References
Aalto, E. A., S. Dedman, M. J. W. Stokesbury, R. J. Schallert, M. Castleton, and B. A. Block. 2023. Evidence of bluefin tuna (Thunnus thynnus) spawning in the Slope Sea region of the Northwest Atlantic from electronic tags. ICES Journal of Marine Science.
Aalto, E. A., F. Ferretti, M. V. Lauretta, J. F. Walter, M. J. W. Stokesbury, R. J. Schallert, and B. A. Block. 2021. Stock-of-origin catch estimation of Atlantic bluefin tuna (Thunnus thynnus) based on observed spatial distributions. Canadian Journal of Fisheries and Aquatic Sciences 78 :1193-1204.
Aarestrup, K., H. Baktoft, K. Birnie-Gauvin, A. Sundelöf, M. Cardinale, G. Quilez-Badia, I. Onandia, M. Casini, E. E. Nielsen, A. Koed, F. Alemany, and B. R. MacKenzie. 2022. First tagging data on large Atlantic bluefin tuna returning to Nordic waters suggest repeated behaviour and skipped spawning. Scientific Reports 12 :11772.
Abbott, R., D. Albach, S. Ansell, J. W. Arntzen, S. J. E. Baird, N. Bierne, J. Boughman, A. Brelsford, C. A. Buerkle, R. Buggs, R. K. Butlin, U. Dieckmann, F. Eroukhmanoff, A. Grill, S. H. Cahan, J. S. Hermansen, G. Hewitt, A. G. Hudson, C. Jiggins, J. Jones, B. Keller, T. Marczewski, J. Mallet, P. Martinez-Rodriguez, M. Möst, S. Mullen, R. Nichols, A. W. Nolte, C. Parisod, K. Pfennig, A. M. Rice, M. G. Ritchie, B. Seifert, C. M. Smadja, R. Stelkens, J. M. Szymura, R. Väinölä, J. B. W. Wolf, and D. Zinner. 2013. Hybridization and speciation. Journal of Evolutionary Biology 26 :229-246.
Alemany, F., L. Quintanilla, P. Velez-Belchí, A. García, D. Cortés, J. M. Rodríguez, M. L. Fernández de Puelles, C. González-Pola, and J. L. López-Jurado. 2010. Characterization of the spawning habitat of Atlantic bluefin tuna and related species in the Balearic Sea (western Mediterranean). Progress in Oceanography 86 :21-38.
Alexander, D. H., J. Novembre, and K. Lange. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome research.
Alvarado Bremer, J. R., J. Viñas, J. Mejuto, B. Ely, and C. Pla. 2005. Comparative phylogeography of Atlantic bluefin tuna and swordfish: the combined effects of vicariance, secondary contact, introgression, and population expansion on the regional phylogenies of two highly migratory pelagic fishes. Molecular Phylogenetics and Evolution 36 :169-187.
Aranda, G., L. Aragón, A. Corriero, C. C. Mylonas, F. d. la Gándara, A. Belmonte, and A. Medina. 2011. GnRHa-induced spawning in cage-reared Atlantic bluefin tuna: An evaluation using stereological quantification of ovarian post-ovulatory follicles. Aquaculture 317 :255-259.
Arnold, M. L., and N. H. Martin. 2009. Adaptation by introgression. Journal of Biology 8 :82.
Arregui, I., B. Galuardi, N. Goñi, C. H. Lam, I. Fraile, J. Santiago, M. Lutcavage, and H. Arrizabalaga. 2018. Movements and geographic distribution of juvenile bluefin tuna in the Northeast Atlantic, described through internal and satellite archival tags. ICES Journal of Marine Science 75 :1560-1572.
Baglin, R. 1976. A preliminary study of the gonadal development and fecundity of the western Atlantic bluefin tuna. Collective Volume of Scientific Papers ICCAT 5 :279-289.
