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Sympatric species of coral trout (Plectropomus) show contrasting patterns of genomic structure across isolated atoll reefs

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Abstract

Understanding patterns of connectivity across remote atoll reefs is important for managing fishery target species, as they often have small population sizes and limited options for replenishment in the event of localised decline. In this study, we used a comprehensive hierarchical sampling design combined with reduced representation genotyping to compare the population genomics of two sympatric species of coral trout (Plectropomus) within and between three isolated offshore atoll reef systems in north-western Australia. The blue spot coral trout, Plectropomus laevis (8979 single nucleotide polymorphisms—SNPs, 223 individuals, 25 sites) and the passionfruit coral trout, P. areolatus (3702 SNPs, 452 individuals, 20 sites) showed high levels of connectivity within reef systems and restricted connectivity between reef systems, indicating that biological stocks primarily occur at the scale of each reef system. Despite being closely related and co-managed species, inter-specific variation in the magnitude of genetic structure was notable. Plectropomus areolatus at the southern-most reef system display modest genetic structure with populations ~ 450 km to the north, whilst P. laevis at the same location show a level of genetic divergence that reflects deep historical isolation. Our results provide the most comprehensive assessment of genetic connectivity across these remote atoll reefs, facilitating management advice that reflect empirically determined population dynamics for these species. We identify contrasting patterns of genetic connectivity among closely related sympatric species, and highlight the role of extrinsic (e.g., geography/environment) and intrinsic (e.g., life history) factors in shaping population dynamics.

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Data availability

The datasets and code associated with this study are available from the corresponding author upon reasonable request.

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Acknowledgements

This research was supported by funding and logistical support from the Department of Primary Industries and Regional Development, Government of Western Australia. The authors would like to thank those involved in sample collection, including Sam Moyle, Craig Skepper, Daniel Yeo, Cameron Dawes-Smith, as well as the captain and crew of the MV Reel Teaser (Chris Rushford, Tracy Newton and Ross Newton), PV Warndoom (Department of Biodiversity, Conservations and Attractions), PV Cape Nelson (Australian Border Force) and HMAS Broome II (Royal Australian Navy). For research permits we would like to thank Parks Australia and the Department of Primary Industries and Regional Development.

Funding

This study was funded by the Department of Primary Industries and Regional Development, Government of Western Australia. The authors have no non-financial competing interests to declare.

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Authors and Affiliations

  1. Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, 6920, Australia

    Samuel D. Payet, Stephen J. Newman, Kelvin J. Rushworth, Corey B. Wakefield & Michael J. Travers

  2. Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia

    Joseph D. DiBattista

  3. Australian Museum Research Institute, Australian Museum, 1 William St., Sydney, NSW, 2010, Australia

    Joseph D. DiBattista

  4. Department of Biodiversity Conservation and Attractions, 17 Dick Perry Ave., Kensington, 6151, Australia

    Richard D. Evans

  5. Oceans Institute, The University of Western Australia, Crawley, WA, 6009, Australia

    Richard D. Evans

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Correspondence to Samuel D. Payet.

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In Western Australia, the Animal Welfare Act 2002 does not require the Department of Primary Industries and Regional Development (DPIRD) to obtain a permit to use animals for scientific purposes unless the species are outside the provisions of the Fish Resources Management Act 1994 and Fish Resources Management Regulations 1995. Nonetheless, all sampling was undertaken in strict adherence to the DPIRD Policy for the handling, use and care of marine fauna for research purposes. Samples were collected under the Commonwealth Government Permits AU-COM2018-420 and AU-COM2020-472, and Australian Marine Park Activity Permit PA2019-00095-1.

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Payet, S.D., DiBattista, J.D., Newman, S.J. et al. Sympatric species of coral trout (Plectropomus) show contrasting patterns of genomic structure across isolated atoll reefs. Rev Fish Biol Fisheries 34, 239–252 (2024). https://doi.org/10.1007/s11160-023-09809-z

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