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    Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO2

    Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science. 1998;281:237–40. https://doi.org/10.1126/science.281.5374.237CAS 
    Article 
    PubMed 

    Google Scholar 
    Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive Earth’s biogeochemical cycles. Science. 2008;320:1034–9. https://doi.org/10.1126/science.1153213CAS 
    Article 
    PubMed 

    Google Scholar 
    Gattuso J-P, Magnan A, Billé R, Cheung WWL, Howes EL, Joos F, et al. Contrasting futures for ocean and society from different anthropogenic CO2 emissions scenarios. Science. 2015;349:aac4722. https://doi.org/10.1126/science.aac4722Steinacher M, Joos F, Frölicher TL, Bopp L, Cadule P, Cocco V, et al. Projected 21st century decrease in marine productivity: a multi-model analysis. Biogeosciences. 2010;7:979–1005. https://doi.org/10.5194/bg-7-979-2010CAS 
    Article 

    Google Scholar 
    Henson SA, Cael BB, Allen SR, Dutkiewicz S. Future phytoplankton diversity in a changing climate. Nat Commun. 2021;12:5372. https://doi.org/10.1038/s41467-021-25699-wCAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Thomas MK, Kremer CT, Klausmeier CA, Litchman E. A global pattern of thermal adaptation in marine phytoplankton. Science. 2012;338:1085–8. https://doi.org/10.1126/science.1224836CAS 
    Article 
    PubMed 

    Google Scholar 
    Collins S, Boyd PW, Doblin MA. Evolution, microbes, and changing ocean conditions. Annu Rev Mar Sci. 2020;12:181–208. https://doi.org/10.1146/annurev-marine-010318-095311Article 

    Google Scholar 
    Schaum CE, Buckling A, Smirnoff N, Studholme DJ, Yvon-Durocher G. Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom. Nat Commun. 2018;9:1719. https://doi.org/10.1038/s41467-018-03906-5CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lohbeck KT, Riebesell U, Reusch TBH. Adaptive evolution of a key phytoplankton species to ocean acidification. Nat Geosci. 2012;5:346–51. https://doi.org/10.1038/ngeo1441CAS 
    Article 

    Google Scholar 
    Jin P, Gao K, Beardall J. Evolutionary responses of a coccolithophorid Gephyrocapsa oceanica to ocean acidification. Evolution. 2013;67:1869–78. https://doi.org/10.1111/evo.12112CAS 
    Article 
    PubMed 

    Google Scholar 
    Schlüter L, Lohbeck KT, Gutowska MA, Gröger JP, Riebesell U, Reusch TBH. Adaptation of a globally important coccolithophore to ocean warming and acidification. Nat Clim Change. 2014;4:1024–30. https://doi.org/10.1038/nclimate2379CAS 
    Article 

    Google Scholar 
    Listmann L, LeRoch M, Schlüter L, Thomas MK, Reusch TBH. Swift thermal reaction norm evolution in a key marine phytoplankton species. Evol Appl. 2016;9:1156–64. https://doi.org/10.1111/eva.12362Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zhong J, Guo Y, Liang Z, Huang Q, Lu H, Pan J, et al. Adaptation of a marine diatom to ocean acidification and warming reveals constraints and trade-offs. Sci Total Environ. 2021;771:145167. https://doi.org/10.1016/j.scitotenv.2021.145167CAS 
    Article 
    PubMed 

    Google Scholar 
    Brennan GL, Colegrave N, Collins S. Evolutionary consequences of multidriver environmental change in an aquatic primary producer. Proc Natl Acad Sci USA. 2017;114:9930–5. https://doi.org/10.1073/pnas.1703375114CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zhang S, Wu Y, Lin L, Wang D. Molecular insights into the circadian clock in marine diatoms. Acta Oceano Sin. 2022;41:1–12. https://doi.org/10.1007/s13131-021-1962-4Article 

    Google Scholar 
    Nagelkerken I, Connell SD. Global alteration of ocean ecosystem functioning due to increasing human CO2 emissions. Proc Natl Acad Sci USA. 2015;112:13272–7. https://doi.org/10.1073/pnas.1510856112CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Boyd PW, Collins S, Dupont S, Fabricius K, Gattuso JP, Havenhand J, et al. Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change-a review. Glob Change Biol. 2018;24:2239–61. https://doi.org/10.1111/gcb.14102Article 

    Google Scholar 
    Matsuda Y, Nakajima K, Tachibana M. Recent progresses on the genetic basis of the regulation of CO2 acquisition systems in response to CO2 concentration. Photosynth Res. 2011;109:191–203. https://doi.org/10.1007/s11120-011-9623-7CAS 
    Article 
    PubMed 

    Google Scholar 
    Ohno N, Inoue T, Yamashiki R, Nakajima K, Kitahara Y, Ishibashi M, et al. CO2-cAMP-responsive cis-elements targeted by a transcription factor with CREB/ATF-like basic zipper domain in the marine diatom Phaeodactylum tricornutum. Plant Physiol. 2012;158:499–513. https://doi.org/10.1104/pp.111.190249CAS 
    Article 
    PubMed 

    Google Scholar 
    Hennon GMM, Ashworth J, Groussman RD, Berthiaume C, Morales RL, Baliga NS, et al. Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression. Nat Clim Change. 2015;5:761–5. https://doi.org/10.1038/nclimate2683CAS 
    Article 

    Google Scholar 
    Toseland A, Daines SJ, Clark JR, Kirkham A, Strauss J, Uhlig C, et al. The impact of temperature on marine phytoplankton resource allocation and metabolism. Nat Clim Change. 2013;3:979–84. https://doi.org/10.1038/nclimate1989CAS 
    Article 

    Google Scholar 
    Gao K, Beardall J, Häder DP, Hall-Spencer JM, Gao G, Hutchins DA. Effects of ocean acidification on marine photosynthetic organisms under the concurrent influences of warming, UV radiation, and deoxygenation. Front Mar Sci. 2019;6:322. https://doi.org/10.3389/fmars.2019.00322Article 

    Google Scholar 
    Tu L, Su P, Zhang Z, Gao L, Wang J, Hu T, et al. Genome of Tripterygium wilfordii and identification of cytochrome P450 involved in triptolide biosynthesis. Nat Commun. 2020;11:971. https://doi.org/10.1038/s41467-020-14776-1CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Treves H, Siemiatkowska B, Luzarowska U, Murik O, Fernandez-Pozo N, Moraes TA, et al. Multi-omics reveals mechanisms of total resistance to extreme illumination of a desert alga. Nat Plants. 2020;6:1031–43. https://doi.org/10.1038/s41477-020-0729-9CAS 
    Article 
    PubMed 

    Google Scholar 
    Van den Bergh B, Swings T, Fauvart M, Michels J. Experimental design, population dynamics, and diversity in microbial experimental evolution. Microbiol Mol Biol Rev. 2018;82:e00008–18.PubMed 
    PubMed Central 

    Google Scholar 
    Elena SF, Lenski RE. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet. 2003;4:457–69. https://doi.org/10.1038/nrg1088CAS 
    Article 
    PubMed 

    Google Scholar 
    Colegrave N, Collins S. Experimental evolution: experimental evolution and evolvability. Heredity. 2008;100:464–70. https://doi.org/10.1038/sj.hdy.6801095CAS 
    Article 
    PubMed 

    Google Scholar 
    Jin P, Ji Y, Huang Q, Li P, Pan J, Lu H, et al. A reduction in metabolism explains the trade‐offs associated with the long‐term adaptation of phytoplankton to high CO2 concentrations. N Phytol. 2022;233:2155–67. https://doi.org/10.1111/nph.17917CAS 
    Article 

    Google Scholar 
    Flombaum P, Gallegos JL, Gordillo RA, Rincón J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci USA. 2013;110:9824–9. https://doi.org/10.1073/pnas.1307701110CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hutchins DA, Walworth NG, Webb EA, Saito MA, Moran D, Mcllvin MR, et al. Irreversibly increased nitrogen fixation in Trichodesmium experimentally adapted to elevated carbon dioxide. Nat Commun. 2015;6:8155. https://doi.org/10.1038/ncomms9155Article 
    PubMed 

    Google Scholar 
    Padfield D, Yvon-Durocher G, Buckling A, Jennings S, Yvon-Durocher G. Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecol Lett. 2016;19:133–42.Article 

    Google Scholar 
    Coles VJ, Stukel MR, Brooks MT, Burd A, Crump BC, Moran MA, et al. Ocean biogeochemistry modeled with emergent trait-based genomics. Science. 2017;358:1149–54. https://doi.org/10.1126/science.aan5712CAS 
    Article 
    PubMed 