Barth, J. M. I., P. R. Berg, P. R. Jonsson, S. Bonanomi, H. Corell, J. Hemmer-Hansen, K. S. Jakobsen, K. Johannesson, P. E. Jorde, H. Knutsen, P.-O. Moksnes, B. Star, N. C. Stenseth, H. Svedäng, S. Jentoft, and C. André. 2017a. Genome architecture enables local adaptation of Atlantic cod despite high connectivity. Molecular Ecology 26 :4452-4466.
Barth, J. M. I., M. Damerau, M. Matschiner, S. Jentoft, and R. Hanel. 2017b. Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations. Genome Biology and Evolution9 :1084-1098.
Barth, J. M. I., D. Villegas-Ríos, C. Freitas, E. Moland, B. Star, C. André, H. Knutsen, I. Bradbury, J. Dierking, C. Petereit, D. Righton, J. Metcalfe, K. S. Jakobsen, E. M. Olsen, and S. Jentoft. 2019. Disentangling structural genomic and behavioural barriers in a sea of connectivity. Molecular Ecology28 :1394-1411.
Begg, G. A., K. D. Friedland, and J. B. Pearce. 1999. Stock identification and its role in stock assessment and fisheries management: an overview. Fisheries Research43 :1-8.
Berg, P. R., B. Star, C. Pampoulie, M. Sodeland, J. M. I. Barth, H. Knutsen, K. S. Jakobsen, and S. Jentoft. 2016. Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod. Scientific Reports 6 :23246.
Bernatchez, L. 2016. On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes. Journal of Fish Biology 89 :2519-2556.
Bernatchez, L., M. Wellenreuther, C. Araneda, D. T. Ashton, J. M. I. Barth, T. D. Beacham, G. E. Maes, J. T. Martinsohn, K. M. Miller, K. A. Naish, J. R. Ovenden, C. R. Primmer, H. Young Suk, N. O. Therkildsen, and R. E. Withler. 2017. Harnessing the Power of Genomics to Secure the Future of Seafood. Trends in Ecology & Evolution 32 :665-680.
Block, B. A., S. L. H. Teo, A. Walli, A. Boustany, M. J. W. Stokesbury, C. J. Farwell, K. C. Weng, H. Dewar, and T. D. Williams. 2005. Electronic tagging and population structure of Atlantic bluefin tuna. Nature 434 :1121-1127.
Bonanomi, S., L. Pellissier, N. O. Therkildsen, R. B. Hedeholm, A. Retzel, D. Meldrup, S. M. Olsen, A. Nielsen, C. Pampoulie, J. Hemmer-Hansen, M. S. Wisz, P. Grønkjær, and E. E. Nielsen. 2015. Archived DNA reveals fisheries and climate induced collapse of a major fishery. Scientific Reports 5 :15395.
Brauer, C. J., J. Sandoval-Castillo, K. Gates, M. P. Hammer, P. J. Unmack, L. Bernatchez, and L. B. Beheregaray. 2023. Natural hybridization reduces vulnerability to climate change. Nature Climate Change 13 :282-289.
Brophy, D., N. Rodríguez-Ezpeleta, I. Fraile, and H. Arrizabalaga. 2020. Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus). Scientific Reports10 :14675.
Brown-Peterson, N. J., D. M. Wyanski, F. Saborido-Rey, B. J. Macewicz, and S. K. Lowerre-Barbieri. 2011. A Standardized Terminology for Describing Reproductive Development in Fishes. Marine and Coastal Fisheries 3 :52-70.
Chow, S., and H. Kishino. 1995. Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae: Teleostei): Inconsistent implications from morphology, nuclear and mitochondrial genomes. Journal of Molecular Evolution41 :741-748.
Ciezarek, A. G., O. G. Osborne, O. N. Shipley, E. J. Brooks, S. R. Tracey, J. D. McAllister, L. D. Gardner, M. J. E. Sternberg, B. Block, and V. Savolainen. 2018. Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas. Molecular Biology and Evolution 36 :84-96.
