Population Genomics Refines Population Structure and Individual Stock Assignment in Atlantic and Mediterranean Swordfish (Xiphias gladius)
Year: 2026
Type: article
Abstract: ) 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.
DOI: 10.3390/ijms27198612
Authors: Giorgia Gioacchini, Kyle Gillespie, Daniela Rosa, Sara Filippi, Luca Marisaldi, Dheeraj Busawon, Natalia Bezerra, Paulo Travassos, Hilário Tiago Campello, Fábio Hissa Vieira Hazin, David Macías, Alexia Gallucci, Francois Poisson, Fulvio Garibaldi, Luis Gustavo Cardoso, Luigi Pappalardo, Paolo Pignalosa, Riccardo Aiese Cigliano, Su Nan-Jay, Dan Parker, George Tserpes, Freddy Arocha, Taimi Shikongo, Tommaso Righi, Andrea Splendiani, Antonio Di Natale, Piero Addis, Adriano Mariani, Miguel Neves dos Santos, Rui Coelho, Alex Hanke, Oliana Carnevali
Institutions: Marche Polytechnic University, Fisheries and Oceans Canada, Portuguese Sea and Atmosphere Institute, Centro de Ciências do Mar do Algarve, University of Algarve, Universidade Federal Rural de Pernambuco, Instituto Español de Oceanografía, Centro Oceanográfico de Málaga, AquaBioTech Group (Malta), Centre National de la Recherche Scientifique, Ifremer, Université de Montpellier, Marine Biodiversity Exploitation and Conservation, Institut de Recherche pour le Développement, University of Genoa, Universidade Federal do Rio Grande, Departament d'Educació, Barcelona Media, National Taiwan Ocean University, University of Cape Town, Hellenic Centre for Marine Research, Universidad de Oriente, Instituto Oceanográfico de Venezuela, University of Cagliari, International Commission for the Conservation of Atlantic Tunas
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Life below water
Open Access status: gold
Estimated APC paid: $3,499
Awards: Centro de Investigação Marinha e Ambiental, G3804113219, Centro de Ciências do Mar do Algarve, Centro de Ciências do Mar do Algarve, Sustainable fisheries management of swordfish (Xiphias gladius) in the Atlantic and Indian Oceans: biology, population dynamics, stock structure, habitat use, and evaluation of alternative management options., G6547834732, G6912052472, G7063316358
OpenAlex ID: W7214667331