological analyses. The myxozoan parasite Enteromyxum scophthalmi, which represents a major challenge to turbot production, was used as a model of infection. The thymus tissues of healthy fish showed overrepresented functions related to its immunological role in T-cell development and maturation. Large differences were observed between the transcriptomes of control and severely infected fish. Evidence of inflammatory response, apoptosis modulation, and declined thymic function associated with loss of cellularity was revealed by both genomic and morphopathological analyses. This study presents the first description of the turbot thymus transcriptome and provides novel insights into the role of this organ in teleosts’ immune responses This research was funded by THE SPANISH MINISTRY OF ECONOMY, INDUSTRY AND COMPETITIVENESS AND THE EUROPEAN REGIONAL DEVELOPMENT FUND (ERDF) through the projects AGL2015–67039–C3–1–R and AGL2015–67039–C3–3–R. DR is supported by BBSRC INSTITUTE STRATEGIC PROGRAM GRANTS to the Roslin Institute (BB/P013732/1, BB/P013740/1, BB/P013759/1) SI

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    Biology
    Other literature type . Article . 2020 . Peer-reviewed
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    Biology
    Article . 2020
    Data sources: DOAJ-Articles
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    Biology
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    Authors: Whitby, H.; Tang, W.; Planquette, H.; Gifford, S.; +5 Authors

    Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the diversity and distribution of nitrogen (N2) fixing marine diazotrophs, knowledge gaps remain regarding ecological interactions between diazotrophs and other community members. Using quantitative 16S and 18S V4 rDNA amplicon sequencing, we surveyed eukaryotic and prokaryotic microbial communities from samples collected in August 2016 and 2017 across the Western North Atlantic. Leveraging and significantly expanding an earlier published 2015 molecular dataset, we examined microbial community structure and ecological co-occurrence relationships associated with intense hotspots of N2 fixation previously reported at sites off the Southern New England Shelf and Mid-Atlantic Bight. Overall, we observed a negative relationship between eukaryotic diversity and both N2 fixation and net community production (NCP). Maximum N2 fixation rates occurred at sites with high abundances of mixotrophic stramenopiles, notably Chrysophyceae. Network analysis revealed such stramenopiles to be keystone taxa alongside the haptophyte diazotroph host Braarudosphaera bigelowii and chlorophytes. Our findings highlight an intriguing relationship between marine stramenopiles and high N2 fixation coastal sites. 4,379 1,24 SCIE Q1 14

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    Scientific Reports
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    UNC Dataverse
    Article . 2021
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      Scientific Reports
      Article
      License: CC BY
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      UNC Dataverse
      Article . 2021
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    Authors: Alexander Nater; Maja Patricia Mattle-Greminger; Anton Nurcahyo; Matthew G. Nowak; +33 Authors

    http://dx.doi.org/10.13039/501100006447 Department of Anthropology at the University of Zurich http://dx.doi.org/10.13039/501100006447 UZH Research Priority Program “Evolution in Action” http://dx.doi.org/10.13039/501100000995 Australian National University (ANU) research fund http://dx.doi.org/10.13039/501100001711 Swiss National Science Foundation http://dx.doi.org/10.13039/501100000996 Australia Awards Scholarship-DFAT http://dx.doi.org/10.13039/501100000995 ANU Vice Chancellor Travel Grant http://dx.doi.org/10.13039/501100006447 University of Zurich (UZH) http://dx.doi.org/10.13039/501100006448 A.H. Schultz Foundation Gates Cambridge Trust http://dx.doi.org/10.13039/501100005370 http://dx.doi.org/10.13039/100005966 Leakey Foundation http://dx.doi.org/10.13039/501100003329 MINECO http://dx.doi.org/10.13039/100004410 EMBO http://dx.doi.org/10.13039/100010663 ERC Julius–Klaus Foundation Fundacio Zoo Barcelona Arcus Foundation MINECO/FEDER

