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Heterogeneous microgeographic genetic structure of the common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean: biogeographic barriers and environmental factors

Heredity volume 131, pages 292–305 (2023)Cite this article

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Abstract

Knowledge of genetic structure at the finest level is essential for the conservation of genetic resources. Despite no visible barriers limiting gene flow, significant genetic structure has been shown in marine species. The common cockle (Cerastoderma edule) is a bivalve of great commercial and ecological value inhabiting the Northeast Atlantic Ocean. Previous population genomics studies demonstrated significant structure both across the Northeast Atlantic, but also within small geographic areas, highlighting the need to investigate fine-scale structuring. Here, we analysed two geographic areas that could represent opposite models of structure for the species: (1) the SW British Isles region, highly fragmented due to biogeographic barriers, and (2) Galicia (NW Spain), a putative homogeneous region. A total of 9250 SNPs genotyped by 2b-RAD on 599 individuals from 22 natural beds were used for the analysis. The entire SNP dataset mostly confirmed previous observations related to genetic diversity and differentiation; however, neutral and divergent SNP outlier datasets enabled disentangling physical barriers from abiotic environmental factors structuring both regions. While Galicia showed a homogeneous structure, the SW British Isles region was split into four reliable genetic regions related to oceanographic features and abiotic factors, such as sea surface salinity and temperature. The information gathered supports specific management policies of cockle resources in SW British and Galician regions also considering their particular socio-economic characteristics; further, these new data will be added to those recently reported in the Northeast Atlantic to define sustainable management actions across the whole distribution range of the species.

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Fig. 1: Geographical distribution of the Cerastoderma edule beds analysed in the present study.
Fig. 2: Population structure of Cerastoderma edule at different geographical scales using fastSTRUCTURE.
Fig. 3: Representation of discriminant analysis of principal components (DAPC) results using complete SNP datasets.

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Data availability

Data for this study are available at Dryad Digital Repository (https://doi.org/10.5061/dryad.xpnvx0kmr) and Supplementary material.

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Acknowledgements

The authors wish to thank L. Insua, S. Sánchez-Darriba and S. Gómez from the ACUIGEN group (USC) for their technical support. Supercomputing Center of Galicia (http://www.cesga.es) provided computing facilities for genotyping. A. Casanova (ACC) was funded by a Xunta de Galicia-Campus Terra postdoctoral fellow. The authors are also indebted to COCKLES Interreg European project partners who provided samples included in this study. Finally, the authors are grateful to Prof. S. Goodacre, Dr X. Zhan and three anonymous reviewers for their helpful comments on the earlier version of this manuscript.

Funding

This study has been supported by the COCKLES project (grant number: EAPA_458/2016) of the INTERREG EUROPEAN PROGRAMME and the NERC-SHEAR project (NE/W001217/1).

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Authors and Affiliations

  1. Department of Zoology, Genetics and Physics Anthropology, ACUIGEN Group, Faculty of Veterinary, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain

    Manuel Vera, Francesco Maroso, Miguel Hermida, Andrés Blanco, Adrián Casanova, Carmen Bouza & Paulino Martínez

  2. School of Ocean Sciences, Marine Centre Wales, Bangor University, Menai Bridge, UK

    Sophie B. Wilmes, Peter E. Robins & Shelagh K. Malham

  3. Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620, Vilanova de Arousa, Spain

    David Iglesias, Asunción Cao & Antonio Villalba

  4. School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, North Mall, Cork, Ireland

    Sarah C. Culloty, Kate Mahony & Sharon Lynch

  5. Environmental Research Institute, University College Cork, Cork, Ireland

    Sarah C. Culloty, Kate Mahony & Sharon Lynch

  6. MaREI Centre, Environmental Research Institute, University College Cork, Cork, Ireland

    Sarah C. Culloty

  7. UNICAEN – UMR BOREA “Biologie des ORganismes et Ecosystèmes Aquatiques” MNHN, UPMC, UCBN, CNRS-7208, IRD-207, University of Caen, Caen, France

    Francis Orvain

  8. Departamento de Ciencias de la Vida, Universidad de Alcalá, 28871, Alcalá de Henares, Spain

    Antonio Villalba

  9. Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620, Plentzia, Basque Country, Spain

    Antonio Villalba

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Contributions

MV, AV and PM designed and supervised the study. DI, AC, KM, FO, SKM and SL performed field collections. PM, SCC, SL, PER, SKM and FO provided funding. FM, MH and AB analysed bioinformatically genomic sequences and created genotyping files. SBW and PER provided information about oceanography, environmental variables and developed geographic maps included in the figures. MV, CB, ACC, AB and PM performed the genetic analyses. MV and PM wrote the manuscript with contributions from all authors. All of them read the manuscript and gave their approval.

Corresponding authors

Correspondence to Manuel Vera or Paulino Martínez.

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Vera, M., Wilmes, S.B., Maroso, F. et al. Heterogeneous microgeographic genetic structure of the common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean: biogeographic barriers and environmental factors. Heredity 131, 292–305 (2023). https://doi.org/10.1038/s41437-023-00646-1

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