A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia)

Z. B.Randolph Quek*, Sudhanshi S. Jain, Zoe T. Richards, Roberto Arrigoni, Francesca Benzoni, Bert W. Hoeksema, Jose I. Carvajal, Nerida G. Wilson, Andrew H. Baird, Marcelo V. Kitahara, Isabela G.L. Seiblitz, Claudia F. Vaga, Danwei Huang

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (less than 38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The “Robust” and “Complex” clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the “Robust” clade, transforming our understanding of the “Basal” clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution.

Original languageEnglish (US)
Article number107867
JournalMolecular phylogenetics and evolution
Volume186
DOIs
StatePublished - Sep 2023

Bibliographical note

Funding Information:
This research is supported by the National Research Foundation, Prime Minister's Office, Singapore under its Marine Science R&D Programme (MSRDP-P03), and the Temasek Foundation under its Singapore Millennium Foundation Research Grant Programme (A-0003203-01-00). MVK thanks the support of the São Paulo Research Foundation (FAPESP #2021/06866-6) and National Council for Scientific and Technological Development (CNPq #305274/2021-0). ZTR was funded by ARC Linkage Project LP1560101508. We are grateful for information and advice on coral taxonomy by Tom Bridge, as well as constructive suggestions by Antonia Monteiro and Daiqin Li. Finally, we wish to thank ML Berumen (KAUST), the captain and crew of the MV Dream-Master, and the KAUST Coastal and Marine Resources Core Lab for their assistance in fieldwork conducted in the Red Sea.

Funding Information:
This research is supported by the National Research Foundation, Prime Minister’s Office, Singapore under its Marine Science R&D Programme (MSRDP-P03), and the Temasek Foundation under its Singapore Millennium Foundation Research Grant Programme (A-0003203-01-00). MVK thanks the support of the São Paulo Research Foundation (FAPESP #2021/06866-6) and National Council for Scientific and Technological Development (CNPq #305274/2021-0). ZTR was funded by ARC Linkage Project LP1560101508. We are grateful for information and advice on coral taxonomy by Tom Bridge, as well as constructive suggestions by Antonia Monteiro and Daiqin Li. Finally, we wish to thank ML Berumen (KAUST), the captain and crew of the MV Dream-Master, and the KAUST Coastal and Marine Resources Core Lab for their assistance in fieldwork conducted in the Red Sea.

Publisher Copyright:
© 2023 The Authors

Keywords

  • Anthozoa
  • Coral
  • Pachyseridae
  • Phylogenomics
  • Transcriptome
  • Tree of life

ASJC Scopus subject areas

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

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