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    ZHAW digitalcollection
    Other literature type . 2017
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    St Andrews Research Repository
    Article . 2017 . Peer-reviewed
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    Current Biology
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    Current Biology
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    Current Biology
    Article . 2017
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Current Biology
    Article . 2017 . Peer-reviewed
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Current Biology; UPF Digital Repository
    Other literature type . Article . 2017 . Peer-reviewed
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    ZHAW digitalcollection
    Other literature type . 2018
    https://doi.org/10.7892/boris....
    Other literature type . 2017
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    Article . 2017
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Current Biology; NAR...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      ZHAW digitalcollection
      Other literature type . 2017
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      St Andrews Research Repository
      Article . 2017 . Peer-reviewed
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      Current Biology
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      Current Biology
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      Current Biology
      Article . 2017
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Current Biology
      Article . 2017 . Peer-reviewed
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Current Biology; UPF Digital Repository
      Other literature type . Article . 2017 . Peer-reviewed
      License: Elsevier Non-Commercial
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      ZHAW digitalcollection
      Other literature type . 2018
      https://doi.org/10.7892/boris....
      Other literature type . 2017
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      Article . 2017
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    Authors: Richter, Daniel J.; Watteaux, Romain; Vannier, Thomas; Leconte, Jade; +45 Authors

    Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated1,2. The most prominent global biogeography of marine plankton was derived by Longhurst3 based on parameters principally associated with photosynthetic plankton. Localized studies of selected plankton taxa or specific organismal sizes1,4–7 have mapped community structure and begun to assess the roles of environment and ocean current transport in shaping these patterns2,8. Here we assess global plankton biogeography and its relation to the biological, chemical and physical context of the ocean (the ‘seascape’) by analyzing 24 terabases of metagenomic sequence data and 739 million metabarcodes from the Tara Oceans expedition in light of environmental data and simulated ocean current transport. In addition to significant local heterogeneity, viral, prokaryotic and eukaryotic plankton communities all display near steady-state, large-scale, size-dependent biogeographical patterns. Correlation analyses between plankto transport time and metagenomic or environmental dissimilarity reveal the existence of basin-scale biological and environmental continua emerging within the main current systems. Across oceans, there is a measurable, continuous change within communities and environmental factors up to an average of 1.5 years of travel time. Modulation of plankton communities during transport varies with organismal size, such that the distribution of smaller plankton best matches Longhurst biogeochemical provinces, whereas larger plankton group into larger provinces. Together these findings provide an integrated framework to interpret plankton community organization in its physico-chemical context, paving the way to a better understanding of oceanic ecosystem functioning in a changing global environment. International audience

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    eLife
    Article . 2022 . Peer-reviewed
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    MPG.PuRe
    Article . 2022
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    MPG.PuRe
    Article . 2022
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    eLife
    Article . 2022
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    https://www.biorxiv.org/conten...
    Preprint
    License: CC BY NC
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    eLife
    Article . 2022
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    HAL AMU
    Article . 2022
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Diego Robledo; Juan A. Rubiolo; Santiago Cabaleiro; Paulino Martínez; +1 Authors

    Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates This work was funded by Spanish Ministry of Economy and Competitiveness and European Regional Development Funds (AGL2012-35904), Ministry of Science and Innovation (Consolider Ingenio, Aquagenomics, CSD2007-00002), and Local Government. Xunta de Galicia (GRC2014/010). DR was supported by a FPU fellowship funded by Spanish Ministry of Education, Culture and Sport (AP2012-0254) and a postdoctoral contract funded by the Biotechnology and Biological Science Research Council (BBSRC) grant BB/N024044/1 SI

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    Authors: Caroline Vernette; Julien Lecubin; Pablo Sánchez; Silvia G Acinas; +31 Authors

