Pauly, D. et al. Towards sustainability in world fisheries. Nature 418, 689–695 (2002).
Google Scholar
Butchart, S. H. M. et al. Global biodiversity: Indicators of recent declines. Science 328, 1164–1168 (2010).
Google Scholar
Pinsky, M. L. & Palumbi, S. R. Meta-analysis reveals lower genetic diversity in overfished populations. Mol. Ecol. 23, 29–39 (2014).
Google Scholar
Neubauer, P., Jensen, O. P., Hutchings, J. A. & Baum, J. K. Resilience and recovery of overexploited marine populations. Science 340, 347–349 (2013).
Google Scholar
Lotze, H. K., Hoffmann, R. & Erlandson, J. Lessons from historical ecology and management. In The Sea, Volume 19: Ecosystem-Based Management (Harvard University Press, 2014).
Erlandson, J. M. & Rick, T. C. Archaeology meets marine ecology: The antiquity of maritime cultures and human impacts on marine fisheries and ecosystems. Ann. Rev. Mar. Sci. 2, 231–251 (2010).
Google Scholar
Schwerdtner Máñez, K. et al. The future of the oceans past: Towards a global marine historical research initiative. PLoS ONE 9, e101466 (2014).
Palsbøll, P. J., Zachariah Peery, M., Olsen, M. T., Beissinger, S. R. & Bérubé, M. Inferring recent historic abundance from current genetic diversity. Mol. Ecol. 22, 22–40 (2013).
Oosting, T. et al. Unlocking the potential of ancient fish DNA in the genomic era. Evol. Appl. 12, 1513–1522 (2019).
Google Scholar
Heino, M., Pauli, B. D. & Dieckmann, U. Fisheries-induced evolution. Annu. Rev. Ecol. Evol. Syst. 46, 461–480 (2015).
Google Scholar
Riccioni, G. et al. Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea. Proc. Natl. Acad. Sci. 107, 2102–2107 (2010).
Google Scholar
Cort, J. L. Age and growth of the bluefin tuna (Thunnus thynnus) of the Northeast Atlantic. In Domestication of the bluefin tuna Thunnus thynnus thynnus. Cahiers Options Méditerranéennes (CIHEAM) 45–49 (2003).
Mather, F. J., Mason, J. M. & Jones, A. C. Historical document: life history and fisheries of Atlantic bluefin tuna. (1995). NOAA Technical Memorandum NMFS-SEFSC – 370.
Puncher, G. N. et al. Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next-generation sequencing. Mol. Ecol. Resour. 18, 620–638 (2018).
Google Scholar
Rodríguez-Ezpeleta, N. et al. Determining natal origin for improved management of Atlantic bluefin tuna. Front. Ecol. Environ. 17, 439–444 (2019).
Google Scholar
Richardson, D. E. et al. Discovery of a spawning ground reveals diverse migration strategies in Atlantic bluefin tuna (Thunnus thynnus). Proc. Natl. Acad. Sci. USA 113, 3299–3304 (2016).
Google Scholar
Piccinetti, C., Di Natale, A. & Arena, P. Eastern bluefin tuna (Thunnus thynnus, L.) reproduction and reproductive areas and season. Collect. Vol. Sci. Pap. ICCAT/Recl. Doc. Sci. CICTA/Colecc. Doc. Cient. CICAA 69, 891–912 (2013).
Cort, J. L. & Abaunza, P. The present state of traps and fisheries research in the strait of Gibraltar. In The Bluefin Tuna Fishery in the Bay of Biscay : Its Relationship with the Crisis of Catches of Large Specimens in the East Atlantic Fisheries from the 1960s (eds. Cort, J. L. & Abaunza, P.) 37–78 (Springer International Publishing, 2019).
Alemany, F., Tensek, S. & Pagà Garcia, A. ICCAT Atlantic-Wide Research programme for Bluefin Tuna (GBYP) activity report for the Phase 9 and the first part of Phase 10. Collect. Vol. Sci. Pap. ICCAT/Recl. Doc. Sci. CICTA/Colecc. Doc. Cient. CICAA 77, 666–700 (2020).
MacKenzie, B. R. & Mariani, P. Spawning of bluefin tuna in the Black Sea: historical evidence, environmental constraints and population plasticity. PLoS ONE 7, e39998 (2012).
Di Natale, A. The Eastern Atlantic bluefin tuna: Entangled in a big mess, possibly far from a conservation red alert. Some comments after the proposal to include bluefin tuna in CITES Appendix I. Collect. Vol. Sci. Pap. ICCAT/Recl. Doc. Sci. CICTA/Colecc. Doc. Cient. CICAA 65(3), 1004–1043 (2010).
Worm, B. & Tittensor, D. P. Range contraction in large pelagic predators. Proc. Natl. Acad. Sci. USA 108, 11942–11947 (2011).