Clarkson, C. S., D. Weetman, J. Essandoh, A. E. Yawson, G. Maslen, M. Manske, S. G. Field, M. Webster, T. Antão, B. MacInnis, D. Kwiatkowski, and M. J. Donnelly. 2014. Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation. Nature Communications 5 :4248.
Collette, B. B., K. E. Carpenter, B. A. Polidoro, M. J. Juan-Jordá, A. Boustany, D. J. Die, C. Elfes, W. Fox, J. Graves, L. R. Harrison, R. McManus, C. V. Minte-Vera, R. Nelson, V. Restrepo, J. Schratwieser, C.-L. Sun, A. Amorim, M. Brick Peres, C. Canales, G. Cardenas, S.-K. Chang, W.-C. Chiang, N. de Oliveira Leite, H. Harwell, R. Lessa, F. L. Fredou, H. A. Oxenford, R. Serra, K.-T. Shao, R. Sumaila, S.-P. Wang, R. Watson, and E. Yáñez. 2011. High Value and Long Life - Double Jeopardy for Tunas and Billfishes. Science333 :291-292.
da Fonseca, R., P. Campos, A. Rey de la Iglesia, G. Barroso, L. Bergeron, M. Nande, F. Tuya, S. Abidli, M. Pérez, I. Riveiro, P. Carrera, A. Jurado-Ruzafa, M. T. G. Santamaria, R. Faria, A. Machado, M. Fonseca, E. Froufe, and L. F. C. Castro. 2022. Population genomics reveals the underlying structure of the small pelagic European sardine and suggests low connectivity within Macaronesia. Authorea.
Díaz-Arce, N., H. Arrizabalaga, H. Murua, X. Irigoien, and N. Rodríguez-Ezpeleta. 2016. RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas. Molecular Phylogenetics and Evolution 102 :202-207.
Durand, E. Y., N. Patterson, D. Reich, and M. Slatkin. 2011. Testing for ancient admixture between closely related populations. Molecular Biology and Evolution28 :2239-2252.
Duranton, M., F. Allal, S. Valière, O. Bouchez, F. Bonhomme, and P.-A. Gagnaire. 2020. The contribution of ancient admixture to reproductive isolation between European sea bass lineages. Evolution Letters 4 :226-242.
Erauskin-Extramiana, M., H. Arrizabalaga, A. J. Hobday, A. Cabré, L. Ibaibarriaga, I. Arregui, H. Murua, and G. Chust. 2019. Large-scale distribution of tuna species in a warming ocean. Global Change Biology 25 :2043-2060.
Etter, P. D., S. Bassham, P. A. Hohenlohe, E. A. Johnson, and W. A. Cresko. 2012. SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Pages 157-178 Molecular methods for evolutionary genetics. Springer.
Faillettaz, R., G. Beaugrand, E. Goberville, and R. R. Kirby. 2019. Atlantic Multidecadal Oscillations drive the basin-scale distribution of Atlantic bluefin tuna. Science Advances 5 :eaar6993.
Foll, M., and O. Gaggiotti. 2008. A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective. Genetics180 :977-993.
Fraser, D. J., and L. Bernatchez. 2001. Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Molecular Ecology 10 :2741-2752.
Fromentin, J.-M. 2009. Lessons from the past: investigating historical data from bluefin tuna fisheries. Fish and Fisheries 10 :197-216.
Fromentin, J.-M., S. Bonhommeau, H. Arrizabalaga, and L. T. Kell. 2014a. The spectre of uncertainty in management of exploited fish stocks: The illustrative case of Atlantic bluefin tuna. Marine Policy 47 :8-14.
Fromentin, J.-M., and J. E. Powers. 2005. Atlantic bluefin tuna: population dynamics, ecology, fisheries and management. Fish and Fisheries 6 :281-306.