    Google Scholar 
    Linnen CR, Kingsley EP, Jensen JD, Hoekstra HE. On the origin and spread of an adaptive allele in deer mice. Science. 2009;325:1095–8. https://doi.org/10.1126/science.1175826CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Van’t Hof AE, Campagne P, Rigden DJ, Yung CJ, Lingley J, Quail MA, et al. The industrial melanism mutation in British peppered moths is a transposable element. Nature. 2016;534:102–5. https://doi.org/10.1038/nature17951CAS 
    Article 
    PubMed 

    Google Scholar 
    Bitter MC, Kapsenberg L, Gattuso JP, Pfister CA. Standing genetic variation fuels rapid adaptation to ocean acidification. Nat Commun. 2019;10:5821. https://doi.org/10.1038/s41467-019-13767-1CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lai YT, Yeung CK, Omland KE, Pang EL, Hao Y, Liao BY, et al. Standing genetic variation as the predominant source for adaptation of a songbird. Proc Natl Acad Sci USA. 2019;116:2152–7. https://doi.org/10.1073/pnas.1813597116Armbrust EV. The life of diatoms in the world’s oceans. Nature. 2009;459:185–92. https://doi.org/10.1038/nature08057CAS 
    Article 
    PubMed 

    Google Scholar 
    Rastogi A, Vieira FRJ, Deton-Cabanillas AF, Veluchamy A, Cantrel C, Wang G, et al. A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum. ISME J. 2020;14:347–63. https://doi.org/10.1038/s41396-019-0528-3Article 
    PubMed 

    Google Scholar 
    Jin P, Agustí S. Fast adaptation of tropical diatoms to increased warming with trade-offs. Sci Rep. 2018;8:17771. https://doi.org/10.1038/s41598-018-36091-yCAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Barton S, Jenkins J, Buckling A, Schaum CE, Smirnoff N, Raven JA, et al. Evolutionary temperature compensation of carbon fixation in marine phytoplankton. Ecol Lett. 2020;23:722–33.Article 

    Google Scholar 
    Guillard RR, Ryther JH. Studies of marine planktonic diatoms: I. Cyclotella nana Hustedt, and Detonula confervacea (Cleve) Gran. Can J Microbiol. 1962;8:229–39. https://doi.org/10.1139/m62-029CAS 
    Article 
    PubMed 

    Google Scholar 
    Huysman MJ, Martens C, Vandepoele K, Gillard J, Rayko E, Heijde M, et al. Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling. Genome Biol. 2010;11:R17. https://doi.org/10.1186/gb-2010-11-2-r17CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    IPCC. Summary for policymakers. In: Masson-Delmotte V, Zhai P, Pirani A, Connors SL, Péan C, Berger S, et al. editors. Climate change 2021: the physical science basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. Switzerland: IPCC; 2021.Jiang H, Gao K. Effects of lowering temperature during culture on the production of polyunsaturated fatty acids in the marine diatom Phaeodactylum tricornutum (Bacillariophyceae). J Phycol. 2004;40:651–4. https://doi.org/10.1111/j.1529-8817.2004.03112.xCAS 
    Article 

    Google Scholar 
    Pérez EB, Pina IC, Rodríguez LP. Kinetic model for growth of Phaeodactylum tricornutum in intensive culture photobioreactor. Biochem Eng J. 2008;40:520–5. https://doi.org/10.1016/j.bej.2008.02.007CAS 
    Article 

    Google Scholar 
    Boyd PW, Rynearson TA, Armstrong EA, Fu F, Hayashi K, Hu Z, et al. Marine phytoplankton temperature versus growth responses from polar to tropical waters-outcome of a scientific community-wide study. PLoS One. 2013;8:e63091 https://doi.org/10.1371/journal.pone.0063091CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zeng X, Jin P, Jiang Y, Yang H, Zhong J, Liang Z, et al. Light alters the responses of two marine diatoms to increased warming. Mar Environ Res. 2020;154:104871. https://doi.org/10.1016/j.marenvres.2019.104871CAS 
    Article 
    PubMed 

    Google Scholar 
    Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–i890. https://doi.org/10.1093/bioinformatics/bty560CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 2008;456:239–44.CAS 
    Article 

    Google Scholar 
    Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60. https://doi.org/10.1093/bioinformatics/btp324CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164. https://doi.org/10.1093/nar/gkq603CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9. https://doi.org/10.1038/nmeth.1923CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357–60. https://doi.org/10.1038/nmeth.3317CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5. https://doi.org/10.1038/nbt.3122CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016;11:1650–67. https://doi.org/10.1038/nprot.2016.095CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. https://doi.org/10.1186/s13059-014-0550-8CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gifford RM. Plant respiration in productivity models: conceptualisation, representation and issues for global terrestrial carbon-cycle research. Funct Plant Biol. 2003;30:171–86. https://doi.org/10.1071/FP02083Article 
    PubMed 

    Google Scholar 
    Jassby AD, Platt T. Mathematical formulation of the relationship between photosynthesis and light for phytoplankton. Limnol Oceanogr. 1976;21:540–7. https://doi.org/10.4319/lo.1976.21.4.0540CAS 
    Article 

    Google Scholar  More

  • in

    The early arrival of spring doesn’t boost annual tree growth

    Dow, C. et al. Nature 608, 552–557 (2022).Article 

    Google Scholar 
    Friedlingstein, P. et al. Earth Syst. Sci. Data 12, 3269–3340 (2020).Article 

    Google Scholar 
    Menzel, A. & Fabian, P. Nature 397, 659 (1999).Article 

    Google Scholar 
    Piao, S. et al. Nature Rev. Earth Environ. 1, 14–27 (2020).Article 

    Google Scholar 
    Cuny, H. E. et al. Nature Plants 1, 15160 (2015).PubMed 
    Article 

    Google Scholar 
    Körner, C. Curr. Opin. Plant Biol. 25, 107–114 (2015).PubMed 
    Article 

    Google Scholar 
    Gessler, A. & Treydte, K. New Phytol. 209, 1338–1340 (2016).PubMed 
    Article 

    Google Scholar 
    Hilty, J., Muller, B., Pantin, F. & Leuzinger, S. New Phytol. 232, 25–41 (2021).PubMed 
    Article 

    Google Scholar 
    Jiang, M. et al. Nature 580, 227–231 (2020).PubMed 
    Article 

    Google Scholar 
    Guillemot, J. et al. New Phytol. 214, 180–193 (2017).PubMed 
    Article 

    Google Scholar 
    Fatichi, S., Pappas, C., Zscheischler, J. & Leuzinger, S. New Phytol. 221, 652–668 (2019).PubMed 
    Article 

    Google Scholar 
    Friend, A. D. et al. Annu. For. Sci. 76, 49 (2019).Article 

    Google Scholar 
    Zuidema, P. A., Poulter, B. & Frank, D. C. Trends Plant Sci. 23, 1006–1015 (2018).PubMed 
    Article 

    Google Scholar 
    Martínez-Sancho, E., Treydte, K., Lehmann, M. M., Rigling, A. & Fonti, P. New Phytol. https://doi.org/10.1111/nph.18224 (2022).Article 

    Google Scholar  More

  • in

    Long-term study on survival and development of successive generations of Mytilus galloprovincialis cryopreserved larvae

    Short-term experimentsPotential toxic and cryoprotection effects of different CPA combinationsFocusing on toxicity bioassays (Figs. 1A, 2A), although there were certain CPA combinations that yielded significant abnormality percentages compared to controls, in general the CPA combinations did not yield any significant toxic effect. The use of Milli-Q Water instead of FSW did not enhance normal larval development after CPA exposure, neither did the addition of PVP at the concentrations tested, even in combination with trehalose (TRE) (p  > 0.05). In fact, the highest concentrations of PVP used in this experiment (9 and 12%) yielded significant abnormal development on exposed trochophores (Fig. 1A) (p  More

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    Potential of microbiome-based solutions for agrifood systems

    German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, GermanyStephanie D. Jurburg, Nico Eisenhauer, François Buscot, Antonis Chatzinotas, Narendrakumar M. Chaudhari, Anna Heintz-Buschart, Kirsten Küsel & Rine C. ReubenInstitute of Biology, Leipzig University, Leipzig, GermanyStephanie D. Jurburg, Nico Eisenhauer, Antonis Chatzinotas & Rine C. ReubenDepartment of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, GermanyStephanie D. Jurburg, Antonis Chatzinotas, Rene Kallies, Susann Müller & Ulisses Nunes da RochaDepartment of Soil Ecology, Helmholtz Centre for Environmental Research–UFZ, Halle, GermanyFrançois Buscot & Anna Heintz-BuschartAquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, GermanyNarendrakumar M. Chaudhari & Kirsten KüselSwammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the NetherlandsAnna Heintz-BuschartKellogg Biological Station, Michigan State University, Hickory Corners, MI, USAElena LitchmanEcology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USAElena LitchmanDepartment of Global Ecology, Carnegie Institution for Science, Stanford, CA, USAElena LitchmanHawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, AustraliaCatriona A. Macdonald & Brajesh K. SinghLeibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, GermanyGianni PanagiotouThe State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Kowloon, Hong Kong SAR, ChinaGianni PanagiotouDepartment of Medicine, The University of Hong Kong, Kowloon, Hong Kong SAR, ChinaGianni PanagiotouInstitut für Biologie, Freie Universität Berlin, Berlin, GermanyMatthias C. RilligBerlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, GermanyMatthias C. RilligGlobal Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, AustraliaBrajesh K. SinghB.K.S. conceived the idea in consultation with N.E. and S.J., and led the discussion which was attended by all authors. S.J. and B.K.S. wrote the manuscript and all contributed to refine it. More