    11 pages, 8 figures, 2 tables.-- Data availability: Ocean Gene Atlas 2.0 is freely available and can be accessed via the following link: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/. Source code is available at GitLab repository: https://gitlab.osupytheas.fr/ocean_atlas/oga. Shotgun sequences are available at the European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) under accession number PRJEB7988 (OM-RGCv1 and v2), PRJEB6609 (MATOU), PRJEB41575 (Tara Arctic metagenome co-assemblies) and PRJEB402 (EUK_SMAGs) (see Table 1). The predicted genes from the OM-RGC are available at ENA under the accession numbers ERZ094224 and ERZ096909 to ERZ097151, and the protein sequences are available at: ftp://ftp.genome.jp/pub/db/mgenes/Environmental/Tara.pep.gz. For OM-RGCv2, all data files can be found through BioStudies with the accession S-BSST297 and for the 530 Tara Arctic metagenome co-assemblies with S-BSST451. All MATOU, EUK_SMAGs, MGT and BAC_ARC_MAGs resources are available at http://www.genoscope.cns.fr/tara/. Registry of all the samples from the Tara Oceans Expedition (2009–2013) with environmental metadata are available at PANGAEA: https://doi.org/10.1594/PANGAEA.875582. For the Global Malaspina 2010 Expedition, all raw sequences are publicly available at both DOE's JGI Integrated Microbial Genomes and Microbiomes (IMG/MER) and the European Nucleotide Archive (ENA). Individual metagenome assemblies, annotation files, and alignment files can be accessed at IMG/MER. All accession numbers are listed at https://www.nature.com/articles/s42003-021-02112–2#MOESM4 in Supplementary Data 1. The metagenomic data can be found through ENA with accession number PRJEB44456 and the co-assembly for the MAG dataset construction with accession number PRJEB40454, the nucleotide sequence for each MAG and their annotation files can be found through BioStudies with accession S-BSST457 and also in the companion publication website at: https://malaspina-public.gitlab.io/malaspina-deep-ocean-microbiome/. The user manual is available at https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/build/pdf/Ocean-Gene-Atlas_User_Manual.pd Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/ French Government ‘Investissements d'Avenir’ programmes OCEANOMICS [ANR-11-BTBR-0008]; FRANCE GENOMIQUE [ANR-10-INBS-09-08]; Institut Français de Bioinformatique (IFB) [ANR-11-INBS-0013]; SeqDigger [ANR-19-CE45-0008]; AO-EMBRC [ANR-21-ESRE-0038]. Funding for open access charge: ANR [ANR-19-CE45-0008] With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S) Peer reviewed

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    Nucleic Acids Research
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    Authors: Rute R. da Fonseca; Alvarina Couto; André M. Machado; Brona Brejova; +40 Authors

    Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments. Rede Nacional de Espectrometria de Massa | Ref. LISBOA-01-0145-FEDER-022125 Biotechnology and Biological Sciences Research Council | Ref. BB/M009122/1 COMPETE and North Portugal Regional Operational Programme | Ref. Norte2020 Biotechnology and Biological Sciences Research Council | Ref. BB/N020146/1 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. SFRH/BD/126560/2016 Netherlands Organization for Scientific Research | Ref. 825.09.016 Rede Nacional de Espectrometria de Massa | Ref. ROTEIRO/0028/2013 European Regional Development Fund | Ref. UID/Multi/04423/2019 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. 1/0458/18 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. 1/0684/16 Portuguese Science Foundation | Ref. PTDC/MAR/115347/2009 Portuguese Science Foundation | Ref. COMPETE-FCOMP-01-012 Portuguese Science Foundation | Ref. FP7-PEOPLE-2010-IEF Deutsche Forschungsgemeinschaft | Ref. HO 5569/2-1 Portuguese Science Foundation | Ref. FEDER-015453 Danish National Research Foundation | Ref. DNRF94 Danish National Research Foundation | Ref. DNRF96 Novo Nordisk Foundation | Ref. NNF14CC0001 DeiC National Life Science Supercomputer European Molecular Biology Laboratory Wellcome Trust | Ref. WT108749/Z/15/Z Lundbeck Foundation | Ref. R52-A4895 Lundbeck Foundation | Ref. R52–5062 David and Lucile Packard Foundation Villum Fonden | Ref. VKR023446 National Science Foundation

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      GigaScience
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      NTNU Open
      Article . 2020
      Data sources: NTNU Open
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      Investigo
      Article . 2020
      Data sources: Investigo
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    Authors: Ingo Braasch; Andrew R. Gehrke; J. Joshua Smith; Kazuhiko Kawasaki; +57 Authors