Google Scholar
Fromentin, J.-M. Lessons from the past: Investigating historical data from bluefin tuna fisheries. Fish Fish. 10, 197–216 (2009).
Google Scholar
Siskey, M. R., Wilberg, M. J., Allman, R. J., Barnett, B. K. & Secor, D. H. 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 J. Mar. Sci. 73, 2518–2528 (2016).
Google Scholar
ICCAT. Report of the 2020 second ICCAT intersessional meeting of the bluefin tuna species group. Online, 20–28 July 2020. SECOND BFT INTERSESSIONAL MEETING – ONLINE 2020 (2020).
Ravier, C. & Fromentin, J.-M. Long-term fluctuations in the eastern Atlantic and Mediterranean bluefin tuna population. ICES J. Mar. Sci. 58, 1299–1317 (2001).
Google Scholar
Garcia, A. P. et al. Report on revised trap data recovered by ICCAT GBYP from Phase 1 to Phase 6. Collect. Vol. Sci. Pap. ICCAT/Recl. Doc. Sci. CICTA/Colecc. Doc. Cient. CICAA 73, 2074–2098 (2017).
Anderson, C. N. K. et al. Why fishing magnifies fluctuations in fish abundance. Nature 452, 835–839 (2008).
Google Scholar
Di Natale, A. & Idrissi, M. Factors to be taken into account for a correct reading of tuna trap catch series. Collect. Vol. Sci. Pap. ICCAT/Recl. Doc. Sci. CICTA/Colecc. Doc. Cient. CICAA 67, 242–261 (2012).
Laconcha, U. et al. New nuclear SNP markers unravel the genetic structure and effective population size of Albacore Tuna (Thunnus alalunga). PLoS ONE 10, e0128247 (2015).
Speller, C. F. et al. High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation. PLoS ONE 7, e51122 (2012).
Montes, I. et al. No loss of genetic diversity in the exploited and recently collapsed population of Bay of Biscay anchovy (Engraulis encrasicolus, L.). Mar. Biol. 163, 98 (2016).
Chapman, D. D. et al. Genetic diversity despite population collapse in a critically endangered marine fish: The smalltooth sawfish (Pristis pectinata). J. Hered. 102, 643–652 (2011).
Google Scholar
Hutchinson, W. F., van Oosterhout, C., Rogers, S. I. & Carvalho, G. R. Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua). Proc. Biol. Sci. 270, 2125–2132 (2003).
Google Scholar
Ólafsdóttir, G. Á., Westfall, K. M., Edvardsson, R. & Pálsson, S. Historical DNA reveals the demographic history of Atlantic cod (Gadus morhua) in medieval and early modern Iceland. Proc. Biol. Sci. 281, 20132976 (2014).
Google Scholar
Bonanomi, S. et al. Archived DNA reveals fisheries and climate induced collapse of a major fishery. Sci. Rep. 5, 15395 (2015).
Google Scholar
Nielsen, E. E., Hansen, M. M. & Loeschcke, V. Analysis of microsatellite DNA from old scale samples of Atlantic salmon Salmo salar : A comparison of genetic composition over 60 years. Mol. Ecol. 6, 487–492 (1997).
Google Scholar
Johnson, B. M., Kemp, B. M. & Thorgaard, G. H. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha. PLoS ONE 13, e0190059 (2018).
Bowles, E., Marin, K., Mogensen, S., MacLeod, P. & Fraser, D. J. Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest?. Evol. Appl. 13, 1128–1144 (2020).
Google Scholar
Royle, T. C. A. et al. Investigating the sex-selectivity of a middle Ontario Iroquoian Atlantic salmon (Salmo salar) and lake trout (Salvelinus namaycush) fishery through ancient DNA analysis. J. Archaeol. Sci. Rep. 31, 102301 (2020).
Therkildsen, N. O. et al. Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod. Mol. Ecol. 22, 2424–2440 (2013).
Google Scholar
Pinsky, M. L. et al. Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic. Proc. Natl. Acad. Sci. USA 118, (2021).
Onar, V., Pazvant, G. & Armutak, A. Radiocarbon dating results of the animal remains uncovered at Yenikapi Excavations. In Istanbul Archaeological Museums, Proceedings of the 1st Symposium on Marmaray-Metro Salvage Excavations 249–256 (2008).
Bernal-Casasola, D., Expósito, J. A. & Díaz, J. J. The Baelo Claudia paradigm: The exploitation of marine resources in Roman cetariae. J. Marit. Archaeol. 13, 329–351 (2018).
Google Scholar
Bernal, D. & Monclova, A. Pescar con Arte. Fenicios y romanos en el origen de los aparejos andaluces. Monografías del Proyecto Sagena 3, (2011).