Fromentin, J.-M., G. Reygondeau, S. Bonhommeau, and G. Beaugrand. 2014b. Oceanographic changes and exploitation drive the spatio-temporal dynamics of Atlantic bluefin tuna (Thunnus thynnus). Fisheries Oceanography 23 :147-156.
Fuentes-Pardo, A. P., E. D. Farrell, M. E. Pettersson, C. G. Sprehn, and L. Andersson. 2022. The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (<em>Trachurus trachurus</em>). bioRxiv:2022.2004.2025.489172.
Gagnaire, P.-A., T. Broquet, D. Aurelle, F. Viard, A. Souissi, F. Bonhomme, S. Arnaud-Haond, and N. Bierne. 2015. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evolutionary Applications 8 :769-786.
Galuardi, B., F. Royer, W. Golet, J. Logan, J. Neilson, and M. Lutcavage. 2010. Complex migration routes of Atlantic bluefin tuna (Thunnus thynnus) question current population structure paradigm. Canadian Journal of Fisheries and Aquatic Sciences67 :966-976.
Green, R. E., J. Krause, A. W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, and M. H.-Y. Fritz. 2010. A draft sequence of the Neandertal genome. science 328 :710-722.
Gutenkunst, R. N., R. D. Hernandez, S. H. Williamson, and C. D. Bustamante. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS genetics 5 :e1000695.
Hauser, L., and G. R. Carvalho. 2008. Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts. Fish and Fisheries 9 :333-362.
Hedrick, P. W. 2013. Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation. Molecular Ecology22 :4606-4618.
Hernández, C. M., D. E. Richardson, I. I. Rypina, K. Chen, K. E. Marancik, K. Shulzitski, and J. K. Llopiz. 2022. Support for the Slope Sea as a major spawning ground for Atlantic bluefin tuna: evidence from larval abundance, growth rates, and particle-tracking simulations. Canadian Journal of Fisheries and Aquatic Sciences 79 :814-824.
Hoban, S., J. A. Arntzen, M. W. Bruford, J. A. Godoy, A. Rus Hoelzel, G. Segelbacher, C. Vilà, and G. Bertorelle. 2014. Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion. Evolutionary Applications 7 :984-998.
Hoey, J. A., K. W. Able, and M. L. Pinsky. 2022. Genetic decline and recovery of a demographically rebuilt fishery species. Molecular Ecology 31 :5684-5698.
Hoffmann, A. A., and C. M. Sgrò. 2011. Climate change and evolutionary adaptation. Nature470 :479-485.
Horton, T. W., B. A. Block, A. Drumm, L. A. Hawkes, M. O’Cuaig, N. Ó. Maoiléidigh, R. O’Neill, R. J. Schallert, M. J. W. Stokesbury, and M. J. Witt. 2020. Tracking Atlantic bluefin tuna from foraging grounds off the west coast of Ireland. ICES Journal of Marine Science 77 :2066-2077.
Huang, K., R. L. Andrew, G. L. Owens, K. L. Ostevik, and L. H. Rieseberg. 2020. Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype. Molecular Ecology 29 :2535-2549.
Huerta-Sánchez, E., X. Jin, Asan, Z. Bianba, B. M. Peter, N. Vinckenbosch, Y. Liang, X. Yi, M. He, M. Somel, P. Ni, B. Wang, X. Ou, Huasang, J. Luosang, Z. X. P. Cuo, K. Li, G. Gao, Y. Yin, W. Wang, X. Zhang, X. Xu, H. Yang, Y. Li, J. Wang, J. Wang, and R. Nielsen. 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512 :194-197.
Hutchinson, W. F. 2008. The dangers of ignoring stock complexity in fishery management: the case of the North Sea cod. Biology Letters 4 :693-695.
ICCAT. 2023. Recommendation by ICCAT establishing a management procedure for Atlantic Bluefin tuna to be used for both the Western Atlantic and Eastern Atlantic and Mediterranean management areas. Page 8,https://www.iccat.int/Documents/Recs/compendiopdf-e/2022-09-e.pdf.