    Funding: We thank the Broad Institute Genomics Platform for constructing and sequencing gar DNA and RNA libraries and J. Turner-Maier for the gar transcriptome assembly. We thank the teams of the Bayousphere Research Laboratory (Nicholls State University) and the University of Oregon Fish Facility for gar work and husbandry. We thank J. Westlund for the design of the species illustrations. The generation of gar sequences and assemblies by the Broad Institute of MIT and Harvard University was supported by US National Institutes of Health (NIH)/National Human Genome Research Institute grant U54 HG03067. This work was further supported by US NIH grants R01 OD011116 (alias R01 RR020833) and R24 OD01119004 (J.H.P.); a Feodor Lynen Fellowship from the Alexander von Humboldt Foundation and the Volkswagen Foundation Initiative Evolutionary Biology, grant I/84 815 (I.B.); US NIH grant T32 HD055164 and National Science Foundation (NSF) Doctoral Dissertation Improvement Grant 1311436 (A.R.G.); Uehara Memorial Foundation Research Fellowship 2013, Japan Society for the Promotion of Science Postdoctoral Research Fellowship 2012-127 and Marine Biological Laboratory Research Award 2014 (T.N.); Brazilian National Council for Scientific and Technological Development (CNPq) grants 402754/2012-3 and 477658/2012-1 (I.S.); the Brinson Foundation and the University of Chicago Biological Sciences Division (N.H.S.); NSF grant BCS0725227 (K.K.); call 'ARISTEIA I' of the National Strategic Reference Framework 2007-2013 (SPARCOMP, 36), Ministry of Education and Religious Affairs of Greece (T.M.); Agence Nationale de la Recherche (ANR) grant ANR-10-GENM-017 (PhyloFish; J.B.); the Wellcome Trust (grants WT095908 and WT098051) and the European Molecular Biology Laboratory (D.B., S.M.J.S. and B.A.); the Biomedical Research Council of the Agency for Science, Technology and Research (A*STAR), Singapore (B.V.); European Research Council grant 268513 (P.W.H.H. and K.J.M.); the Ministerio de Ciencia e Innovacion (BFU2010-14875 and BFU2015-71340) and the Generalitat de Catalunya, AGAUR (SGR2014-290) (C. C.); US NIH grant R01 AI057559 (G.W.L. and J.A.Y.); US NIH grants R24 OD010922 and R01 GM079492 (C. T. A.); and the National Basic Research Program of China (973 Program) (2012CB947600) and the National Natural Science Foundation of China (NSFC) (31030062) (H.W.). To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

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    Oxford University Research Archive
    Article . 2016
    License: CC BY NC SA
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    Nature Genetics
    Article . 2016 . Peer-reviewed
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    Nature Genetics
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    Nature Genetics
    Article . 2016 . Peer-reviewed
    License: CC BY NC SA
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    Authors: Mikkel-Holger S. Sinding; Shyam Gopalakrishnan; Jazmín Ramos-Madrigal; Marc de Manuel; +31 Authors

    This work is embedded in “The Qimmeq Project,” funded by the Velux Foundations and Aage og Johanne Louis-Hansens Fond, and supported by ArchSci2020, funded by the European Union’s EU Framework Programme for Research and Innovation Horizon 2020 under Marie Curie Actions grant no. 676154. We thank the Rock Foundation of New York for funding excavations at the Zhokhov and Yana sites in a 15-year-long effort starting in 2000. M.-H.S.S. was supported by the Independent Research Fund Denmark (8028-00005B) and NHM Oslo. S.G. was supported by Marie Skłodowska-Curie Actions (H2020 655732 - WhereWolf) and Carlsberg (CF14 - 0995). M.d.M.M. was supported by a Formació de Personal Investigador fellowship from Generalitat de Catalunya (FI_B01111). V.V.P., E.Y.P., and P.A.N. were supported by the Russian Science Foundation project no. 16-18-10265-RNF. T.M.B. was supported by BFU2017-86471-P (MINECO/FEDER, UE), Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). M.T.P.G. was supported by a European Research Council grant (ERC-2015-CoG-681396–Extinction Genomics). G.L. and L.A.F. were supported by the ERC (Grant ERC-2013-StG-337574-UNDEAD) and the Natural Environmental Research Council (Grants NE/K005243/1 and NE/K003259/1). P.S. was supported by the Francis Crick Institute (FC001595). Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.

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    Europe PubMed Central
    Other literature type . 2020
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    Authors: Julien Kincaid-Smith; Alan Tracey; Ronaldo de Carvalho Augusto; Ingo Bulla; +11 Authors

