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Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia)

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Abstract

Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RAD-sequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e., PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.

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Data availability

Raw sequences are available in Genbank under BioProject ID PRJNA689941 and SRA accession number SRA PRJNA689941. The mitochondrial ORF sequences, microsatellite genotypes and SliM scripts are available in Zenodo: https://zenodo.org/record/4748346. The scripts used for SLiM simulations are also available at: https://gitlab.osupytheas.fr/aurelle/slim-simulations. The scripts used for the analyses of RAD-sequencing data are available at: https://gitlab.osupytheas.fr/aurelle/rad_pocillopora.git

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Acknowledgements

We thank Nicolas Fernandez and Béatrice Loriod from the Marseille TGML platform for their invaluable help and advices with the preparation of the RAD libraries. We thank the team of the MGX platform for the sequencing of the RAD libraries. We acknowledge Stéphanie Rialle, Maurine Bonabaud from the MGX sequencing platform (CNRS, Montpellier, France) for help with data production and quality controls. The authors thank the UMR 8199 LIGAN-PM Genomics group (Lille, France, especially Véronique Dhennin), who belongs to the ‘Federation de Recherche’ 3508 Labex EGID (European Genomics Institute for Diabetes; ANR-10-LABX-46) and was supported by the ANR Equipex 2010 session (ANR-10-EQPX-07-01; ‘LIGAN-PM’). The LIGAN-PM Genomics platform (Lille, France) is also supported by the FEDER and the Region Nord-Pas-de-Calais-Picardie. We acknowledge the staff of the “Cluster de calcul intensif HPC” Platform of the OSU Institut Pythéas (Aix-Marseille Université, INSU-CNRS) for facilitating the use of computing facilities. We gratefully acknowledge Julien Lecubin and Christophe Yohia from the Informatic Service of Pythéas Institute (SIP) for their technical assistance. We thank the molecular biology service of the IMBE. We are grateful to the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12) for providing help and computing resources.

Funding

This work is a contribution to the Labex OT-Med (n° ANR-11-LABX-0061) funded by the French Government “Investissements d’Avenir” program of the French National Research Agency (ANR) through the A*MIDEX project (n° ANR-11-IDEX-0001–02). This project has been funded by the ADACNI program of the French National Research Agency (ANR) (project n°ANR-12-ADAP-0016; http://adacni.imbe.fr). The project leading to this publication has received funding from the European FEDER Fund under project 1166–39417. The authors acknowledge the financial support from the France Génomique National Infrastructure, funded as part of “Investissement d’Avenir” program managed by the Agence Nationale de la Recherche (contract ANR-10-INBS-09). This study was set within the framework of the Laboratoire d’Excellence (LABEX) TULIP (ANR-10-LABX-41).

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Authors and Affiliations

  1. Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France

    Didier Aurelle, Marine Pratlong & Lauric Reynes

  2. Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France

    Didier Aurelle & Anne Haguenauer

  3. Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, 75005, Paris, France

    Didier Aurelle

  4. Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France

    Marine Pratlong

  5. UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, Saint-Denis La Réunion, France

    Nicolas Oury, Pauline Gélin, Hélène Magalon & Mehdi Adjeroud

  6. PSL Université Paris, USR CRIOBE—EPHE-UPVD-CNRS, 3278, Perpignan, France

    Anne Haguenauer & Mehdi Adjeroud

  7. Laboratoire d’Excellence “CORAIL”, Paris, France

    Pauline Gélin, Hélène Magalon & Mehdi Adjeroud

  8. Centre de Ressources Biologiques Marines, Sorbonne Universités, UPMC Univ Paris 06, Observatoire Océanologique, UMS 2348, Banyuls/Mer, France

    Pascal Romans

  9. IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Montpellier France, Montpellier, France

    Jeremie Vidal-Dupiol & Eve Toulza

  10. Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, 123, Muscat, Sultanate of Oman

    Michel Claereboudt

  11. Laboratoire Cogitamus, Paris, France

    Camille Noûs

  12. ISEM, Univ Montpellier, CNRS, IRD, EPHE, 34000, Montpellier, France

    François Bonhomme

  13. EIO, Univ Polynesie Francaise, ILM, IRD, Ifremer, 98719, Tahiti, French Polynesia, France

    Guillaume Mitta

  14. Aix Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005, Marseille, France

    Pierre Pontarotti

  15. SNC5039 CNRS, 19–21 Boulevard Jean Moulin, 13005, Marseille, France

    Pierre Pontarotti

  16. Campus de Luminy—Oceanomed, 13288, Marseille cedex 09, France

    Didier Aurelle

  17. Equipe Evolution Biologique et Modélisation, Marseille, France

    Marine Pratlong

  18. IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France

    Eve Toulza & Guillaume Mitta

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  1. Didier Aurelle
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  2. Marine Pratlong
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  3. Nicolas Oury
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Contributions

D.A. G.M. and P.P. designed the project. M.P., A.H., N.O. and H.M. performed the molecular analyses. J.V.D., M.A. and G.M. were responsible for the sampling. D.A., M.P., H.M., N.O., L.R., F.B. analysed the data. All authors reviewed the manuscript.

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Correspondence to Didier Aurelle.

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Aurelle, D., Pratlong, M., Oury, N. et al. Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia). Genetica 150, 247–262 (2022). https://doi.org/10.1007/s10709-022-00165-7

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