Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next-generation sequencing

Puncher, Gregory N., Cariani, Alessia, Maes, Gregory E., Van Houdt, Jeroen, HertenKatho, Koen, Cannas, Rita, Rodriguez-Ezpeleta, Naiara, Albaina, Aitor, Estonba, Andone, Lutcavage, Molly, Hanke, Alex, Rooker, Jay, Franks, James S., Quattro, Joseph S., Basilone, Gualtiero, Fraile, Igaratza, Laconcha, Urtzi, Goni, Nicolas, Kimoto, Ai, Macias, David, Alemany, Francisco, Deguara, Simeon, Zgozi, Salem W., Garibaldi, Fulvio, Oray, Isik K., Karakulak, Firdes Saadet, Abid, Noureddine, Santos, Miguel N., Addis, Piero, Arrizabalaga, Haritz, and Tinti, Fausto (2018) Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next-generation sequencing. Molecular Ecology Resources, 18 (3). pp. 620-638.

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Abstract

The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species' stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n =326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (F-ST = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n =184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts.

Item ID: 53887
Item Type: Article (Research - C1)
ISSN: 1755-0998
Keywords: mixed-stock analysis, origin assignment, population structure, reduced representation sequencing, single nucleotide polymorphisms, Thunnus thynnus
Funders: International Commission for the Conservation of Atlantic Tunas (ICCAT), Erasmus Mundus
Projects and Grants: ICCAT Atlantic-wide Research Program for Bluefin Tuna
Date Deposited: 06 Jun 2018 07:48
FoR Codes: 05 ENVIRONMENTAL SCIENCES > 0502 Environmental Science and Management > 050202 Conservation and Biodiversity @ 20%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 40%
07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070405 Fish Physiology and Genetics @ 40%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8302 Fisheries - Wild Caught > 830207 Wild Caught Tuna @ 30%
96 ENVIRONMENT > 9605 Ecosystem Assessment and Management > 960507 Ecosystem Assessment and Management of Marine Environments @ 35%
96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 35%
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