    Schistosomes cause schistosomiasis, the world’s second most important parasitic disease after malaria in terms of public health and social-economic impacts. A peculiar feature of these dioecious parasites is their ability to produce viable and fertile hybrid offspring. Originally only present in the tropics, schistosomiasis is now also endemic in southern Europe. Based on the analysis of two genetic markers the European schistosomes had previously been identified as hybrids between the livestock- and the human-infective species Schistosoma bovis and Schistosoma haematobium, respectively. Here, using PacBio long-read sequencing technology we performed genome assembly improvement and annotation of S. bovis, one of the parental species for which no satisfactory genome assembly was available. We then describe the whole genome introgression levels of the hybrid schistosomes, their morphometric parameters (eggs and adult worms) and their compatibility with two European snail strains used as vectors (Bulinus truncatus and Planorbarius metidjensis). Schistosome-snail compatibility is a key parameter for the parasites life cycle progression, and thus the capability of the parasite to establish in a given area. Our results show that this Schistosoma hybrid is strongly introgressed genetically, composed of 77% S. haematobium and 23% S. bovis origin. This genomic admixture suggests an ancient hybridization event and subsequent backcrosses with the human-specific species, S. haematobium, before its introduction in Corsica. We also show that egg morphology (commonly used as a species diagnostic) does not allow for accurate hybrid identification while genetic tests do. PLoS Neglected Tropical Diseases, 15 (12) ISSN:1935-2727 ISSN:1935-2735

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    Research Collection
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    PLoS Neglected Tropical Diseases
    Article . 2021 . Peer-reviewed
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    PLoS Neglected Tropical Diseases
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    ETH Zürich Research Collection
    Article . 2021
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      PLoS Neglected Tropical Diseases
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      PLoS Neglected Tropical Diseases
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      Article . 2021
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    Authors: Paolo Ronza; Diego Robledo; Ana Paula Losada; Roberto Bermúdez; +3 Authors

    The thymus is a primary lymphoid organ that plays a pivotal role in the adaptive immune system. The immunobiology of the thymus in fish is considered to be similar to that of mammals, but it is actually poorly characterized in several cultured teleost species. In particular, while investigations in human and veterinary medicine have highlighted that the thymus can be affected by different pathological conditions, little is known about its response during disease in fish. To better understand the role of the thymus under physiological and pathological conditions, we conducted a study in turbot (Scophthalmus maximus), a commercially valuable flatfish species, combining transcriptomic and histopathological analyses. The myxozoan parasite Enteromyxum scophthalmi, which represents a major challenge to turbot production, was used as a model of infection. The thymus tissues of healthy fish showed overrepresented functions related to its immunological role in T-cell development and maturation. Large differences were observed between the transcriptomes of control and severely infected fish. Evidence of inflammatory response, apoptosis modulation, and declined thymic function associated with loss of cellularity was revealed by both genomic and morphopathological analyses. This study presents the first description of the turbot thymus transcriptome and provides novel insights into the role of this organ in teleosts’ immune responses This research was funded by THE SPANISH MINISTRY OF ECONOMY, INDUSTRY AND COMPETITIVENESS AND THE EUROPEAN REGIONAL DEVELOPMENT FUND (ERDF) through the projects AGL2015–67039–C3–1–R and AGL2015–67039–C3–3–R. DR is supported by BBSRC INSTITUTE STRATEGIC PROGRAM GRANTS to the Roslin Institute (BB/P013732/1, BB/P013740/1, BB/P013759/1) SI

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    Biology
    Other literature type . Article . 2020 . Peer-reviewed
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    Biology
    Article . 2020
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    Authors: Whitby, H.; Tang, W.; Planquette, H.; Gifford, S.; +5 Authors

    Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the diversity and distribution of nitrogen (N2) fixing marine diazotrophs, knowledge gaps remain regarding ecological interactions between diazotrophs and other community members. Using quantitative 16S and 18S V4 rDNA amplicon sequencing, we surveyed eukaryotic and prokaryotic microbial communities from samples collected in August 2016 and 2017 across the Western North Atlantic. Leveraging and significantly expanding an earlier published 2015 molecular dataset, we examined microbial community structure and ecological co-occurrence relationships associated with intense hotspots of N2 fixation previously reported at sites off the Southern New England Shelf and Mid-Atlantic Bight. Overall, we observed a negative relationship between eukaryotic diversity and both N2 fixation and net community production (NCP). Maximum N2 fixation rates occurred at sites with high abundances of mixotrophic stramenopiles, notably Chrysophyceae. Network analysis revealed such stramenopiles to be keystone taxa alongside the haptophyte diazotroph host Braarudosphaera bigelowii and chlorophytes. Our findings highlight an intriguing relationship between marine stramenopiles and high N2 fixation coastal sites. 4,379 1,24 SCIE Q1 14

