{ "abstract": "Swordfish (Xiphias gladius) is managed in the Atlantic Ocean and Mediterranean Sea as three major stocks, although their correspondence with underlying genomic population structure remains uncertain. Here, we combined a newly assembled reference genome with ddRAD sequencing of 575 swordfish from 14 Atlantic and Mediterranean areas to characterize genomic population structure and genetic differentiation relative to the current ICCAT management framework, evaluate individual stock assignment and ancestry across management boundaries, and compare genetic-diversity patterns among stocks and sampling areas. After quality control, 504 individuals were retained, with 26,324 SNPs used for diversity analyses and 15,049 LD-pruned SNPs for population-structure and assignment analyses. Multivariate analyses, pairwise differentiation, AMOVA, and ADMIXTURE consistently identified strong Mediterranean-Atlantic differentiation, whereas North and South Atlantic swordfish showed much weaker and partly continuous genomic structure. Formal stock identification, DAPC, and ADMIXTURE consistently assigned 11 individuals from Portugal and the Canary Islands to the Mediterranean stock. Within the Atlantic, ancestry patterns were more diffuse and included individuals with assignments discordant with their a priori management stock. Heterozygosity was broadly similar among stocks, whereas rarefied allelic richness was lower in the Mediterranean than in either Atlantic stock. Overall, the current management framework captures the major Mediterranean-Atlantic differentiation but only partially reflects the weaker genomic structure within the Atlantic. These findings show that population-genomic analyses can refine stock-structure inference and individual assignment while providing complementary information for swordfish assessment and monitoring.", "abstract_shown": true, "affiliations": [ "Dipartimento di Scienze della Vita e dell'Ambiente, Universita' Politecnica delle Marche, 60131 Ancona, Italy.", "Fisheries and Oceans Canada, St. Andrews Biological Station, 125 Marine Science Drive, St. Andrews, NB E5B 0E4, Canada.", "Instituto Português do Mar e da Atmosfera (IPMA), Av. 5 de Outubro s/n, 8700-305 Olhão, Portugal.", "Centro de Ciências do Mar da Universidade do Algarve (CCMar), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.", "Instituto de Oceanografia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n Dois Irmãos, 52171-900 Recife, PE, Brazil.", "Centro Oceanográfico de Málaga, Instituto Español de Oceanografía (IEO-CSIC), Puerto Pesquero s/n, 29640 Fuengirola, Spain.", "AquaBioTech Group, Central Complex, Naggar Street, Targa Gap, MST 1761 Mosta, Malta.", "MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34203 Sète, France.", "Department of Earth, Environment and Life Sciences, University of Genoa, Corso Europa, 26, 16132 Genova, Italy.", "Laboratório de Recursos Pesqueiros Demersais e Cefalópodes, Instituto de Oceanografia, Universidade Federal do Rio Grande, Av. Itália, sn, Campus Carreiros, 96203-900 Rio Grande, RS, Brazil.", "OCEANIS SRL, 80056 Ercolano, Italy.", "Sequentia Biotech SL, 08005 Barcellona, Spain.", "Department of Environmental Biology and Fishery Science, National Taiwan Ocean University, Keelung 20224, Taiwan.", "Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa.", "Hellenic Centre for Marine Research, Athens Sounio Ave., P.O. Box 712, Anavyssos, 19013 Attiki, Greece.", "Instituto Oceanográfico de Venezuela, Universidad de Oriente, A.P. 204, 6101 Cumana, Venezuela.", "Ministry of Fisheries and Marine Resources, National Marine Information and Research Centre, Swakopmund P.O. Box 912, Namibia.", "Aquastudio Research Institute, Via Trapani, 6, 98121 Messina, Italy.", "Department of Life Science and Environment, University of Cagliari, Via Fiorelli 