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    Boreal forest on the move

    Settele, J. et al. in Climate Change 2014 Impacts, Adaptation and Vulnerability. Part A: Global and Sectoral Aspects (eds Field, C. et al.) 271–360 (IPCC, Cambridge Univ. Press, 2015).
    Google Scholar 
    Rees, W. G. et al. Glob. Change Biol. 26, 3965–3977 (2020).Article 

    Google Scholar 
    Anderson, L. L., Hu, F. S., Nelson, D. S., Petit, R. J. & Paige, K. N. Proc. Natl Acad. Sci. USA 103, 12447–12450 (2006).PubMed 
    Article 

    Google Scholar 
    Clark, J. S., Lewis, M. & Horvath, L. Am. Nat. 157, 537–554 (2001).PubMed 
    Article 

    Google Scholar 
    Edwards, M., Hamilton, T. D., Elias, S. A., Bigelow, N. H. & Krumhardt, A. P. Arct. Antarct. Alp. Res. 35, 460–468 (2003).Article 

    Google Scholar  More

  • in

    Unexpected high carbon losses in a continental glacier foreland on the Tibetan Plateau

    Arias PA, Bellouin N, Coppola E, Jones RG, Krinner G, Marotzke J, et al. Technical Summary. In Climate Change 2021: The Physical Science Basis, the Working Group I contribution to the Sixth Assessment Report. Cambridge University Press: Cambridge, UK; New York, NY, USA, 2021. 42–4.Donhauser J, Frey B. Alpine soil microbial ecology in a changing world. FEMS Microbiol Ecol. 2018;94:1–31.Article 
    CAS 

    Google Scholar 
    Bradley JA, Singarayer JS, Anesio AM. Microbial community dynamics in the forefield of glaciers. Proc R Soc B. 2014; 281.Hood E, Battin TJ, Fellman J, O’neel S, Spencer RGM. Storage and release of organic carbon from glaciers and ice sheets. Nat Geosci. 2015;8:91–96.CAS 
    Article 

    Google Scholar 
    Harden JW, Mark RK, Sundquist ET, Stallard RF. Dynamics of Soil Carbon During Deglaciation of the Laurentide Ice Sheet. Science. 1992;258:1921–4.CAS 
    PubMed 
    Article 

    Google Scholar 
    Egli M, Favilli F, Krebs R, Pichler B, Dahms D. Soil organic carbon and nitrogen accumulation rates in cold and alpine environments over 1 Ma. Geoderma. 2012;183-4:109–23.Article 
    CAS 

    Google Scholar 
    Khedim N, Cécillon L, Poulenard J, Barré P, Baudin F, Marta S, et al. Topsoil organic matter build-up in glacier forelands around the world. Glob Chang. Biol. 2021;27:1662–77.
    Google Scholar 
    Amico MED, Freppaz M, Filippa G, Zanini E. Vegetation in fluence on soil formation rate in a proglacial chronosequence (Lys Glacier, NW Italian Alps). Catena. 2014;113:122–37.Article 
    CAS 

    Google Scholar 
    Mateos-Rivera A, Yde JC, Wilson B, Finster KW, Reigstad LJ, Øvreås L The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway). FEMS Microbiol Ecol. 2016; 92. https://doi.org/10.1093/femsec/fiw038.Vilmundardóttir OK, Gísladóttir G, Lal R. Soil carbon accretion along an age chronosequence formed by the retreat of the Skaftafellsjökull glacier. SE-Iceland. Geomorphology. 2015;228:124–33.Article 

    Google Scholar 
    Strauss SL, Ruhland CT, Day TA. Trends in soil characteristics along a recently deglaciated foreland on Anvers Island, Antarctic Peninsula. Polar Biol. 2009;32:1779–88.Article 

    Google Scholar 
    Kabala C, Zapart J. Initial soil development and carbon accumulation on moraines of the rapidly retreating Werenskiold Glacier, SW Spitsbergen, Svalbard archipelago. Geoderma. 2012;175-6:9–20.Article 
    CAS 

    Google Scholar 
    Fernández-martínez MA, Pointing SB, Pérez-ortega S, Arróniz-crespo M, Green TGA, Rozzi R, et al. Functional ecology of soil microbial communities along a glacier forefield in Tierra del Fuego (Chile). Int Microbiol. 2016;19:161–73.PubMed 

    Google Scholar 
    Kazemi S, Hatam I, Lanoil B. Bacterial community succession in a high-altitude subarctic glacier foreland is a three-stage process. Mol Ecol. 2016;25:5557–67.CAS 
    PubMed 
    Article 

    Google Scholar 
    He L, Tang Y. Soil development along primary succession sequences on moraines of Hailuogou Glacier, Gongga Mountain, Sichuan, China. Catena. 2008;72:259–69.Article 

    Google Scholar 
    Zhou J, Bing HJ, Wu YH, Yang ZJ, Wang JP, Sun HY, et al. Rapid weathering processes of a 120-year-old chronosequence in the Hailuogou Glacier foreland, Mt. Gongga, SW China Jun. Geoderma. 2016;267:78–91.CAS 
    Article 

    Google Scholar 
    Zeng J, Lou K, Zhang CJ, Wang JT, Hu HW, Shen JP, et al. Primary succession of nitrogen cycling microbial communities along the deglaciated forelands of Tianshan Mountain, China. Front Microbiol. 2016; 7. https://doi.org/10.3389/fmicb.2016.01353.Wei TF, Shangguan DH, Yi SH, Ding YJ. Characteristics and controls of vegetation and diversity changes monitored with an unmanned aerial vehicle (UAV) in the foreland of the Urumqi Glacier No. 1, Tianshan, China. Sci Total Environ. 2021;771:145433.CAS 
    PubMed 
    Article 

    Google Scholar 
    Huang MH, Shi YF. Progress in the study on basic features of glaciers in China in the last thirty years. J Glaciol Geocryol. 1988;10:228–37.
    Google Scholar 
    Xu XK, Pan BL, Hu E, Li YJ, Liang YH. Responses of two branches of Glacier No. 1 to climate change from 1993 to 2005, Tianshan, China. Quat Int. 2011;236:143–50.Article 

    Google Scholar 
    Liu YS, Qin X, Chen JZ, Li ZL, Wang J, Du WT, et al. Variations of Laohugou Glacier No. 12 in the western Qilian Mountains, China, from 1957 to 2015. J Mt Sci. 2018;15:25–32.Article 

    Google Scholar 
    Schulz S, Brankatschk R, Dümig A, Kögel-Knabner I, Schloter M, Zeyer J. The role of microorganisms at different stages of ecosystem development for soil formation. Biogeosciences. 2013;10:3983–96.Article 

    Google Scholar 
    Odum EP. The strategy of ecosystem development. Science. 1969;164:262–70.CAS 
    PubMed 
    Article 

    Google Scholar 
    Schmidt SK, Reed SC, Nemergut DR, Grandy AS, Cleveland CC, Weintraub MN, et al. The earliest stages of ecosystem succession in high-elevation (5000 metres above sea level), recently deglaciated soils. Proc R Soc B. 2008;275:2793–802.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Knelman JE, Legg TM, O’Neill SP, Washenberger CL, González A, Cleveland CC, et al. Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield. Soil Biol Biochem. 2012;46:172–80.CAS 
    Article 

    Google Scholar 
    Rime T, Hartmann M, Frey B. Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier. ISME J. 2016;10:1625–41.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, et al. Genome-centric view of carbon processing in thawing permafrost. Nature. 2018;560:49–54.CAS 
    PubMed 
    Article 

    Google Scholar 
    Chen H, Wang F, Kong WD, Jia HZ, Zhou TQ, Xu R, et al. Soil microbial CO2 fixation plays a significant role in terrestrial carbon sink in a dryland ecosystem: A four-year small-scale field-plot observation on the Tibetan Plateau. Sci Total Environ. 2021; 761. https://doi.org/10.1016/j.scitotenv.2020.143282.Bond-lamberty B, Wang CK, Gower ST. A global relationship between the heterotrophic and autotrophic components of soil respiration? Gloal Chang. Biol. 2004;10:1756–66.
    Google Scholar 
    Barnett SE, Youngblut ND, Koechli CN, Buckley DH. Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling. Proc Natl Acad Sci USA. 2021; 118. https://doi.org/10.1073/pnas.2115292118/-/DCSupplemental.Published.Margesin R, Jud M, Tscherko D, Schinner F. Microbial communities and activities in alpine and subalpine soils. FEMS Microbiol Ecol. 2009;67:208–18.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhou ZH, Wang CK, Luo YQ. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat Commun. 2020;11:3072.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Guelland K, Hagedorn F, Smittenberg RH, Göransson H, Bernasconi SM, Hajdas I, et al. Evolution of carbon fluxes during initial soil formation along the forefield of Damma glacier, Switzerland. Biogeochemistry. 2013;113:545–61.CAS 
    Article 