Puncher, G. N. et al. Comparison and optimization of genetic tools used for the identification of ancient fish remains recovered from archaeological excavations and museum collections in the Mediterranean region. Int J Osteoarchaeol 29, 365–376 (2019).
Google Scholar
Kemp, B. M. & Smith, D. G. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci. Int. 154, 53–61 (2005).
Google Scholar
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. USA 110, 15758–15763 (2013).
Google Scholar
Serventi, P. et al. Iron Age Italic population genetics: The Piceni from Novilara (8th–7th century BC). Ann. Hum. Biol. 45, 34–43 (2018).
Google Scholar
Star, B. et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207–210 (2011).
Google Scholar
Tine, M. et al. European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation. Nat. Commun. 5, 5770 (2014).
Google Scholar
Chini, V. et al. Genes expressed in bluefin tuna (Thunnus thynnus) liver and gonads. Gene 410, 207–213 (2008).
Google Scholar
Gardner, L. D., Jayasundara, N., Castilho, P. C. & Block, B. Microarray gene expression profiles from mature gonad tissues of Atlantic bluefin tuna, Thunnus thynnus in the Gulf of Mexico. BMC Genomics 13, 530 (2012).
Google Scholar
Kamvar, Z. N., Tabima, J. F. & Grünwald, N. J. Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2, e281 (2014).
Team, R. C. R development core team. RA Lang. Environ. Stat. Comput. 55, 275–286 (2013).
Paradis, E. pegas: An R package for population genetics with an integrated–modular approach. Bioinformatics 26, 419–420 (2010).
Google Scholar
Rousset, F. genepop’007: A complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106 (2008).
Google Scholar
Foll, M. & Gaggiotti, O. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics 180, 977–993 (2008).
Google Scholar
Whitlock, M. C. & Lotterhos, K. E. Reliable detection of loci responsible for local adaptation: Inference of a null model through trimming the distribution of FST. Am. Nat. 186, S24–S36 (2015).
Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. (1995).
Goudet, J. hierfstat, a package for r to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184–186 (2005).
Google Scholar
Waples, R. S. A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conserv. Genet. 7, 167–184 (2006).
Google Scholar
Do, C. et al. NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data. Mol. Ecol. Resour. 14, 209–214 (2014).
Google Scholar
Wang, J., Santiago, E. & Caballero, A. Prediction and estimation of effective population size. Heredity 117, 193–206 (2016).
Google Scholar
Jenkins, T. L., Ellis, C. D., Triantafyllidis, A. & Stevens, J. R. Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster. Evol. Appl. 12, 1881–1899 (2019).
Google Scholar
Jombart, T. et al. Package ‘adegenet’. Bioinform. Appl. Note 24, 1403–1405 (2008).
Google Scholar
Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).
Google Scholar
Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14, 2611–2620 (2005).
Google Scholar
Earl, D. A. & vonHoldt, B. M. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361 (2012).
Kopelman, N. M., Mayzel, J., Jakobsson, M., Rosenberg, N. A. & Mayrose, I. Clumpak: A program for identifying clustering modes and packaging population structure inferences across K. Mol. Ecol. Resour. 15, 1179–1191 (2015).
Google Scholar
Nei, M. Molecular Evolutionary Genetics. (Columbia University Press, 1987). https://doi.org/10.7312/nei-92038.
Frankham, R., Scientist Emeritus Jonathan, Briscoe, D. A. & Ballou, J. D. Introduction to Conservation Genetics. (Cambridge University Press, 2002).
Di Natale, A. Due to the new scientific knowledge, is it time to reconsider the stock composition of the Atlantic bluefin tuna? Collect. Vol. Sci. Pap. ICCAT/Recl. Doc. Sci. CICTA/Colecc. Doc. Cient. CICAA 75, 1282–1292 (2019).
Di Natale, A., Tensek, S. & Pagá García, A. ICCAT Atlantic-wide research programme for bluefin tuna (GBYP) activity report for the last part of phase and the first part of phase (2016–2017). https://www.iccat.int/Documents/CVSP/CV074_2017/n_6/CV074063100.pdf (2017).
Leonard, J. A. Ancient DNA applications for wildlife conservation. Mol. Ecol. 17, 4186–4196 (2008).
Google Scholar
Alter, S. E., Newsome, S. D. & Palumbi, S. R. Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: Insights from ancient DNA and stable isotopes. PLoS ONE 7, e35039 (2012).
Cole, T. L. et al. Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world’s most diverse penguin clade. Mol. Phylogenet. Evol. 131, 72–79 (2019).
Google Scholar
Dures, S. G. et al. A century of decline: Loss of genetic diversity in a southern African lion-conservation stronghold. Divers. Distrib. 25, 870–879 (2019).
Google Scholar
Thomas, J. E. et al. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. Elife 8, (2019).
