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Comparative population genomics confirms little population structure in two commercially targeted carcharhinid sharks

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Abstract

Many shark species are at risk of overexploitation due to their high economic value, slow maturation, and low recruitment compared to most teleosts. However, there is insufficient knowledge about population structure at different spatial scales necessary to optimise fisheries models. We used single-nucleotide polymorphisms (SNPs) obtained through complexity-reduction genome sequencing to quantify the population structure of two highly mobile and commercially fished shark species: bronze whalers (Carcharhinus brachyurus) and dusky sharks (C. obscurus). We applied a comprehensive approach to test several population-structure hypotheses and signal consistency across methods and marker type. We found that C. obscurus was panmictic across Australia and Indonesia and across the Indian Ocean to South Africa based on neutral loci, whereas for C. brachyurus, the westernmost Australian samples appeared to be separate from the rest. The southernmost east Australian samples indicated some difference from the rest of Australia and New Zealand based on candidate loci for C. brachyurus, and potentially also C. obscurus; however, the lack of a reference genome makes the interpretation difficult. Despite similar patterns in both species, subtle and potentially important structure differences emphasise the importance of studying each target species independently rather than assuming similar patterns from closely related species with similar dispersal abilities, as well as considering different marker types in future studies. We found evidence of connectivity across the regions sampled, suggesting that the cumulative effects of regional fisheries and the potential for cross-jurisdictional fishery assessments and management should be considered for Australian, Indonesian, and New Zealand populations.

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Fig. 1
Fig. 2
Fig. 3

(modified from Duffy and Gordon 2003a) with sample sets indicated: 3–W_SW1, 5–S_GAB, 6–S_SG, 7–S_GSV, 8–S_Vic, 9–E_South, and 10–E_NZ (see Table 1 for abbreviation definitions)

Fig. 4

(modified from Musick et al. 2009) with the sample sets indicated: 1–W_North, 2–W_Perth, 3–W_SW1, 4–W_SW2, 5–S_GAB, 6–S_SG, 7–S_GSV, 9–E_South, 11–E_Mid, 12–E_North, 13–E_NORF, 14–N_IDN, and 15–N_NT) (see Table 1 for abbreviation definitions)

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Acknowledgements

We thank W White, M Scott, S Tindale, J Ovenden, and Auckland museum for providing samples, R Keane for the distance estimations, A Loi for help in the lab, and JCA Pistevos for the shark artwork in Figs. 3 and 4. The project received funding from the Australian Research Council (LP120100652), the Neiser Foundation, and the Nature Foundation of South Australia. BMG and CJAB were supported by ARC Future Fellowships FT100100767 and FT110100306, respectively). Unpublished acoustic tracking data was sourced from the Acoustic Tracking Database (animaltracking.aodn.org.au) of the Integrated Marine Observing System (IMOS; www.imos.org.au)—IMOS is a national collaborative research infrastructure supported by Australian Government.

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Authors and Affiliations

  1. Southern Seas Ecology Laboratories, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia

    Claudia Junge, Alexis Simon & Bronwyn M. Gillanders

  2. The Environment Institute and School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia

    Claudia Junge & Bronwyn M. Gillanders

  3. Havforskningsinstituttet (Institute of Marine Research, IMR), Postboks 6606, Framsenteret, Langnes, 9296, Tromsö, Norway

    Claudia Junge

  4. Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, SA, 5005, Australia

    Stephen C. Donnellan

  5. South Australian Museum, North Terrace, Adelaide, SA, 5000, Australia

    Stephen C. Donnellan

  6. South Australian Research and Development Institute, Adelaide, SA, 5024, Australia

    Charlie Huveneers & Paul Rogers

  7. Southern Shark Ecology Group, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia

    Charlie Huveneers & Michael Drew

  8. Global Ecology, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia

    Corey J. A. Bradshaw

  9. École Normale Supérieure, Formation Interuniversitaire de Biologie, 75230, Paris Cedex 05, France

    Alexis Simon

  10. Aquatic and Reporting Unit, Department of Conservation, Auckland, 1010, New Zealand

    Clinton Duffy

  11. Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, GPO Box 3000, Darwin, NT, 0801, Australia

    Grant Johnson

  12. KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa and Biomedical Resource Unit, University of KwaZulu-Natal, Durban, South Africa

    Geremy Cliff

  13. Western Australian Fisheries and Marine Research Laboratories, PO Box 20, North Beach, WA, 6920, Australia

    Matias Braccini & Rory McAuley

  14. School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia

    Scott C. Cutmore

  15. New South Wales Department of Industry, Department of Primary Industries, DPI Fisheries, Coffs Harbour, NSW, 2450, Australia

    Paul Butcher

  16. New South Wales of Department of Primary Industries, Sydney Institute of Marine Science, 19 Chowder Bay Road, Mosman, NSW, 2088, Australia

    Vic Peddemors

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  1. Claudia Junge
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Correspondence to Claudia Junge.

Ethics declarations

No sharks were sacrificed for this study. All tissue samples were approximately 2 × 2 cm and were taken from pectoral fins (unless otherwise indicated). All samples were obtained legally (see Electronic Supplementary Material 10).

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All authors declare that they have no conflict of interest and all applicable international, national and/or institutional guidelines for the care and use of animals were followed.

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Junge, C., Donnellan, S.C., Huveneers, C. et al. Comparative population genomics confirms little population structure in two commercially targeted carcharhinid sharks. Mar Biol 166, 16 (2019). https://doi.org/10.1007/s00227-018-3454-4

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