From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals

Nicolas Oury, Cyril Noel, Stefano Mona, Didier Aurelle, Helene Magalon

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.
Original languageEnglish (US)
Pages (from-to)107803
JournalMolecular Phylogenetics and Evolution
StatePublished - May 11 2023
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2023-06-21
Acknowledgements: This work was supported in part through grants from the LabEx CORAIL (AI PocillopoRAD). Coral sampling in New Caledonia was carried out during COBELO (, BIBELOT (, and CHEST ( oceanographic campaigns on board of RV Alis (IRD), and in the northeastern and northwestern of Madagascar during MAD ( oceanographic campaign on board of RV Antea (IRD). Sampling in Reunion Island was supported by program CONPOCINPA (LabEx CORAIL fund); in the south of Madagascar in collaboration with the Institut Halieutique des Sciences Marines (Tulear); and in Rodrigues Island with the collaboration of the Rodrigues Regional Assembly and the South-East Marine Protected Area supported by project Biodiversity (POCT FEDER fund); in Europa, Juan de Nova, and Glorioso Islands by program BIORECIE (financial supports from INEE, INSU, IRD, AAMP, FRB, TAAF, and the foundation Veolia Environnement); in Tromelin Island by program ORCIE (INEE), and in Mayotte by program SIREME (FED). HM thanks all the buddies who helped in photographs during diving (J. Butscher, S. Andréfouët, L. Bigot, and M. Pinault). We acknowledge the Plateforme Gentyane (microsatellite genotyping) of the Institut National de Recherche pour l’Agriculture, l’alimentation et l’Environnement (INRAE, Clermont-Ferrand, France), GenoScreen (Sanger sequencing; Lille, France), the Plateforme iGenSeq (library preparations and NGS sequencing) of the Institut du Cerveau et de la Moelle épinière (ICM, Paris, France), and G. Toutirais from the Plateau technique de Microscopie Électronique (scanning electron microscopy) of the Muséum National d’Histoire Naturelle (MNHN, Paris, France) for technical supports. We would also like to acknowledge A. Quattrini for her valuable advice on UCE target enrichment and analyses and S. Schmidt-Roach for his guidance on preparing SEM samples. Bioinformatics analyses were performed on the Genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, NO was financially supported by a PhD contract from the Doctoral School “Sciences, Technologies, Santé” of Reunion Island University. DA has received funding from the European FEDER Fund under project 1166-39417 and from the Excellence Initiative of Aix-Marseille University - A*MIDEX, a French “Investissements d’Avenir” program.

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Molecular Biology


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