ICCAT, S. 2017. Report of the Standing Committee on Research and Statistics (SCRS), Madrid, Spain, 2017. ICCAT.
ICCAT, S. 2019. Report of the Standing Committee on Resarch and Statistics. ICCAT ICCAT, Madrid, Spain .
ICCAT, S. 2021. 2020 SRCS Advice to the Comission. ICCAT,https://www.iccat.int/Documents/BienRep/REP_EN_20-21_I-1.pdf.
Jansen, T., E. E. Nielsen, N. Rodriguez-Ezpeleta, H. Arrizabalaga, S. Post, and B. R. MacKenzie. 2021. Atlantic bluefin tuna (Thunnus thynnus) in Greenland — mixed-stock origin, diet, hydrographic conditions, and repeated catches in this new fringe area. Canadian Journal of Fisheries and Aquatic Sciences78 :400-408.
Jay, P., A. Whibley, L. Frézal, M. Á. Rodríguez de Cara, R. W. Nowell, J. Mallet, K. K. Dasmahapatra, and M. Joron. 2018. Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion. Current Biology 28 :1839-1845.e1833.
Jiménez-Mena, B., A. Le Moan, A. Christensen, M. van Deurs, H. Mosegaard, J. Hemmer-Hansen, and D. Bekkevold. 2020. Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea. Evolutionary Applications13 :376-387.
Johnstone, C., M. Pérez, E. Malca, J. M. Quintanilla, T. Gerard, D. Lozano-Peral, F. Alemany, J. Lamkin, A. García, and R. Laiz-Carrión. 2021. Genetic connectivity between Atlantic bluefin tuna larvae spawned in the Gulf of Mexico and in the Mediterranean Sea. PeerJ 9 :e11568.
Jombart, T., and I. Ahmed. 2011. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27 :3070-3071.
Kerr, L. A., N. T. Hintzen, S. X. Cadrin, L. W. Clausen, M. Dickey-Collas, D. R. Goethel, E. M. C. Hatfield, J. P. Kritzer, and R. D. M. Nash. 2016. Lessons learned from practical approaches to reconcile mismatches between biological population structure and stock units of marine fish. ICES Journal of Marine Science 74 :1708-1722.
Kerr, L. A., Z. T. Whitener, S. X. Cadrin, M. R. Morse, D. H. Secor, and W. Golet. 2020. Mixed stock origin of Atlantic bluefin tuna in the U.S. rod and reel fishery (Gulf of Maine) and implications for fisheries management. Fisheries Research224 :105461.
Kulathinal, R. J., L. S. Stevison, and M. A. Noor. 2009. The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing. PLoS genetics 5 :e1000550.
Le Moan, A., D. Bekkevold, and J. Hemmer-Hansen. 2020. Evolution at two time-frames: ancient and singular origin of two structural variants involved in local adaptation of the European plaice (<em>Pleuronectes platessa</em>). bioRxiv:662577.
Li, H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997.
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and G. P. D. P. Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 :2078-2079.
Lischer, H. E. L., and L. Excoffier. 2011. PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics28 :298-299.
Lowe, W. H., and F. W. Allendorf. 2010. What can genetics tell us about population connectivity? Molecular Ecology 19 :3038-3051.
Luu, K., E. Bazin, and M. G. B. Blum. 2017. pcadapt: an R package to perform genome scans for selection based on principal component analysis. Molecular Ecology Resources17 :67-77.
Mamoozadeh, N. R., J. E. Graves, and J. R. McDowell. 2020. Genome-wide SNPs resolve spatiotemporal patterns of connectivity within striped marlin (Kajikia audax), a broadly distributed and highly migratory pelagic species. Evolutionary Applications 13 :677-698.
Mather, F. J., J. M. Mason, and A. C. Jones. 1995. Historical document : life history and fisheries of Atlantic bluefin tuna.
