{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T04:56:40Z","timestamp":1790657800234,"version":"4.1.0"},"reference-count":68,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T00:00:00Z","timestamp":1790380800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union","id":[{"id":"https:\/\/ror.org\/019w4f821","id-type":"ROR","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/019w4f821","id-type":"ROR","asserted-by":"publisher"}]},{"name":"International Commission for the Conservation of Atlantic Tunas","id":[{"id":"https:\/\/ror.org\/01fxs2165","id-type":"ROR","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/01fxs2165","id-type":"ROR","asserted-by":"publisher"}]},{"name":"ICCAT","id":[{"id":"https:\/\/ror.org\/01fxs2165","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Funds and the European Social Fund","award":["SFRH\/BD\/136074\/2018"],"award-info":[{"award-number":["SFRH\/BD\/136074\/2018"]}],"id":[{"id":"https:\/\/ror.org\/048snh465","id-type":"ROR","asserted-by":"crossref"}]},{"name":"FCT","award":["UIDB\/04326\/2020"],"award-info":[{"award-number":["UIDB\/04326\/2020"]}]},{"name":"FCT","award":["UIDP\/04326\/2020"],"award-info":[{"award-number":["UIDP\/04326\/2020"]}]},{"name":"FCT","award":["LA\/P\/0101\/2020"],"award-info":[{"award-number":["LA\/P\/0101\/2020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>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\u2013Atlantic 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\u2013Atlantic 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.<\/jats:p>","DOI":"10.3390\/ijms27198612","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T16:50:54Z","timestamp":1790614254000},"page":"8612","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Population Genomics Refines Population Structure and Individual Stock Assignment in Atlantic and Mediterranean Swordfish (Xiphias gladius)"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1187-7302","authenticated-orcid":false,"given":"Giorgia","family":"Gioacchini","sequence":"first","affiliation":[{"name":"Dipartimento di Scienze della Vita e dell\u2019Ambiente, Universita\u2019 Politecnica delle Marche, 60131 Ancona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4221-3173","authenticated-orcid":false,"given":"Kyle","family":"Gillespie","sequence":"additional","affiliation":[{"name":"Fisheries and Oceans Canada, St. Andrews Biological Station, 125 Marine Science Drive, St. Andrews, NB E5B 0E4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Rosa","sequence":"additional","affiliation":[{"name":"Instituto Portugu\u00eas do Mar e da Atmosfera (IPMA), Av. 5 de Outubro s\/n, 8700-305 Olh\u00e3o, Portugal"},{"name":"Centro de Ci\u00eancias do Mar da Universidade do Algarve (CCMar), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Filippi","sequence":"additional","affiliation":[{"name":"Dipartimento di Scienze della Vita e dell\u2019Ambiente, Universita\u2019 Politecnica delle Marche, 60131 Ancona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Marisaldi","sequence":"additional","affiliation":[{"name":"Dipartimento di Scienze della Vita e dell\u2019Ambiente, Universita\u2019 Politecnica delle Marche, 60131 Ancona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dheeraj","family":"Busawon","sequence":"additional","affiliation":[{"name":"Fisheries and Oceans Canada, St. Andrews Biological Station, 125 Marine Science Drive, St. Andrews, NB E5B 0E4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Bezerra","sequence":"additional","affiliation":[{"name":"Instituto de Oceanografia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s\/n Dois Irm\u00e3os, 52171-900 Recife, PE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8667-5292","authenticated-orcid":false,"given":"Paulo","family":"Travassos","sequence":"additional","affiliation":[{"name":"Instituto de Oceanografia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s\/n Dois Irm\u00e3os, 52171-900 Recife, PE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hil\u00e1rio Tiago","family":"Campello","sequence":"additional","affiliation":[{"name":"Instituto de Oceanografia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s\/n Dois Irm\u00e3os, 52171-900 Recife, PE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F\u00e1bio Hissa","family":"Vieira Hazin","sequence":"additional","affiliation":[{"name":"Instituto de Oceanografia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s\/n Dois Irm\u00e3os, 52171-900 Recife, PE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Mac\u00edas","sequence":"additional","affiliation":[{"name":"Centro Oceanogr\u00e1fico de M\u00e1laga, Instituto Espa\u00f1ol de Oceanograf\u00eda (IEO-CSIC), Puerto Pesquero s\/n, 29640 Fuengirola, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexia","family":"Gallucci","sequence":"additional","affiliation":[{"name":"AquaBioTech