Marine Biology

, 166:16 | Cite as

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

  • Claudia JungeEmail author
  • Stephen C. Donnellan
  • Charlie Huveneers
  • Corey J. A. Bradshaw
  • Alexis Simon
  • Michael Drew
  • Clinton Duffy
  • Grant Johnson
  • Geremy Cliff
  • Matias Braccini
  • Scott C. Cutmore
  • Paul Butcher
  • Rory McAuley
  • Vic Peddemors
  • Paul Rogers
  • Bronwyn M. Gillanders
Original paper


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.



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 ( of the Integrated Marine Observing System (IMOS;—IMOS is a national collaborative research infrastructure supported by Australian Government.

Compliance with ethical standards

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).

Conflict of interest

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.

Supplementary material

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Supplementary material 1 (PDF 1911 kb)
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Supplementary material 5 (PDF 621 kb)
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Supplementary material 9 (PDF 1041 kb)
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Supplementary material 10 (PDF 1092 kb)
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Supplementary material 11 (PDF 878 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Claudia Junge
    • 1
    • 2
    • 3
    Email author
  • Stephen C. Donnellan
    • 4
    • 5
  • Charlie Huveneers
    • 6
    • 7
  • Corey J. A. Bradshaw
    • 8
  • Alexis Simon
    • 1
    • 9
  • Michael Drew
    • 7
  • Clinton Duffy
    • 10
  • Grant Johnson
    • 11
  • Geremy Cliff
    • 12
  • Matias Braccini
    • 13
  • Scott C. Cutmore
    • 14
  • Paul Butcher
    • 15
  • Rory McAuley
    • 13
  • Vic Peddemors
    • 16
  • Paul Rogers
    • 6
  • Bronwyn M. Gillanders
    • 1
    • 2
  1. 1.Southern Seas Ecology Laboratories, School of Biological SciencesThe University of AdelaideAdelaideAustralia
  2. 2.The Environment Institute and School of Biological Sciences, The University of AdelaideAdelaideAustralia
  3. 3.Havforskningsinstituttet (Institute of Marine Research, IMR)TromsöNorway
  4. 4.Australian Centre for Evolutionary Biology and BiodiversityThe University of AdelaideAdelaideAustralia
  5. 5.South Australian MuseumAdelaideAustralia
  6. 6.South Australian Research and Development InstituteAdelaideAustralia
  7. 7.Southern Shark Ecology Group, College of Science and EngineeringFlinders UniversityAdelaideAustralia
  8. 8.Global Ecology, College of Science and EngineeringFlinders UniversityAdelaideAustralia
  9. 9.École Normale Supérieure, Formation Interuniversitaire de BiologieParis Cedex 05France
  10. 10.Aquatic and Reporting Unit, Department of ConservationAucklandNew Zealand
  11. 11.Department of Primary Industry and FisheriesAquatic Resource Research UnitDarwinAustralia
  12. 12.KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa and Biomedical Resource UnitUniversity of KwaZulu-NatalDurbanSouth Africa
  13. 13.Western Australian Fisheries and Marine Research LaboratoriesNorth BeachAustralia
  14. 14.School of Biological SciencesThe University of QueenslandSt LuciaAustralia
  15. 15.New South Wales Department of Industry, Department of Primary IndustriesDPI FisheriesCoffs HarbourAustralia
  16. 16.New South Wales of Department of Primary IndustriesSydney Institute of Marine ScienceMosmanAustralia

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