McPherson, G. 1991. Reproductive biology of yellowfin tuna in the eastern Australian Fishing Zone, with special reference to the north-western Coral Sea. Marine and Freshwater Research 42 :465-477.
Mérot, C., E. L. Berdan, H. Cayuela, H. Djambazian, A.-L. Ferchaud, M. Laporte, E. Normandeau, J. Ragoussis, M. Wellenreuther, and L. Bernatchez. 2021. Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly. Molecular Biology and Evolution 38 :3953-3971.
Muhling, B. A., S.-K. Lee, J. T. Lamkin, and Y. Liu. 2011. Predicting the effects of climate change on bluefin tuna (Thunnus thynnus) spawning habitat in the Gulf of Mexico. ICES Journal of Marine Science 68 :1051-1062.
Nikolic, N., F. Devloo-Delva, D. Bailleul, E. Noskova, C. Rougeux, C. Delord, P. Borsa, C. Liautard-Haag, M. Hassan, A. D. Marie, P. Feutry, P. Grewe, C. Davies, J. Farley, D. Fernando, S. Biton-Porsmoguer, F. Poisson, D. Parker, A. Leone, J. Aulich, M. Lansdell, F. Marsac, and S. Arnaud-Haond. 2023. Stepping up to genome scan allows stock differentiation in the worldwide distributed blue shark Prionace glauca. Molecular Ecology 32 :1000-1019.
Nøttestad, L., E. Boge, and K. Ferter. 2020. The comeback of Atlantic bluefin tuna (Thunnus thynnus) to Norwegian waters. Fisheries Research 231 :105689.
Oosting, T., B. Star, J. H. Barrett, M. Wellenreuther, P. A. Ritchie, and N. J. Rawlence. 2019. Unlocking the potential of ancient fish DNA in the genomic era. Evolutionary Applications 12 :1513-1522.
Ovenden, J. R., O. Berry, D. J. Welch, R. C. Buckworth, and C. M. Dichmont. 2015. Ocean’s eleven: a critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries. Fish and Fisheries 16 :125-159.
Patterson, N. J., P. Moorjani, Y. Luo, S. Mallick, N. Rohland, Y. Zhan, T. Genschoreck, T. Webster, and D. Reich. 2012. Ancient admixture in human history. Genetics:genetics. 112.145037.
Pickrell, J. K., and J. K. Pritchard. 2012. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. PLOS Genetics 8 :e1002967.
Porch, C. E., S. Bonhommeau, G. A. Diaz, A. Haritz, and G. Melvin. 2019. The journey from overfishing to sustainability for Atlantic bluefin tuna, Thunnus thynnus. The future of bluefin tunas: Ecology, fisheries management, and conservation:3-44.
Portik, D. M., A. D. Leaché, D. Rivera, M. F. Barej, M. Burger, M. Hirschfeld, M.-O. Rödel, D. C. Blackburn, and M. K. Fujita. 2017. Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection. Molecular Ecology 26 :5245-5263.
Puncher, G. N., A. Cariani, G. E. Maes, J. Van Houdt, K. Herten, R. Cannas, N. Rodriguez-Ezpeleta, A. Albaina, A. Estonba, M. Lutcavage, A. Hanke, J. Rooker, J. S. Franks, J. M. Quattro, G. Basilone, I. Fraile, U. Laconcha, N. Goñi, A. Kimoto, D. Macías, F. Alemany, S. Deguara, S. W. Zgozi, F. Garibaldi, I. K. Oray, F. S. Karakulak, N. Abid, M. N. Santos, P. Addis, H. Arrizabalaga, and F. Tinti. 2018. Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next-generation sequencing. Molecular Ecology Resources 18 :620-638.