    Google Scholar 
    Chen QL, Ding J, Li CY, Yan ZZ, He JZ, Hu HW. Microbial functional attributes, rather than taxonomic attributes, drive top soil respiration, nitrification and denitrification processes. Sci Total Environ. 2020;734:139479.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zheng BX, Zhu YG, Sardans J, Peñuelas J, Su JQ. QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling. Sci China (Life Sciences). 2018;61:1451–62.CAS 
    Article 

    Google Scholar 
    Fan KK, Delgado-Baquerizo M, Guo XS, Wang DZ, Zhu YG, Chu HY. Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment. ISME J. 2021;15:550–61.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhou JZ, Xue K, Xie JP, Deng Y, Wu LY, Cheng XH, et al. Microbial mediation of carbon-cycle feedbacks to climate warming. Nat Clim Chang. 2012;2:106–10.CAS 
    Article 

    Google Scholar 
    Chen JZ, Qin X, Kang SC, Du WT, Sun WJ, Liu YS. Potential effect of black carbon on glacier mass balance during the past 55 years of Laohugou Glacier No. 12, western Qilian Mountains. J Earth Sci. 2020;31:410–8.CAS 
    Article 

    Google Scholar 
    Zhang LN, Jiang Y, Zhao SD, Jiao L, Wen Y. Relationships between tree age and climate sensitivity of radial growth in different drought conditions of Qilian Mountains, northwestern China. Forests. 2018; 9. https://doi.org/10.3390/f9030135.Sun WJ, Qin X, Ren JW, Yang XG, Zhang T, Liu YS, et al. The surface energy budget in the accumulation zone of the laohugou glacier No. 12 in the western Qilian mountains, China, in summer 2009. Arctic, Antarct Alp Res. 2012;44:296–305.Article 

    Google Scholar 
    Wang YW, Ma AZ, Liu GH, Ma JP, Wei J, Zhou HC, et al. Potential feedback mediated by soil microbiome response to warming in a glacier forefield. Glob Chang Biol. 2020;26:697–708.PubMed 
    Article 

    Google Scholar 
    Harris D, Horwa WR, Van Kessel C. Acid fumigation of soils to remove carbonates prior to total organic carbon or carbon-13 isotopic analysis. Soil Sci Soc Am J.2001;65:1853–6.CAS 
    Article 

    Google Scholar 
    Zhou HC, Ma AZ, Liu GH, Zhou XR, Yin J, Liang Y, et al. Reduced interactivity during microbial community degradation leads to the extinction of Tricholomas matsutake. L Degrad Dev. 2021;32:5118–28.Article 

    Google Scholar 
    Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F, et al. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol Ecol. 2016;92:fiw018.PubMed 
    Article 
    CAS 

    Google Scholar 
    Feng K, Zhang ZJ, Cai WW, Liu WZ, Xu MY, Yin HQ, et al. Biodiversity and species competition regulate the resilience of microbial biofilm community. Mol Ecol. 2017;26:6170–82.PubMed 
    Article 

    Google Scholar 
    McDonald D, Price MN, Goodrich J, Nawrocki EP, Desantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.CAS 
    PubMed 
    Article 

    Google Scholar 
    Mackelprang R, Burkert A, Haw M, Mahendrarajah T, Conaway CH, Douglas TA, et al. Microbial survival strategies in ancient permafrost: insights from metagenomics. ISME J. 2017;11:2305–18.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang YW, Ma AZ, Zhong GS, Xie F, Zhou HC, Liu GH, et al. Effect of Simulated Warming on Microbial Community in Glacier Forefield. Environ Sci. 2020;41:2918–23.
    Google Scholar 
    Lei YB, Zhou J, Xiao HF, Duan BL, Wu YH, Korpelainen H, et al. Soil nematode assemblages as bioindicators of primary succession along a 120-year-old chronosequence on the Hailuogou Glacier forefield, SW China. Soil Biol Biochem. 2015;88:362–71.CAS 
    Article 

    Google Scholar 
    Sigler WV, Crivii S, Zeyer J. Bacterial succession in glacial forefield soils characterized by community structure, activity and opportunistic growth dynamics. Microb Ecol. 2002;44:306–16.CAS 
    PubMed 
    Article 

    Google Scholar 
    Hu WM, Schmidt SK, Sommers P, Darcy JL, Porazinska DL. Multiple-trophic patterns of primary succession following retreat of a high-elevation glacier. Ecosphere. 2021; 12. https://doi.org/10.1002/ecs2.3400.Nemergut DR, Anderson SP, Cleveland CC, Martin AP, Miller AE, Seimon A, et al. Microbial community succession in an unvegetated, recently deglaciated soil. Microb Ecol. 2007;53:110–22.PubMed 
    Article 

    Google Scholar 
    Whelan P, Bach AJ. Retreating glaciers, incipient soils, emerging forests: 100 years of landscape change on Mount Baker, Washington, USA. Ann Am Assoc Geogr. 2017;107:336–49.
    Google Scholar 
    Cleveland CC, Liptzin ÆD. C:N:P stoichiometry in soil: is there a ‘Redfield ratio’ for the microbial biomass? Biogeochemistry. 2007;85:235–52.Article 

    Google Scholar 
    Manzoni S, Taylor P, Richter A, Porporato A, Ågren GI. Environmental and stoichiometric controls on microbial carbon-use efficiency in soils. New Phytol. 2012;196:79–91.CAS 
    PubMed 
    Article 

    Google Scholar 
    Tian J, Zong N, Hartley IP, He NP, Zhang JJ, Powlson D, et al. Microbial metabolic response to winter warming stabilizes soil carbon. Gloal Chang Biol. 2021;27:2011–28.CAS 
    Article 

    Google Scholar 
    Zhu XF, Liang C, Masters MD, Kantola IB, DeLucia EH. The impacts of four potential bioenergy crops on soil carbon dynamics as shown by biomarker analyses and DRIFT spectroscopy. Glob Chang Biol Bioenergy. 2018;10:489–500.CAS 
    Article 

    Google Scholar 
    Evans MCW, Buchanan BB, Arnon DI. A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Biochemistry. 1966;55:928–34.CAS 

    Google Scholar 
    Menendez C, Bauer Z, Huber H, Gad’on N, Stetter K, Fuchs G. Presence of acetyl coenzyme A (CoA) carboxylase and propionyl-CoA carboxylase in autotrophic crenarchaeota and indication for operation of a 3-hydroxypropionate cycle in autotrophic carbon fixation. J Bacteriol. 1999;181:1088–98.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Li Y, Cha QQ, Dang YR, Chen XL, Wang M, Mcminn A, et al. Reconstruction of the functional ecosystem in the high light, low temperature union glacier region, Antarctica. Front Microbiol. 2019;10:1–14.Article 

    Google Scholar 
    Lazzaro A, Hilfiker D, Zeyer J. Structures of microbial communities in alpine soils: Seasonal and elevational effects. Front Microbiol. 2015; 6. https://doi.org/10.3389/fmicb.2015.01330.Aylward FO, McDonald BR, Adams SM, Valenzuela A, Schmidt RA, Goodwin LA, et al. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Appl Environ Microbiol. 2013;79:3724–33.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bardgett RD, Freeman C, Ostle NJ. Microbial contributions to climate change through carbon cycle feedbacks. ISME J. 2008;2:805–14.CAS 
    PubMed 
    Article 

    Google Scholar 
    Liang C, Schimel JP, Jastrow JD. The importance of anabolism in microbial control over soil carbon storage. Nat Microbiol. 2017;2:17105.CAS 
    PubMed 
    Article 

    Google Scholar 
    Schäfer A, Konrad R, Kuhnigk T, Kämpfer P, Hertel H, König H. Hemicellulose-degrading bacteria and yeasts from the termite gut. J Appl Bacteriol. 1996;80:471–8.PubMed 
    Article 

    Google Scholar 
    Lange M, Roth V-N, Nico E, Roscher C, Thorsten D, Fischer-bedtke C, et al. Plant diversity enhances production and downward transport of biodegradable dissolved organic matter. J Ecol. 2021;109:1284–97.CAS 
    Article 

    Google Scholar 
    Ho A, Di Lonardo DP, Bodelier PLE. Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiol Ecol. 2017;93:1–14.CAS 

