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Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean

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  • 1.

    Pauly, D. et al. Towards sustainability in world fisheries. Nature 418, 689–695 (2002).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 2.

    Butchart, S. H. M. et al. Global biodiversity: Indicators of recent declines. Science 328, 1164–1168 (2010).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 3.

    Pinsky, M. L. & Palumbi, S. R. Meta-analysis reveals lower genetic diversity in overfished populations. Mol. Ecol. 23, 29–39 (2014).

    PubMed 
    Article 

    Google Scholar 

  • 4.

    Neubauer, P., Jensen, O. P., Hutchings, J. A. & Baum, J. K. Resilience and recovery of overexploited marine populations. Science 340, 347–349 (2013).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 5.

    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).

  • 6.

    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).

    PubMed 
    Article 

    Google Scholar 

  • 7.

    Schwerdtner Máñez, K. et al. The future of the oceans past: Towards a global marine historical research initiative. PLoS ONE 9, e101466 (2014).

  • 8.

    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).

  • 9.

    Oosting, T. et al. Unlocking the potential of ancient fish DNA in the genomic era. Evol. Appl. 12, 1513–1522 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 10.

    Heino, M., Pauli, B. D. & Dieckmann, U. Fisheries-induced evolution. Annu. Rev. Ecol. Evol. Syst. 46, 461–480 (2015).

    Article 

    Google Scholar 

  • 11.

    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).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 12.

    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).

  • 13.

    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.

  • 14.

    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).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 15.

    Rodríguez-Ezpeleta, N. et al. Determining natal origin for improved management of Atlantic bluefin tuna. Front. Ecol. Environ. 17, 439–444 (2019).

    Article 

    Google Scholar 

  • 16.

    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).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 17.

    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).

  • 18.

    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).

  • 19.

    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).

  • 20.

    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).

  • 21.

    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).

  • 22.

    Worm, B. & Tittensor, D. P. Range contraction in large pelagic predators. Proc. Natl. Acad. Sci. USA 108, 11942–11947 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 23.

    Fromentin, J.-M. Lessons from the past: Investigating historical data from bluefin tuna fisheries. Fish Fish. 10, 197–216 (2009).

    Article 

    Google Scholar 

  • 24.

    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).

    Article 

    Google Scholar 

  • 25.

    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).

  • 26.

    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).

    Article 

    Google Scholar 

  • 27.

    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).

  • 28.

    Anderson, C. N. K. et al. Why fishing magnifies fluctuations in fish abundance. Nature 452, 835–839 (2008).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 29.

    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).

  • 30.

    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).

  • 31.

    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).

  • 32.

    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).

  • 33.

    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).

    PubMed 
    Article 

    Google Scholar 

  • 34.

    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).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 35.

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 36.

    Bonanomi, S. et al. Archived DNA reveals fisheries and climate induced collapse of a major fishery. Sci. Rep. 5, 15395 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 37.

    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).

    CAS 
    Article 

    Google Scholar 

  • 38.

    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).

  • 39.

    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).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 40.

    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).

  • 41.

    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).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 42.

    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).

  • 43.

    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).

  • 44.

    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).

    ADS 
    Article 

    Google Scholar 

  • 45.

    Bernal, D. & Monclova, A. Pescar con Arte. Fenicios y romanos en el origen de los aparejos andaluces. Monografías del Proyecto Sagena 3, (2011).

  • 46.

    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).

    Article 

    Google Scholar 

  • 47.

    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).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 48.

    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).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 49.

    Serventi, P. et al. Iron Age Italic population genetics: The Piceni from Novilara (8th–7th century BC). Ann. Hum. Biol. 45, 34–43 (2018).

    PubMed 
    Article 

    Google Scholar 

  • 50.

    Star, B. et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207–210 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 51.

    Tine, M. et al. European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation. Nat. Commun. 5, 5770 (2014).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 52.

    Chini, V. et al. Genes expressed in bluefin tuna (Thunnus thynnus) liver and gonads. Gene 410, 207–213 (2008).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 53.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 54.

    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).

  • 55.