Puncher, G. N., A. Hanke, D. Busawon, E. V. A. Sylvester, W. Golet, L. C. Hamilton, and S. A. Pavey. 2022. Individual assignment of Atlantic bluefin tuna in the northwestern Atlantic Ocean using single nucleotide polymorphisms reveals an increasing proportion of migrants from the eastern Atlantic Ocean. Canadian Journal of Fisheries and Aquatic Sciences 79 :111-123.
Puncher, G. N., S. Rowe, G. A. Rose, N. M. Leblanc, G. J. Parent, Y. Wang, and S. A. Pavey. 2019. Chromosomal inversions in the Atlantic cod genome: Implications for management of Canada’s Northern cod stock. Fisheries Research 216 :29-40.
Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. Ferreira, D. Bender, J. Maller, P. Sklar, P. I. de Bakker, M. J. Daly, and P. C. Sham. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81 :559-575.
Ravier, C., and J.-M. Fromentin. 2004. Are the long-term fluctuations in Atlantic bluefin tuna (Thunnus thynnus) population related to environmental changes? Fisheries Oceanography 13 :145-160.
Raymond, M. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86 :248-249.
Reiss, H., G. Hoarau, M. Dickey-Collas, and W. J. Wolff. 2009. Genetic population structure of marine fish: mismatch between biological and fisheries management units. Fish and Fisheries 10 :361-395.
Richardson, D. E., K. E. Marancik, J. R. Guyon, M. E. Lutcavage, B. Galuardi, C. H. Lam, H. J. Walsh, S. Wildes, D. A. Yates, and J. A. Hare. 2016a. Discovery of a spawning ground reveals diverse migration strategies in Atlantic bluefin tuna (<em>Thunnus thynnus</em>). Proceedings of the National Academy of Sciences 113 :3299-3304.
Richardson, D. E., K. E. Marancik, J. R. Guyon, M. E. Lutcavage, B. Galuardi, C. H. Lam, H. J. Walsh, S. Wildes, D. A. Yates, and J. A. Hare. 2016b. Reply to Safina and Walter et al.: Multiple lines of evidence for size-structured spawning migrations in western Atlantic bluefin tuna. Proceedings of the National Academy of Sciences 113 :E4262-E4263.
Roberts, D. G., C. A. Gray, R. J. West, and D. J. Ayre. 2010. Marine genetic swamping: hybrids replace an obligately estuarine fish. Molecular Ecology 19 :508-520.
Rochette, N. C., A. G. Rivera-Colón, and J. M. Catchen. 2019. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Molecular Ecology28 :4737-4754.
Rodríguez-Ezpeleta, N., N. Díaz-Arce, J. F. Walter III, D. E. Richardson, J. R. Rooker, L. Nøttestad, A. R. Hanke, J. S. Franks, S. Deguara, M. V. Lauretta, P. Addis, J. L. Varela, I. Fraile, N. Goñi, N. Abid, F. Alemany, I. K. Oray, J. M. Quattro, F. N. Sow, T. Itoh, F. S. Karakulak, P. J. Pascual-Alayón, M. N. Santos, Y. Tsukahara, M. Lutcavage, J.-M. Fromentin, and H. Arrizabalaga. 2019. Determining natal origin for improved management of Atlantic bluefin tuna. Frontiers in Ecology and the Environment 17 :439-444.
Rooker, J. R., H. Arrizabalaga, I. Fraile, D. H. Secor, D. L. Dettman, N. Abid, P. Addis, S. Deguara, F. S. Karakulak, A. Kimoto, O. Sakai, D. Macías, and M. N. Santos. 2014. Crossing the line: migratory and homing behaviors of Atlantic bluefin tuna. Marine Ecology Progress Series 504 :265-276.
Rooker, J. R., I. Fraile, H. Liu, N. Abid, M. A. Dance, T. Itoh, A. Kimoto, Y. Tsukahara, E. Rodriguez-Marin, and H. Arrizabalaga. 2019. Wide-ranging temporal variation in transoceanic movement and population mixing of bluefin tuna in the North Atlantic Ocean. Frontiers in Marine Science 6 :398.