    Google Scholar 
    Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology. 2007;88:1354–64.PubMed 
    Article 

    Google Scholar 
    Jansson JK, Hofmockel KS. Soil microbiomes and climate change. Nat Rev Microbiol. 2020;18:35–46.CAS 
    PubMed 
    Article 

    Google Scholar 
    Yan BS, Sun LP, Li JJ, Liang CQ, Wei FR, Xue S, et al. Change in composition and potential functional genes of soil bacterial and fungal communities with secondary succession in Quercus liaotungensis forests of the Loess Plateau, western China. Geoderma. 2020;364:114199.CAS 
    Article 

    Google Scholar 
    Wu MH, Chen SY, Chen JW, Xue K, Chen SL, Wang XM, et al. Reduced microbial stability in the active layer is associated with carbon loss under alpine permafrost degradation. Proc Natl Acad Sci USA. 2021;118:1–9.
    Google Scholar  More

  • in

    Effects of oceanographic environment on the distribution and migration of Pacific saury (Cololabis saira) during main fishing season

    NPFC. 8th Meeting of the Small Scientific Committee on Pacific Saury Report. NPFC-2021-SSC PS08-Final Report. Preprint at https://www.npfc.int/meetings/8th-ssc-ps-meeting (2021).Hubbs, C. L. & Wisner, R. L. Revision of the sauries (Pisces, Scomberesocidae) with descriptions of two new genera and one new species. Fish. Bull. 77, 521–566 (1980).
    Google Scholar 
    Tian, Y., Akamine, T. & Suda, M. Variations in the abundance of Pacific saury (Cololabis saira) from the northwestern Pacific in relation to oceanic-climate changes. Fish. Res. 60, 439–454 (2003).Article 

    Google Scholar 
    Huang, W. B. Comparisons of monthly and geographical variations in abundance and size composition of Pacific saury between the high-seas and coastal fishing grounds in the northwestern Pacific. Fish. Sci. 76, 21–31 (2010).CAS 
    Article 

    Google Scholar 
    Watanabe, Y., Builer, J. L. & Mori, T. Growth of Pacific saury, Cololabis saira, in the northeastern and northwestern Pacific Ocean. Fish. Bull. 86, 489–498 (1988).
    Google Scholar 
    Nakaya, M. et al. Growth and maturation of Pacific saury Cololabis saira under laboratory conditions. Fish. Sci. 76, 45–53 (2010).CAS 
    Article 

    Google Scholar 
    Kosaka, S. Life history of Pacific saury Cololabis saira in the Northwest Pacific and consideration of resource fluctuation based on it. Bull. Tohoku Natl. Fish. Res. Inst. 63, 1–96 (2000).
    Google Scholar 
    Suyama, S. Study on the age, growth, and maturation process of Pacific saury Cololabis saira (Brevoort) in the north Pacific. Bull. Fish. Res. Agen. 5, 68–113 (2002).
    Google Scholar 
    Huang, W. B., Lo, N. C. H., Chiu, T. S. & Chen, C. S. Geographical distribution and abundance of Pacific saury fishing stock in the Northwestern Pacific in relation to sea temperature. Zool. Stud. 46, 705–716 (2007).
    Google Scholar 
    Liu, S. et al. Using novel spawning ground indices to analyze the effects of climate change on Pacifc saury abundance. J. Mar. Syst. 191, 13–23 (2019).Article 

    Google Scholar 
    Tian, Y., Akamine, T. & Suda, M. Long-term variability in the abundance of Pacific Saury in the Northwestern Pacific Ocean and climate changes during the last century. Bull. Jpn. Soc. Fish. Oceanogr. 66, 16–25 (2002).
    Google Scholar 
    Tian, Y., Ueno, Y., Suda, M. & Akamine, T. Decadal variability in the abundance of Pacific saury and its response to climatic/oceanic regime shifts in the northwestern subtropical Pacific during the last half century. J. Mar. Syst. 52, 235–257 (2004).Article 

    Google Scholar 
    Yasuda, I. & Watanabe, T. Chlorophyll a variation in the Kuroshio Extension revealed with a mixed-layer tracking float: Implication on the long-term change of Pacific saury (Cololabis saira). Fish. Oceanogr. 16, 482–488 (2007).Article 

    Google Scholar 
    Fuji, T., Kurita, Y., Suyama, S. & Ambe, D. Estimating the spawning ground of Pacific saury Cololabis saira by using the distribution and geographical variation in maturation status of adult fish during the main spawning season. Fish. Oceanogr. 30, 382–396 (2020).Article 

    Google Scholar 
    Yasuda, I. & Watanabe, Y. On the relationship between the Oyashio front and saury fishing grounds in the northewestern Pacific: A forecasting method for fishing ground locations. Fish. Oceanogr. 3, 172–181 (1994).Article 

    Google Scholar 
    Kuroda, H. & Yokouchi, K. Interdecadal decrease in potential fishing areas for Pacific saury off the southeastern coast of Hokkaido, Japan. Fish. Oceanogr. 26, 439–454 (2017).Article 

    Google Scholar 
    Fukushima, S. Synoptic analysis of migration and fishing conditions of saury in the northwestern Pacific Ocean. Bull. Tohoku. Reg. Fish. Res. Lab 41, 1–70 (1979).
    Google Scholar 
    Sugisaki, H. & Kurita, Y. Daily rhythm and seasonal variation of feeding habit of Pacific saury (Cololabis saira) in relation to their migration and oceanographic conditions off Japan. Fish. Oceanogr. 13, 63–73 (2004).Article 

    Google Scholar 
    Huang, W. B. & Huang, Y. C. Maturity characteristics of Pacific saury during fishing season in the Northwest pacific. J. Mar. Sci. Tech. 23, 819–826 (2015).
    Google Scholar 
    Tseng, C. T. et al. Influence of climate-driven sea surface temperature increase on potential habitats of the Pacific saury (Cololabis saira). ICES J. Mar. Sci. 68, 1105–1113 (2011).Article 

    Google Scholar 
    Tseng, C. T. et al. Sea surface temperature fronts affect distribution of Pacific saury (Cololabis saira) in the Northwestern Pacific Ocean. Deep Sea Res II Top. Stud. Oceanogr. 107, 15–21 (2014).ADS 
    Article 

    Google Scholar 
    Hua, C., Li, F., Zhu, Q., Zhu, G. & Meng, L. Habitat suitability of Pacific saury (Cololabis saira) based on a yield-density model and weighted analysis. Fish. Res. 221, 105408. https://doi.org/10.1016/j.fishres.2019.105408 (2020).Article 

    Google Scholar 
    Mugo, R., Saitoh, S. I., Nihira, A. & Kuroyama, T. Habitat characteristics of skipjack tuna (Katsuwonus pelamis) in the western North Pacific: A remote sensing perspective. Fish. Oceanogr. 19, 382–396 (2010).Article 

    Google Scholar 
    Yu, W., Chen, X., Chen, Y., Yi, Q. & Zhang, Y. Effects of environmental variations on the abundance of western winter-spring cohort of neon flying squid (Ommastrephes bartramii) in the Northwest Pacific Ocean. Acta Oceanol. Sin. 34, 43–51 (2015).CAS 
    Article 

    Google Scholar 
    Kakehi, S. et al. Forecasting Pacific saury (Cololabis saira) fishing grounds off Japan using a migration model driven by an ocean circulation model. Ecol. Model. 431, 109150. https://doi.org/10.1016/j.ecolmodel.2020.109150 (2020).Article 

    Google Scholar 
    Swain, D. P. & Wade, E. J. Spatial distribution of catch and effort in a fishery for snow crab (Chionoecetes opilio): Tests of predictions of the ideal free distribution. Can. J. Fish. Aquat. Sci. 60, 897–909 (2003).Article 

    Google Scholar 
    Chang, Y. J. et al. Modelling the impacts of environmental variation on habitat suitability for Pacific saury in the Northwestern Pacific Ocean. Fish. Oceanogr. 28, 291–304 (2018).Article 

    Google Scholar 
    Bakun, A. Fronts and eddies as key structures in the habitat of marine fish larvae: Opportunity, adaptive response and competitive advantage. Sci. Mar. 70, 105–122 (2006).Article 

    Google Scholar 
    Oozeki, Y., Watanabe, Y. & Kitagawa, D. Environmental factors affecting larval growth of Pacific saury, Cololabis saira, in the northwestern Pacific Ocean. Fish. Oceanogr. 13, 44–53 (2004).Article 

    Google Scholar 
    Ito, S. I. et al. Initial design for a fish bioenergetics model of Pacific saury coupled to a lower trophic ecosystem model. Fish. Oceanogr. 13, 111–124 (2004).Article 

    Google Scholar 
    Miyamoto, H. et al. Geographic variation in feeding of Pacific saury Cololabis saira in June and July in the North Pacific Ocean. Fish. Oceanogr. 29, 558–571 (2020).CAS 
    Article 

