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Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi

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Abstract

Genetic differentiation is characteristically weak in marine species making assessments of population connectivity and structure difficult. However, the advent of genomic methods has increased genetic resolution, enabling studies to detect weak, but significant population differentiation within marine species. With an increasing number of studies employing high resolution genome-wide techniques, we are realising that the connectivity of marine populations is often complex and quantifying this complexity can provide an understanding of the processes shaping marine species genetic structure and to inform long-term, sustainable management strategies. This study aims to assess the genetic structure, connectivity, and local adaptation of the Eastern Rock Lobster (Sagmariasus verreauxi), which has a maximum pelagic larval duration of 12 months and inhabits both subtropical and temperate environments. We used 645 neutral and 15 outlier SNPs to genotype lobsters collected from the only two known breeding populations and a third episodic population—encompassing S. verreauxi’s known range. Through examination of the neutral SNP panel, we detected genetic homogeneity across the three regions, which extended across the Tasman Sea encompassing both Australian and New Zealand populations. We discuss differences in neutral genetic signature of S. verreauxi and a closely related, co-distributed rock lobster, Jasus edwardsii, determining a regional pattern of genetic disparity between the species, which have largely similar life histories. Examination of the outlier SNP panel detected weak genetic differentiation between the three regions. Outlier SNPs showed promise in assigning individuals to their sampling origin and may prove useful as a management tool for species exhibiting genetic homogeneity.

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Data accessibility

Reference loci sequences are available through Dryad, https://doi.org/10.5061/dryad.d4q57s5.

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Acknowledgements

We would like to thank Marcus Miller and Giles Ballinger for collecting and organising the New South Wales S. verreauxi samples, which were obtained during fishery independent spawning stock survey and commercial catch observer survey routinely undertaken by the New South Wales Department of Primary Industries. We thank Irina Ilyushkina and Darrel Sykes for collection and organisation of New Zealand S. verreauxi samples. Thanks to the Tasmanian Rock Lobster Fishing Industry, University of Tasmania students, dive team and recreational divers that collected specimens in Tasmania. We are grateful to Michael Amor for laboratory assistance and Cecilia Villacorta-Rath for assistance in RAD-LOCI pipeline development. We thank the editor and two reviewers for their time and their constructive feedback.

Funding

This research was funded by ARC DP 150101491, a La Trobe University Securing Food, Water and Environment Grant, the Holsworth Wildlife Research Endowment, the Institute for Marine and Antarctic Studies, the NSW Department of Primary Industries and shareholders in the NSW Rock Lobster Fishery.

Author information

Authors and Affiliations

  1. Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia

    Laura N. Woodings, Nicholas P. Murphy & Jan M. Strugnell

  2. Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK

    Stephen R. Doyle

  3. Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, VIC, 3086, Australia

    Nathan E. Hall

  4. Genomics Research Platform, La Trobe University, Melbourne, VIC, 3086, Australia

    Andrew J. Robinson

  5. Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Melbourne, VIC, 3053, Australia

    Andrew J. Robinson

  6. NSW Department of Primary Industries, Sydney Institute of Marine Science, Mosman, NSW, 2088, Australia

    Geoffrey W. Liggins

  7. Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7001, Australia

    Bridget S. Green

  8. Department of Molecular and Cell Biology, and Comparative Genomics Centre, James Cook University, Townsville, QLD, 4810, Australia

    Ira R. Cooke

  9. School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand

    James J. Bell

  10. Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia

    Jan M. Strugnell

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  1. Laura N. Woodings
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  2. Nicholas P. Murphy
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  3. Stephen R. Doyle
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  4. Nathan E. Hall
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  5. Andrew J. Robinson
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  6. Geoffrey W. Liggins
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  7. Bridget S. Green
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  8. Ira R. Cooke
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  9. James J. Bell
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  10. Jan M. Strugnell
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Corresponding author

Correspondence to Laura N. Woodings.

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The authors declare that they have no conflict of interest.

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All applicable international, national, and/or institutional guidelines for the care and use of animals were followed and all necessary approvals were obtained.

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Responsible Editor: O. Puebla.

Reviewed by N. Jeffery and an undisclosed expert.

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Woodings, L.N., Murphy, N.P., Doyle, S.R. et al. Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi. Mar Biol 165, 185 (2018). https://doi.org/10.1007/s00227-018-3443-7

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  • DOI: https://doi.org/10.1007/s00227-018-3443-7

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