Rooker, J. R., D. H. Secor, G. DeMetrio, A. J. Kaufman, A. B. Ríos, and V. Ticina. 2008. Evidence of trans-Atlantic movement and natal homing of bluefin tuna from stable isotopes in otoliths. Marine Ecology Progress Series368 :231-239.
Rypina, I. I., K. Chen, C. M. Hernández, L. J. Pratt, and J. K. Llopiz. 2019. Investigating the suitability of the Slope Sea for Atlantic bluefin tuna spawning using a high-resolution ocean circulation model. ICES Journal of Marine Science76 :1666-1677.
Safina, C. 2016. Data do not support new claims about bluefin tuna spawning or abundance. Proceedings of the National Academy of Sciences 113 :E4261-E4261.
Schaefer, K. 1996. Spawning time, frequency, and batch fecundity of yellowfin tuna, Thunnus albacares, near Clipperton Atoll in the eastern Pacific ocien. Fish. Bull.94 :98-112.
Secor, D. H., J. R. Rooker, B. I. Gahagan, M. R. Siskey, and R. W. Wingate. 2015. Depressed resilience of bluefin tuna in the western atlantic and age truncation. Conservation Biology 29 :400-408.
Siskey, M. R., M. J. Wilberg, R. J. Allman, B. K. Barnett, and D. H. Secor. 2016. Forty years of fishing: changes in age structure and stock mixing in northwestern Atlantic bluefin tuna (Thunnus thynnus) associated with size-selective and long-term exploitation. ICES Journal of Marine Science73 :2518-2528.
Stephenson, R. L. 1999. Stock complexity in fisheries management: a perspective of emerging issues related to population sub-units. Fisheries Research 43 :247-249.
Suda, A., I. Nishiki, Y. Iwasaki, A. Matsuura, T. Akita, N. Suzuki, and A. Fujiwara. 2019. Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers. Scientific Reports9 :14450.
Thorstensen, M. J., P. T. Euclide, J. D. Jeffrey, Y. Shi, J. R. Treberg, D. A. Watkinson, E. C. Enders, W. A. Larson, Y. Kobayashi, and K. M. Jeffries. 2022. A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish. Ecology and Evolution 12 :e8898.
Tigano, A., and V. L. Friesen. 2016. Genomics of local adaptation with gene flow. Molecular Ecology25 :2144-2164.
Valenzuela-Quiñonez, F. 2016. How fisheries management can benefit from genomics? Briefings in Functional Genomics 15 :352-357.
Viñas, J., A. Gordoa, R. Fernández-Cebrián, C. Pla, Ü. Vahdet, and R. M. Araguas. 2011. Facts and uncertainties about the genetic population structure of Atlantic bluefin tuna (Thunnus thynnus) in the Mediterranean. Implications for fishery management. Reviews in Fish Biology and Fisheries 21 :527-541.
Walter, J. F., C. E. Porch, M. V. Lauretta, S. L. Cass-Calay, and C. A. Brown. 2016. Implications of alternative spawning for bluefin tuna remain unclear. Proceedings of the National Academy of Sciences 113 :E4259-E4260.
Waples, R. 1998. Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity 89 :438-450.
Waples, R. S. 2022. What Is Ne, Anyway? Journal of Heredity 113 :371-379.
Wellenreuther, M., and L. Bernatchez. 2018. Eco-Evolutionary Genomics of Chromosomal Inversions. Trends in Ecology & Evolution 33 :427-440.
Xuereb, A., C. C. D’Aloia, M. Andrello, L. Bernatchez, and M.-J. Fortin. 2021. Incorporating putatively neutral and adaptive genomic data into marine conservation planning. Conservation Biology 35 :909-920.
Yang, J., S. H. Lee, M. E. Goddard, and P. M. Visscher. 2011. GCTA: A Tool for Genome-wide Complex Trait Analysis. The American Journal of Human Genetics 88 :76-82.