    Google Scholar 
    Tseng, C. T. et al. Spatial and temporal variability of the Pacific saury (Cololabis saira) distribution in the northwestern Pacific Ocean. ICES J. Mar. Sci. 70, 991–999 (2013).Article 

    Google Scholar 
    Ichii, T. et al. Oceanographic factors affecting interannual recruitment variability of Pacific saury (Cololabis saira) in the central and western North Pacific. Fish. Oceanogr. 27, 445–457 (2018).Article 

    Google Scholar 
    Coletto, J. L., Pinho, M. P. & Madureira, L. S. P. Operational oceanography applied to skipjack tuna (Katsuwonus pelamis) habitat monitoring and fishing in south-western Atlantic. Fish. Oceanogr. 28, 82–93 (2018).Article 

    Google Scholar 
    Shi, Y., Zhu, Q., Hua, C. & Zhang, Y. Evaluation of saury stick-held net performance between model test and on-sea measurements. Haiyang Xuebao 41, 123–133 (2019).CAS 

    Google Scholar 
    Semedi, B., Saitoh, S., Saitoh, K. & Yoneta, K. Application of multi-sensor satellite remote sensing for determining distribution and movement of Pacific saury, Cololabis saira. Fish. Sci. 68, 1781–1784 (2002).Article 

    Google Scholar 
    Syah, A. F., Saitoh, S. I., Alabia, I. D. & Hirawake, T. Detection of potential fishing zone for Pacific saury (Cololabis saira) using generalized additive model and remotely sensed data. IOP Conf. Ser. Earth Env. Sci. 54, 012074. https://doi.org/10.1088/1755-1315/54/1/012074 (2017).Article 

    Google Scholar 
    Xing, Q. et al. Application of a fish habitat model considering mesoscale oceanographic features in evaluating climatic impact on distribution and abundance of Pacific saury (Cololabis saira). Prog. Oceanogr. 201, 102743. https://doi.org/10.1016/j.pocean.2022.102743 (2022).Article 

    Google Scholar 
    Tittensor, D. P. et al. Global patterns and predictors of marine biodiversity across taxa. Nature 466, 1098–1101 (2010).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Prants, S. V., Budyansky, M. V. & Uleysky, M. Y. Identifying Lagrangian fronts with favourable fishery conditions. Deep Sea Res. Part I Oceanogr. Res. Pap. 90, 27–35 (2014).ADS 
    Article 

    Google Scholar 
    Saito, H., Tsuda, A. & Kasai, H. Nutrient and plankton dynamics in the Oyashio region of the western subarctic Pacific Ocean. Deep Sea Res. II Top. Stud. Oceanogr. 49, 5463–5486 (2002).ADS 
    CAS 
    Article 

    Google Scholar 
    Watanabe, Y., Kurita, Y., Noto, M., Oozeki, Y. & Kitagawa, D. Growth and survival of Pacific Saury Cololabis saira in the Kuroshio-Oyashio transitional waters. J. Oceanogr. 59, 403–414 (2003).Article 

    Google Scholar 
    Bakun, A. Ocean eddies, predator pits and bluefin tuna: Implications of an inferred ‘low risk-limited payoff’ reproductive scheme of a (former) archetypical top predator. Fish Fish. 14, 424–438 (2013).Article 

    Google Scholar 
    Iwahashi, M., Isoda, Y., Ito, S. I., Oozeki, Y. & Suyama, S. Estimation of seasonal spawning ground locations and ambient sea surface temperatures for eggs and larvae of Pacific saury (Cololabis saira) in the western North Pacific. Fish. Oceanogr. 15, 128–138 (2006).Article 

    Google Scholar 
    Oozeki, Y., Okunishi, T., Takasuka, A. & Ambe, D. Variability in transport processes of Pacific saury Cololabis saira larvae leading to their broad dispersal: Implications for their ecological role in the western North Pacific. Prog. Oceanogr. 138, 448–458 (2015).ADS 
    Article 

    Google Scholar 
    Polovina, J. J., Kleiber, P. & Kobayashi, D. R. Application of TOPEX-Poseidon satellite altimetry to simulate transport dynamics of larvae of spiny lobster, Panulirus marginatus, in the Northwestern Hawaiian Islands, 1993–1996. Fish. Bull. 97, 132–143 (1999).
    Google Scholar 
    Kawai, H. Hydrography of the Kuroshio extension. In Kuroshio—Its Physical Aspects (eds Stommel, H. & Yoshida, K.) 235–352 (University of Tokyo, 1972).
    Google Scholar 
    Yamada, F. & Sekine, Y. Variations in sea surface temperature and 500 hPa height over the north Pacific with reference to the occurrence of anomalous southward Oyashio intrusion east of Japan. J. Meteorol. Soc Jpn. Ser. II 75, 995–1000 (1997).Article 

    Google Scholar 
    Ellis, N., Smith, S. J. & Pitcher, C. R. Gradient forests: Calculating importance gradients on physical predictors. Ecology 93, 156–168 (2012).PubMed 
    Article 

    Google Scholar 
    Hastie, T. J. & Tibshirani, R. J. Generalized additive models. Stat. Sci. 1, 297–310 (1986).MathSciNet 
    MATH 

    Google Scholar 
    Litzow, M. A., Hobday, A. J., Frusher, S. D., Dann, P. & Tuck, G. N. Detecting regime shifts in marine systems with limited biological data: An example from southeast Australia. Prog. Oceanogr. 141, 96–108 (2016).ADS 
    Article 

    Google Scholar 
    Pang, Y. et al. Variability of coastal cephalopods in overexploited China Seas under climate change with implications on fisheries management. Fish. Res. 208, 22–33 (2018).Article 

    Google Scholar  More

  • in

    Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas

    Roberson, L. A., Watson, R. A. & Klein, C. J. Over 90 endangered fish and invertebrates are caught in industrial fisheries. Nat. Commun. 11, 1–8 (2020).Article 
    CAS 

    Google Scholar 
    Pacoureau, N. et al. Half a century of global decline in oceanic sharks and rays. Nature 589, 567–571 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Dulvy, N. K. et al. Overfishing drives over one-third of all sharks and rays toward a global extinction crisis. Curr. Biol. 31, 1–15 (2021).Article 
    CAS 

    Google Scholar 
    MacNeil, M. A. et al. Global status and conservation potential of reef sharks. Nature 583, 801–806 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Dent, F. & Clarke, S. State of the global market for shark products. FAO Fish. Aquac. Tech. Pap. No. 590. 187 (2015).FAO. 2008. The State of World Fisheries and Aquaculture. Food and Agriculture Organization of the United Nations, Rome (2008).Davidson, L. N. K., Krawchuk, M. A. & Dulvy, N. K. Why have global shark and ray landings declined: improved management or over fishing? Fish Fish 17, 438–458 (2016).Article 

    Google Scholar 
    Clarke, S. C. et al. Global estimates of shark catches using trade records from commercial markets. Ecol. Lett. 9, 1115–1126 (2006).PubMed 
    Article 

    Google Scholar 
    Dulvy, N. K. et al. Extinction risk and conservation of the world’ s sharks and rays. Elife 3, 1–35 (2014).Article 

    Google Scholar 
    FAO. The State of World Fisheries and Aquaculture. Sustainability in action. Rome https://doi.org/10.4060/ca9229en (2020).Smith, H. et al. Ecology and the science of small-scale fisheries: A synthetic review of research effort for the Anthropocene. Biol. Conserv. 254, 108895 (2021).Article 

    Google Scholar 
    Worm, B. et al. Global catches, exploitation rates, and rebuilding options for sharks. Mar. Policy 40, 194–204 (2013).Article 

    Google Scholar 
    Queiroz, N. et al. Global spatial risk assessment of sharks under the footprint of fisheries. Nature 572, 461–466 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Leurs, G. et al. Industrial fishing near West African marine protected areas and its potential effects on mobile marine predators. Fron. Mar. Sci. 8, 1–13 (2021).ADS 

    Google Scholar 
    White, W. T. et al. Shark longline fishery of Papua New Guinea: Size and species composition and spatial variation of the catches. Mar. Freshw. Res. 71, 662–669 (2020).Article 

    Google Scholar 
    Jacquet, J. & Pauly, D. Funding priorities: Big barriers to small-scale fisheries. Conserv. Biol. 22, 832–835 (2008).PubMed 
    Article 

    Google Scholar 
    Moore, J. E. et al. An interview-based approach to assess marine mammal and sea turtle captures in artisanal fisheries. Biol. Conserv. 143, 795–805 (2010).Article 

    Google Scholar 
    Soykan, C. U. et al. Why study bycatch? An introduction to the Theme Section on fisheries bycatch. Endanger. Species Res. 5, 91–102 (2008).Article 