Colson, I. & Hughes, R. N. Rapid recovery of genetic diversity of dogwhelk (Nucella lapillus L.) populations after local extinction and recolonization contradicts predictions from life-history characteristics. Mol. Ecol. 13, 2223–2233 (2004).
McEachern, M. B., Van Vuren, D. H., Floyd, C. H., May, B. & Eadie, J. M. Bottlenecks and rescue effects in a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis). Conserv. Genet. 12, 285–296 (2011).
Google Scholar
Jangjoo, M., Matter, S. F., Roland, J. & Keyghobadi, N. Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network. Proc. Natl. Acad. Sci. USA 113, 10914–10919 (2016).
Google Scholar
Porch, C. E., Bonhommeau, S., Diaz, G. A., Haritz, A. & Melvin, G. The journey from overfishing to sustainability for Atlantic bluefin tuna, Thunnus thynnus. In The Future of Bluefin Tunas: Ecology, Fisheries Management, and Conservation 3–44 (2019).
Di Natale, A., Macias, D. & Cort, J. L. Atlantic bluefin tuna fisheries: temporal changes in the exploitation pattern, feasibility of sampling, factors that can influence our ability to understand spawning structure and dynamics. Collect. Vol. Sci. Pap. ICCAT/Recl. Doc. Sci. CICTA/Colecc. Doc. Cient. CICAA 76, 354–388 (2020).
Viñas, J. & Tudela, S. A validated methodology for genetic identification of tuna species (genus Thunnus). PLoS ONE 4, e7606 (2009).
MacKenzie, B. R., Mosegaard, H. & Rosenberg, A. A. Impending collapse of bluefin tuna in the northeast Atlantic and Mediterranean. Conserv. Lett. 2, 26–35 (2009).
Google Scholar
Collette, B. B. Bluefin tuna science remains vague. Science 358, 879–880 (2017).
Google Scholar
Nøttestad, L., Boge, E. & Ferter, K. The comeback of Atlantic bluefin tuna (Thunnus thynnus) to Norwegian waters. Fish. Res. 231, 105689 (2020).
Lehodey, P. et al. Climate variability, fish, and fisheries. J. Clim. 19, 5009–5030 (2006).
Google Scholar
Kuwae, M. et al. Sedimentary DNA tracks decadal-centennial changes in fish abundance. Commun Biol 3, 558 (2020).
Google Scholar
Domingues, R. et al. Variability of preferred environmental conditions for Atlantic bluefin tuna (Thunnus thynnus) larvae in the Gulf of Mexico during 1993–2011. Fish. Oceanogr. 25, 320–336 (2016).
Google Scholar
Reglero, P. et al. Pelagic habitat and offspring survival in the eastern stock of Atlantic bluefin tuna. ICES J. Mar. Sci. 76, 549–558 (2019).
Google Scholar
Faillettaz, R., Beaugrand, G., Goberville, E. & Kirby, R. R. Atlantic Multidecadal Oscillations drive the basin-scale distribution of Atlantic bluefin tuna. Sci. Adv. 5, eaar6993 (2019).
Hanke, A. et al. Stock mixing rates of bluefin tuna from Canadian landings: 1975–2015. Collect. Vol. Sci. Pap. ICCAT/Recl. Doc. Sci. CICTA/Colecc. Doc. Cient. CICAA 74, 2622–2634 (2017).
Fraser, D. J. et al. Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems. Mol. Ecol. 16, 3866–3889 (2007).
Google Scholar
Albrechtsen, A., Nielsen, F. C. & Nielsen, R. Ascertainment biases in SNP chips affect measures of population divergence. Mol. Biol. Evol. 27, 2534–2547 (2010).
Google Scholar
Clark, A. G., Hubisz, M. J., Bustamante, C. D., Williamson, S. H. & Nielsen, R. Ascertainment bias in studies of human genome-wide polymorphism. Genome Res. 15, 1496–1502 (2005).
Google Scholar
Lachance, J. & Tishkoff, S. A. SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it. BioEssays 35, 780–786 (2013).
Google Scholar
Hofreiter, M. et al. The future of ancient DNA: Technical advances and conceptual shifts. BioEssays 37, 284–293 (2015).
Google Scholar
Malomane, D. K. et al. Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies. BMC Genomics 19, 22 (2018).
Google Scholar
Bradbury, I. R. et al. Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod, Gadus morhua. Mol. Ecol. Resour. 11, 218–225 (2011).
Google Scholar
Lou, R. N., Jacobs, A., Wilder, A. & Therkildsen, N. O. A beginner’s guide to low-coverage whole genome sequencing for population genomics. Mol. Ecol. https://doi.org/10.1111/mec.16077 (2020).
Google Scholar
Schlötterer, C. Hitchhiking mapping–functional genomics from the population genetics perspective. Trends Genet. 19, 32–38 (2003).
Google Scholar
Source: Ecology - nature.com