1, 09126 Cagliari, Italy.", "UNIMAR Società Cooperative, Via Nazionale, 243, 00184 Roma, Italy.", "ICCAT Secretariat, Calle Corazón de Maria 8, Planta 6, 28002 Madrid, Spain." ], "article_type": "research article", "arxiv": null, "author_total": 32, "authors": [ { "affs": [ 0 ], "name": "Giorgia Gioacchini", "orcid": "0000-0003-1187-7302" }, { "affs": [ 1 ], "name": "Kyle Gillespie", "orcid": "0000-0002-4221-3173" }, { "affs": [ 2, 3 ], "name": "Daniela Rosa" }, { "affs": [ 0 ], "name": "Sara Filippi" }, { "affs": [ 0 ], "name": "Luca Marisaldi" }, { "affs": [ 1 ], "name": "Dheeraj Busawon" }, { "affs": [ 4 ], "name": "Natalia Bezerra" }, { "affs": [ 4 ], "name": "Paulo Travassos", "orcid": "0000-0001-8667-5292" }, { "affs": [ 4 ], "name": "Hilário Tiago Campello" }, { "affs": [ 4 ], "name": "Fábio Hissa Vieira Hazin" }, { "affs": [ 5 ], "name": "David Macías" }, { "affs": [ 6 ], "name": "Alexia Gallucci" }, { "affs": [ 7 ], "name": "Francois Poisson", "orcid": "0000-0002-3618-7220" }, { "affs": [ 8 ], "name": "Fulvio Garibaldi" }, { "affs": [ 9 ], "name": "Luis Gustavo Cardoso", "orcid": "0000-0003-1026-0853" }, { "affs": [ 10 ], "name": "Luigi Pappalardo" }, { "affs": [ 10 ], "name": "Paolo Pignalosa" }, { "affs": [ 11 ], "name": "Riccardo Aiese Cigliano", "orcid": "0000-0002-9058-6994" }, { "affs": [ 12 ], "name": "Su Nan-Jay", "orcid": "0000-0003-1370-0842" }, { "affs": [ 13 ], "name": "Dan Parker" }, { "affs": [ 14 ], "name": "George Tserpes", "orcid": "0000-0001-9052-4091" }, { "affs": [ 15 ], "name": "Freddy Arocha", "orcid": "0000-0002-5814-0626" }, { "affs": [ 16 ], "name": "Taimi Shikongo" }, { "affs": [ 0 ], "name": "Tommaso Righi" }, { "affs": [ 0 ], "name": "Andrea Splendiani" }, { "affs": [ 17 ], "name": "Antonio Di Natale" }, { "affs": [ 18 ], "name": "Piero Addis", "orcid": "0000-0002-0464-0270" }, { "affs": [ 19 ], "name": "Adriano Mariani" }, { "affs": [ 20 ], "name": "Miguel Neves Dos Santos" }, { "affs": [ 2, 3 ], "name": "Rui Coelho" }, { "affs": [ 1 ], "name": "Alex Hanke" }, { "affs": [ 0 ], "name": "Oliana Carnevali", "orcid": "0000-0001-5994-0572" } ], "bibtex": "https://research.draconitic.com/paper/18xmt5xf8jrxb.bib", "cited_by": 0, "doi": "10.3390/ijms27198612", "fulltext_url": "https://europepmc.org/articles/PMC13665000", "id": "18xmt5xf8jrxb", "issns": [ "1422-0067", "1661-6596" ], "landing_url": "https://europepmc.org/article/MED/42883862", "language": "eng", "licence": "CC-BY", "licence_label": "CC BY", "licence_source": "article", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "hal", "0.sdv" ], [ "openalex", "1311|Genetic diversity and population structure" ] ], "openalex": "W7214667331", "pdf_url": "https://europepmc.org/articles/PMC13665000?pdf=render", "pmcid": "PMC13665000", "pmid": "42883862", "published": "2026-09-26", "publisher": "MDPI", "ris": "https://research.draconitic.com/paper/18xmt5xf8jrxb.ris", "sources": [ { "first_seen": "2026-10-30T12:19:16Z", "native_id": "MED:42883862", "source": "europepmc", "url": "https://europepmc.org/article/MED/42883862" }, { "first_seen": "2026-11-06T12:20:44Z", "native_id": "hal-05854064", "source": "hal", "url": "https://hal.science/hal-05854064v1" } ], "subjects": [ { "field": "biology", "origin": "openalex:1311|Genetic diversity and population structure", "subfield": "genetics-genomics" } ], "title": "Population Genomics Refines Population Structure and Individual Stock Assignment in Atlantic and Mediterranean Swordfish (Xiphias gladius).", "title_text": "Population Genomics Refines Population Structure and Individual Stock Assignment in Atlantic and Mediterranean Swordfish (Xiphias gladius).", "type": "peer-reviewed", "updated_at": "2026-11-07T12:20:25Z", "url": "https://research.draconitic.com/paper/18xmt5xf8jrxb", "venue": "International journal of molecular sciences", "versions": [] }