    Google Scholar 
    Haque, A. B. et al. Socio-ecological approach on the fishing and trade of rhino rays (Elasmobranchii: Rhinopristiformes) for their biological conservation in the Bay of Bengal, Bangladesh. Ocean Coast. Manag. 210, 105690 (2021).Article 

    Google Scholar 
    Barausse, A. et al. The role of fisheries and the environment in driving the decline of elasmobranchs in the nor-thern Adriatic Sea. ICES J. Mar. Sci. 71, 1593–1603 (2014).Article 

    Google Scholar 
    Pérez-Jiménez, J. C. & Mendez-Loeza, I. The small-scale shark fisheries in the southern Gulf of Mexico: Understanding their heterogeneity to improve their management. Fish. Res. 172, 96–104 (2015).Article 

    Google Scholar 
    Saidi, B., Enajjar, S. & Bradai, M. N. Elasmobranch captures in shrimps trammel net fishery off the Gulf of Gabès (Southern Tunisia, Mediterranean Sea). J. Appl. Ichthyol. 32, 421–426 (2016).Article 

    Google Scholar 
    Vögler, R., González, C. & Segura, A. M. Spatio-temporal dynamics of the fish community associated with artisanal fisheries activities within a key marine protected area of the Southwest Atlantic (Uruguay). Ocean Coast. Manag. 190, 105175 (2020).Dulvy, N. K. et al. Challenges and priorities in Shark and Ray conservation. Curr. Biol. 27, R565–R572 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Davidson, L. N. K. & Dulvy, N. K. Global marine protected areas to prevent extinctions. Nat. Ecol. Evol. 1, 1–6 (2017).Article 

    Google Scholar 
    Edgar, G. J. et al. Global conservation outcomes depend on marine protected areas with five key features. Nature 506, 216–220 (2014).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Giakoumi, S. et al. Ecological effects of full and partial protection in the crowded Mediterranean Sea: A regional meta-analysis. Sci. Rep. 7, 1–12 (2017).ADS 
    CAS 
    Article 

    Google Scholar 
    Grorud-Colvert, K. et al. The MPA Guide: A framework to achieve global goals for the ocean. Science 373, 6560 (2021).Article 
    CAS 

    Google Scholar 
    Di Franco, A. et al. Five key attributes can increase marine protected areas performance for small-scale fisheries management. Sci. Rep. 6, 38135 (2016).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Ban, N. C., Kushneryk, K., Falk, J., Vachon, A. & Sleigh, L. Improving compliance of recreational fishers with Rockfish Conservation Areas: community–academic partnership to achieve and evaluate conservation. ICES J. Mar. Sci. 77, 2308–2318 (2019).Di Lorenzo, M., Guidetti, P., Di Franco, A., Calò, A. & Claudet, J. Assessing spillover from marine protected areas and its drivers: A meta-analytical approach. Fish Fish. 15, 1–10 (2020).Belharet, M. et al. Extending full protection inside existing marine protected areas, or reducing fishing effort outside, can reconcile conservation and fisheries goals. J. Appl. Ecol. 57, 1948–1957 (2020).Article 

    Google Scholar 
    McCauley, D. J. et al. Marine defaunation: Animal loss in the global ocean. Science 347, 247–254 (2015).CAS 
    Article 

    Google Scholar 
    Di Franco, A. et al. Linking home ranges to protected area size: The case study of the Mediterranean Sea. Biol. Conserv. 221, 175–181 (2018).MacKeracher, T., Diedrich, A. & Simpfendorfer, C. A. Sharks, rays and marine protected areas: A critical evaluation of current perspectives. Fish Fish 20, 255–267 (2019).Article 

    Google Scholar 
    Ward-Paige, C. A., Keith, D. M., Worm, B. & Lotze, H. K. Recovery potential and conservation options for elasmobranchs. J. Fish. Biol. 80, 1844–1869 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Lester, S. E. et al. Biological effects within no-take marine reserves: a global synthesis. MEPS 384, 33–46 (2009).ADS 
    Article 

    Google Scholar 
    O’Leary, B. C. et al. Addressing criticisms of large-scale marine protected areas. Bioscience 68, 359–370 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Collins, C. et al. Understanding persistent non-compliance in a remote, large-scale marine protected area. Front. Mar. Sci. 8, 1–13 (2021).ADS 
    Article 

    Google Scholar 
    White, T. D. et al. Assessing the effectiveness of a large marine protected area for reef shark conservation. Biol. Conserv. 207, 64–71 (2017).Article 

    Google Scholar 
    Speed, C. W., Cappo, M. & Meekan, M. G. Evidence for rapid recovery of shark populations within a coral reef marine protected area. Biol. Conserv. 220, 308–319 (2018).Article 

    Google Scholar 
    Escalle, L. et al. Restricted movements and mangrove dependency of the nervous shark Carcharhinus cautus in nearshore coastal waters. J. Fish. Biol. 87, 323–341 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    O’Leary, B. C. et al. Effective coverage targets for ocean protection. Conserv. Lett. 9, 398–404 (2016).Article 

    Google Scholar 
    Guidetti, P., Danovaro, R., Bottaro, M. & Ciccolella, A. Marine protected areas and endangered shark conservation. Aquat. Conserv. Mar. Freshw. Ecosyst. 31, 2671–2672 (2021).Article 

    Google Scholar 
    Lubchenco, J. & Grorud-Colvert, K. Making waves: The science and politics of ocean protection. Science 350, 382–383 (2015).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Zupan, M. et al. Marine partially protected areas: drivers of ecological effectiveness. Front. Ecol. Environ. 16, 381–387 (2018).Article 

    Google Scholar 
    Dulvy, N. K., Allen, D. J., Ralph, G. M. & Walls, R. H. L. The Conservation Status of Sharks, Rays, and Chimaeras in the Mediterranean Sea. IUCN, Malaga, Spain. pp. 236 (2016).Morales-Muñiz, A. & Roselló, E. 20,000 years of fishing in the Strait: archaeological fish and shellfish assemblages from southern Iberia. In Human Impacts on Ancient Marine Ecysosytems: a Global Perspective (eds Torben, R. C. & Erlandson, J. M.), pp. 243–278 (University of California Press, Berkeley, 2008).Coll, M. et al. The biodiversity of the Mediterranean Sea: estimates, patterns, and threats. PLoS One 5, e11842 (2010).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Cashion, M. S., Bailly, N. & Pauly, D. Official catch data underrepresent shark and ray taxa caught in Mediterranean and Black Sea fisheries. Mar. Pol. 105, 1–9 (2019).Article 

    Google Scholar 
    Ferretti, F., Myers, R. A., Serena, F. & Lotze, H. K. Loss of large predatory sharks from the Mediterranean Sea. Conserv. Biol. 22, 952–964 (2008).PubMed 
    Article 

    Google Scholar 
    Colloca, F., Enea, M., Ragonese, S. & Di Lorenzo, M. A century of fishery data documenting the collapse of smooth-hounds (Mustelus spp.) in the Mediterranean Sea. Aquat. Conserv. Mar. Freshw. Ecosyst. 27, 1145–1155 (2017).Article 

    Google Scholar 
    Colloca, F., Carrozzi, V., Simonetti, A. & Lorenzo, M. D. Using local ecological knowledge of fishers to reconstruct abundance trends of Elasmobranch populations in the Strait of Sicily. Front. Mar. Sci. 7, 1–8 (2020).Article 

    Google Scholar 
    FAO. The State of World Fisheries and Aquaculture.Contributing to food security and nutrition for all. Rome. pp 200 (2016).Milazzo, M., Cattano, C., Al Mabruk, S. A. A. & Giovos, I. Mediterranean sharks and rays need action. Science 371, 355–356 (2021).ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar 
    Claudet, J., Loiseau, C., Sostres, M. & Zupan, M. Underprotected marine protected areas in a global biodiversity hotspot. One Earth 2, 380–384 (2020).ADS 
    Article 

    Google Scholar 
    Maynou, F. et al. Estimating trends of population decline in long-lived marine species in the Mediterranean Sea based on fishers’ perceptions. PLoS One 6, e21818 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Serena, F. et al. Species diversity, taxonomy and distribution of Chondrichthyes in the Mediterranean and Black Sea. Eur. Zool. J. 87, 497–536 (2020).Article 

    Google Scholar 
    Morey, G., Moranta, J., Riera, F., Grau, A. M. & Morales-NIN, B. Elasmobranchs in trammel net fishery associated to marine reserves in the Balearic Islands (NW Mediterranean). Cybium 30, 125–132 (2006).
    Google Scholar 
    Temple, A. J. et al. Marine megafauna interactions with small-scale fisheries in the southwestern Indian Ocean: a review of status and challenges for research and management. Rev. Fish. Biol. Fish. 28, 89–115 (2018).Article 

    Google Scholar 
    Siskey, M. R., Shipley, O. N. & Frisk, M. G. Skating on thin ice: Identifying the need for species- ­ specific data and defined migration ecology of Rajidae spp. Fish Fish 20, 286–302 (2019).Article 