    Team, R. C. R development core team. RA Lang. Environ. Stat. Comput. 55, 275–286 (2013).

  • 56.

    Paradis, E. pegas: An R package for population genetics with an integrated–modular approach. Bioinformatics 26, 419–420 (2010).

    CAS 
    Article 

    Google Scholar 

  • 57.

    Rousset, F. genepop’007: A complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106 (2008).

    Article 

    Google Scholar 

  • 58.

    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).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 59.

    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).

    PubMed 
    Article 

    Google Scholar 

  • 60.

    Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. (1995).

  • 61.

    Goudet, J. hierfstat, a package for r to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184–186 (2005).

    Article 

    Google Scholar 

  • 62.

    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).

    Article 

    Google Scholar 

  • 63.

    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).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 64.

    Wang, J., Santiago, E. & Caballero, A. Prediction and estimation of effective population size. Heredity 117, 193–206 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 65.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 66.

    Jombart, T. et al. Package ‘adegenet’. Bioinform. Appl. Note 24, 1403–1405 (2008).

    CAS 
    Article 

    Google Scholar 

  • 67.

    Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 68.

    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).

    CAS 
    Article 

    Google Scholar 

  • 69.

    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).

  • 70.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 71.

    Nei, M. Molecular Evolutionary Genetics. (Columbia University Press, 1987). https://doi.org/10.7312/nei-92038.

  • 72.

    Frankham, R., Scientist Emeritus Jonathan, Briscoe, D. A. & Ballou, J. D. Introduction to Conservation Genetics. (Cambridge University Press, 2002).

  • 73.

    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).

  • 74.

    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).

  • 75.

    Leonard, J. A. Ancient DNA applications for wildlife conservation. Mol. Ecol. 17, 4186–4196 (2008).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 76.

    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).

  • 77.

    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).

    PubMed 
    Article 

    Google Scholar 

  • 78.

    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).

    Article 

    Google Scholar 

  • 79.

    Thomas, J. E. et al. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. Elife 8, (2019).

  • 80.

    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).

  • 81.

    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).

    Article 

    Google Scholar 

  • 82.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 83.

    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).

  • 84.

    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).

  • 85.

    Viñas, J. & Tudela, S. A validated methodology for genetic identification of tuna species (genus Thunnus). PLoS ONE 4, e7606 (2009).

  • 86.

    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).

    Article 

    Google Scholar 

  • 87.

    Collette, B. B. Bluefin tuna science remains vague. Science 358, 879–880 (2017).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • 88.

    Nøttestad, L., Boge, E. & Ferter, K. The comeback of Atlantic bluefin tuna (Thunnus thynnus) to Norwegian waters. Fish. Res. 231, 105689 (2020).

  • 89.

    Lehodey, P. et al. Climate variability, fish, and fisheries. J. Clim. 19, 5009–5030 (2006).

    ADS 
    Article 

    Google Scholar 

  • 90.

    Kuwae, M. et al. Sedimentary DNA tracks decadal-centennial changes in fish abundance. Commun Biol 3, 558 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 91.

    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).

    Article 

    Google Scholar 

  • 92.

    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).

    Article 

    Google Scholar 

  • 93.

    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).

  • 94.

    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).

  • 95.

    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).

    PubMed 
    Article 

    Google Scholar 

  • 96.

    Albrechtsen, A., Nielsen, F. C. & Nielsen, R. Ascertainment biases in SNP chips affect measures of population divergence. Mol. Biol. Evol. 27, 2534–2547 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 97.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 98.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 99.

    Hofreiter, M. et al. The future of ancient DNA: Technical advances and conceptual shifts. BioEssays 37, 284–293 (2015).

    PubMed 
    Article 

    Google Scholar 

  • 100.

    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).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 101.

    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).

    PubMed 
    Article 

    Google Scholar 

  • 102.

    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).

    Article 

    Google Scholar 

  • 103.

    Schlötterer, C. Hitchhiking mapping–functional genomics from the population genetics perspective. Trends Genet. 19, 32–38 (2003).

    PubMed 
    Article 

    Google Scholar 


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