Group, Central Complex, Naggar Street, Targa Gap, MST 1761 Mosta, Malta"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3618-7220","authenticated-orcid":false,"given":"Francois","family":"Poisson","sequence":"additional","affiliation":[{"name":"MARBEC, Universit\u00e9 de Montpellier, CNRS, Ifremer, IRD, 34203 S\u00e8te, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fulvio","family":"Garibaldi","sequence":"additional","affiliation":[{"name":"Department of Earth, Environment and Life Sciences, University of Genoa, Corso Europa, 26, 16132 Genova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1026-0853","authenticated-orcid":false,"given":"Luis Gustavo","family":"Cardoso","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Recursos Pesqueiros Demersais e Cefal\u00f3podes, Instituto de Oceanografia, Universidade Federal do Rio Grande, Av. It\u00e1lia, sn, Campus Carreiros, 96203-900 Rio Grande, RS, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luigi","family":"Pappalardo","sequence":"additional","affiliation":[{"name":"OCEANIS SRL, 80056 Ercolano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Pignalosa","sequence":"additional","affiliation":[{"name":"OCEANIS SRL, 80056 Ercolano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9058-6994","authenticated-orcid":false,"given":"Riccardo","family":"Aiese Cigliano","sequence":"additional","affiliation":[{"name":"Sequentia Biotech SL, 08005 Barcellona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1370-0842","authenticated-orcid":false,"given":"Su","family":"Nan-Jay","sequence":"additional","affiliation":[{"name":"Department of Environmental Biology and Fishery Science, National Taiwan Ocean University, Keelung 20224, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Parker","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9052-4091","authenticated-orcid":false,"given":"George","family":"Tserpes","sequence":"additional","affiliation":[{"name":"Hellenic Centre for Marine Research, Athens Sounio Ave., P.O. Box 712, Anavyssos, 19013 Attiki, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5814-0626","authenticated-orcid":false,"given":"Freddy","family":"Arocha","sequence":"additional","affiliation":[{"name":"Instituto Oceanogr\u00e1fico de Venezuela, Universidad de Oriente, A.P. 204, 6101 Cumana, Venezuela"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taimi","family":"Shikongo","sequence":"additional","affiliation":[{"name":"Ministry of Fisheries and Marine Resources, National Marine Information and Research Centre, Swakopmund P.O. Box 912, Namibia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tommaso","family":"Righi","sequence":"additional","affiliation":[{"name":"Dipartimento di Scienze della Vita e dell\u2019Ambiente, Universita\u2019 Politecnica delle Marche, 60131 Ancona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Splendiani","sequence":"additional","affiliation":[{"name":"Dipartimento di Scienze della Vita e dell\u2019Ambiente, Universita\u2019 Politecnica delle Marche, 60131 Ancona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Di Natale","sequence":"additional","affiliation":[{"name":"Aquastudio Research Institute, Via Trapani, 6, 98121 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0464-0270","authenticated-orcid":false,"given":"Piero","family":"Addis","sequence":"additional","affiliation":[{"name":"Department of Life Science and Environment, University of Cagliari, Via Fiorelli 1, 09126 Cagliari, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriano","family":"Mariani","sequence":"additional","affiliation":[{"name":"UNIMAR Societ\u00e0 Cooperative, Via Nazionale, 243, 00184 Roma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miguel Neves dos","family":"Santos","sequence":"additional","affiliation":[{"name":"ICCAT Secretariat, Calle Coraz\u00f3n de Maria 8, Planta 6, 28002 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Coelho","sequence":"additional","affiliation":[{"name":"Instituto Portugu\u00eas do Mar e da Atmosfera (IPMA), Av. 5 de Outubro s\/n, 8700-305 Olh\u00e3o, Portugal"},{"name":"Centro de Ci\u00eancias do Mar da Universidade do Algarve (CCMar), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Hanke","sequence":"additional","affiliation":[{"name":"Fisheries and Oceans Canada, St. Andrews Biological Station, 125 Marine Science Drive, St. Andrews, NB E5B 0E4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5994-0572","authenticated-orcid":false,"given":"Oliana","family":"Carnevali","sequence":"additional","affiliation":[{"name":"Dipartimento di Scienze della Vita e dell\u2019Ambiente, Universita\u2019 Politecnica delle Marche, 60131 Ancona, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Cadrin, S.X., Kerr, L.A., and Mariani, S. 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