    Google Scholar 
    Chapman, D. D., Feldheim, K. A., Papastamatiou, Y. P. & Hueter, R. E. There and back again: a review of residency and return migrations in Sharks, with implications for population structure and management. Ann. Rev. Mar. Sci. 7, 547–570 (2015).PubMed 
    Article 

    Google Scholar 
    Heupel, M. R., Carlson, J. K. & Simpfendorfer, C. A. Shark nursery areas: Concepts, definition, characterization and assumptions. Mar. Ecol. Prog. Ser. 337, 287–297 (2007).ADS 
    Article 

    Google Scholar 
    Speed, C., Field, I., Meekan, M. & Bradshaw, C. Complexities of coastal shark movements and their implications for management. Mar. Ecol. Prog. Ser. 408, 275–293 (2010).ADS 
    Article 

    Google Scholar 
    Knip, D. M., Heupel, M. R. & Simpfendorfer, C. A. Mortality rates for two shark species occupying a shared coastal environment. Fish. Res. 125–126, 184–189 (2012).Article 

    Google Scholar 
    Espinoza, M., Farrugia, T. J. & Lowe, C. G. Habitat use, movements and site fidelity of the gray smooth-hound shark (Mustelus californicus Gill 1863) in a newly restored southern California estuary. J. Exp. Mar. Bio. Ecol. 401, 63–74 (2011).Article 

    Google Scholar 
    Myers, R. A. & Mertz, G. The limits of exploitation: A precautionary approach. Ecol. Appl. 8, 165–169 (1998).Article 

    Google Scholar 
    Ferretti, F., Osio, G., Jenkins, C., Rosenberg, A. A. & Lotze, H. K. Long-term change in a meso-predator community in response to prolonged and heterogeneous human impact. Sci. Rep. 3, 1057 (2013).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Lotze, H. K. et al. Depletion, degradation, and recovery potential of estuaries and coastal seas. Science 312, 1806–1809 (2006).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Di Lorenzo, M. et al. Ontogenetic trophic segregation between two threatened smooth ‑ hound sharks in the Central Mediterranean Sea. Sci. Rep. 10, 1–15 (2020).Article 
    CAS 

    Google Scholar 
    Mulas, A. et al. Resource partitioning among sympatric elasmobranchs in the central-western Mediterranean continental shelf. Mar. Biol. 166, 1–16 (2019).Article 

    Google Scholar 
    Silva, P. M., Teixeira, C. M., Pita, C., Cabral, H. N. & França, S. Portuguese artisanal fishers’ knowledge about Elasmobranchs—A case study. Front. Mar. Sci. 8, 1–9 (2021).
    Google Scholar 
    Cortés, E. & Brooks, E. N. Stock status and reference points for sharks using data-limited methods and life history. Fish Fish 19, 1110–1129 (2018).Article 

    Google Scholar 
    Prince, J. D. Gauntlet fisheries for elasmobranchs – The secret of sustainable shark fisheries. J. Northwest Atl. Fish. 37, 407–416 (2005).Article 

    Google Scholar 
    Booth, H., Squires, D. & Milner-Gulland, E. J. The neglected complexities of shark fisheries, and priorities for holistic risk-based management. Ocean Coast. Manag. 182, 104994 (2019).Article 

    Google Scholar 
    Juhel, J. B. et al. Reef accessibility impairs the protection of sharks. J. Appl. Ecol. 55, 673–683 (2018).Article 

    Google Scholar 
    Espinoza, M., Cappo, M., Heupel, M. R., Tobin, A. J. & Simpfendorfer, C. A. Quantifying shark distribution patterns and species-habitat associations: Implications of Marine Park zoning. PLoS One 9, e106885 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Cattano, C., Turco, G., Di Lorenzo, M., Visconti, G. & Milazzo, M. Sandbar shark aggregation in the central Mediterranean Sea and potential effects of tourism. Aquat. Conserv. Mar. Freshw. Ecosyst. 31, 1420–1428 (2021).Article 

    Google Scholar 
    O’Connell, C. P., Stroud, E. M. & He, P. The emerging field of electrosensory and semiochemical shark repellents: Mechanisms of detection, overview of past studies, and future directions. Ocean Coast. Manag. 97, 2–11 (2014).Article 

    Google Scholar 
    Barbato, M. et al. The use of fishers’ Local Ecological Knowledge to reconstruct fish behavioural traits and fishers’ perception of conservation relevance of elasmobranchs in the Mediterranean Sea. Mediterr. Mar. Sci. 22, 603–622 (2021).Article 

    Google Scholar 
    Gill, D. A. et al. Capacity shortfalls hinder the performance of marine protected areas globally. Nature 543, 665–669 (2017).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Booth, H., Squires, D. & Milner-Gulland, E. J. The mitigation hierarchy for sharks: A risk-based framework for reconciling trade-offs between shark conservation and fisheries objectives. Fish Fish 21, 269–289 (2020).Article 

    Google Scholar 
    Sala, E. et al. Author correction: protecting the global ocean for biodiversity, food and climate. Nature 592, 397–402 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Di Franco, A. et al. Improving marine protected area governance through collaboration and co-production. J. Environ. Manag. 269, 110757 (2020).Article 

    Google Scholar 
    Abràmoff, M. D., Magalhães, P. J. & Ram, S. J. Image processing with imageJ. Biophotonics Int 11, 36–41 (2004).
    Google Scholar 
    Froese, R., & Pauly, D. FishBase. https://www.fishbase.org (2021).Micheli, F. et al. Cumulative human impacts on Mediterranean and Black Sea marine ecosystems: assessing current pressures and opportunities. PLoS ONE 8, e79889 (2013).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Atwood, T. B. et al. Herbivores at the highest risk of extinction among mammals, birds, and reptiles. Sci. Adv. 6, eabb8458 (2020).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Munstermann, M. J. et al. A global ecological signal of extinction risk in terrestrial vertebrates. Cons. Biol. 36, 1–13 (2021).
    Google Scholar 
    Martin, T. G., Wintle, A., Rhodes, J. R., Field, A. & Low-choy, S. J. REVIEWS AND Zero tolerance ecology: improving ecological inference by modelling the source of zero observations. Ecol. Lett. 8, 1235–1246 (2005).PubMed 
    Article 

    Google Scholar 
    Rigby, R. A., Stasinopoulos, D. M. & Lane, P. W. Generalized additive models for location, scale and shape. J. R. Stat. Soc. Ser. C. Appl. Stat. 54, 507–554 (2005).MathSciNet 
    MATH 
    Article 

    Google Scholar 
    Wickham, H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org (2016).Zuur, A. F., Ieno, E. N. & Elphick, C. S. A protocol for data exploration to avoid common statistical problems. Methods Ecol. Evol. 1, 3–14 (2010).Article 

    Google Scholar 
    Akaike, H. A new look at the Statistical Model Identification. IEEE Trans. Autom. Contr. 19, 716–723 (1974).ADS 
    MathSciNet 
    MATH 
    Article 

    Google Scholar 
    Kariya, T. Institute of Mathematical Statistics is collaborating with JSTOR to digitize, preserve, and extend access to The Annals of Statistics. Ann. Stat. 19, 1403–1433, www.jstor.org (1991). ®.
    Google Scholar 
    Stasinopoulos, D. M. & Rigby, R. A. Generalized additive models for location scale and shape (GAMLSS) in R. J. Stat. Softw. 23, 1–46 (2007).Article 

    Google Scholar 
    Van Buuren, S. & Fredriks, M. Worm plot: A simple diagnostic device for modelling growth reference curves. Stat. Med. 20, 1259–1277 (2001).PubMed 
    Article 

    Google Scholar 
    R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. (2020).Legendre, P. & Legendre, L. Numerical ecology, 2nd English edn. Elsevier, Amsterdam (1998).Peres-Neto, P. R., Legendre, P., Dray, S. & Borcard, D. Variation partitioning of species data matrices: Estimation and comparison of fractions. Ecology 87, 2614–2625 (2006).PubMed 
    Article 

    Google Scholar 
    Oksanen, A. J. et al. Vegan: Community Ecology Package. R package Version 2.0-2 (2011). Available at: http://cran.r-project.org/. (2012).Di Lorenzo et al. Dataset1: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318878.v1 (2022).Di Lorenzo et al. Dataset2: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318881.v3 (2022).Di Lorenzo et al. Dataset3: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare. https://doi.org/10.6084/m9.figshare.18318884.v1 (2022).Di Lorenzo et al. Dataset4: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare. https://doi.org/10.6084/m9.figshare.18318887.v1 (2022).Di Lorenzo et al. Code1: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318875.v2 (2022).Di Lorenzo et al. Code2: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318890.v1 (2022).Di Lorenzo et al. Code3: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318893.v1 (2022). More