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    Scientific Reports
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    UNC Dataverse
    Article . 2021
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Scientific Reports
      Article
      License: CC BY
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      UNC Dataverse
      Article . 2021
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    Authors: Alexander Nater; Maja Patricia Mattle-Greminger; Anton Nurcahyo; Matthew G. Nowak; +33 Authors

    http://dx.doi.org/10.13039/501100006447 Department of Anthropology at the University of Zurich http://dx.doi.org/10.13039/501100006447 UZH Research Priority Program “Evolution in Action” http://dx.doi.org/10.13039/501100000995 Australian National University (ANU) research fund http://dx.doi.org/10.13039/501100001711 Swiss National Science Foundation http://dx.doi.org/10.13039/501100000996 Australia Awards Scholarship-DFAT http://dx.doi.org/10.13039/501100000995 ANU Vice Chancellor Travel Grant http://dx.doi.org/10.13039/501100006447 University of Zurich (UZH) http://dx.doi.org/10.13039/501100006448 A.H. Schultz Foundation Gates Cambridge Trust http://dx.doi.org/10.13039/501100005370 http://dx.doi.org/10.13039/100005966 Leakey Foundation http://dx.doi.org/10.13039/501100003329 MINECO http://dx.doi.org/10.13039/100004410 EMBO http://dx.doi.org/10.13039/100010663 ERC Julius–Klaus Foundation Fundacio Zoo Barcelona Arcus Foundation MINECO/FEDER

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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZHAW digitalcollection
    Other literature type . 2017
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    St Andrews Research Repository
    Article . 2017 . Peer-reviewed
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    Current Biology
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    Current Biology
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    Current Biology
    Article . 2017
    Data sources: NARCIS
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Current Biology
    Article . 2017 . Peer-reviewed
    License: Elsevier Non-Commercial
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Current Biology; UPF Digital Repository
    Other literature type . Article . 2017 . Peer-reviewed
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    ZHAW digitalcollection
    Other literature type . 2018
    https://doi.org/10.7892/boris....
    Other literature type . 2017
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    ZENODO
    Article . 2017
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZHAW digitalcollection
      Other literature type . 2017
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      St Andrews Research Repository
      Article . 2017 . Peer-reviewed
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      Current Biology
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      License: Elsevier Non-Commercial
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      Current Biology
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Current Biology
      Article . 2017
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Current Biology
      Article . 2017 . Peer-reviewed
      License: Elsevier Non-Commercial
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Current Biology; UPF Digital Repository
      Other literature type . Article . 2017 . Peer-reviewed
      License: Elsevier Non-Commercial
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      ZHAW digitalcollection
      Other literature type . 2018
      https://doi.org/10.7892/boris....
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      ZENODO
      Article . 2017
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Richter, Daniel J.; Watteaux, Romain; Vannier, Thomas; Leconte, Jade; +45 Authors

    Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated1,2. The most prominent global biogeography of marine plankton was derived by Longhurst3 based on parameters principally associated with photosynthetic plankton. Localized studies of selected plankton taxa or specific organismal sizes1,4–7 have mapped community structure and begun to assess the roles of environment and ocean current transport in shaping these patterns2,8. Here we assess global plankton biogeography and its relation to the biological, chemical and physical context of the ocean (the ‘seascape’) by analyzing 24 terabases of metagenomic sequence data and 739 million metabarcodes from the Tara Oceans expedition in light of environmental data and simulated ocean current transport. In addition to significant local heterogeneity, viral, prokaryotic and eukaryotic plankton communities all display near steady-state, large-scale, size-dependent biogeographical patterns. Correlation analyses between plankto transport time and metagenomic or environmental dissimilarity reveal the existence of basin-scale biological and environmental continua emerging within the main current systems. Across oceans, there is a measurable, continuous change within communities and environmental factors up to an average of 1.5 years of travel time. Modulation of plankton communities during transport varies with organismal size, such that the distribution of smaller plankton best matches Longhurst biogeochemical provinces, whereas larger plankton group into larger provinces. Together these findings provide an integrated framework to interpret plankton community organization in its physico-chemical context, paving the way to a better understanding of oceanic ecosystem functioning in a changing global environment. International audience

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    eLife
    Article . 2022 . Peer-reviewed
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    MPG.PuRe
    Article . 2022
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    MPG.PuRe
    Article . 2022
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    eLife
    Article . 2022
    Data sources: DOAJ
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    https://www.biorxiv.org/conten...
    Preprint
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    eLife
    Article . 2022
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    HAL AMU
    Article . 2022
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