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Genome skimming resolves the giant clam (Bivalvia: Cardiidae: Tridacninae) tree of life

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Abstract

Giant clams are conspicuous bivalves inhabiting Indo-Pacific reefs. Since Rosewater’s seminal paper in 1965, the number of giant clam species described or resurrected has exactly doubled. The increased number of species reported and accessibility to genetic material of rare or uncommon species therefore call for a reappraisal of the phylogenetic relationships within the Tridacninae subfamily. Here, we aim to reconstruct the evolutionary relationships among all 12 extant species by performing a comprehensive phylogenetic analysis of mitochondrial genome and nuclear 18S rRNA data from a combination of genome skimming, Sanger sequencing and previously published sequences. Comparing the mitogenomes among Tridacninae species, we report two new findings: (1) the T. crocea mitogenome length obtained here (18,266 bp) is shorter than previously known, and (2) the mitochondrial gene order in T. crocea and T. squamosa differs from the other species. Our phylogeny based on a concatenated 16-gene dataset (15 mitochondrial markers and nuclear 18S rRNA) reveals highly supported relationships within and between the three subgenera, Tridacna (Tridacna), Tridacna (Persikima) and Tridacna (Chametrachea). Overall, the inclusion of new molecular markers greatly improves the confidence and support for the subfamily’s phylogeny. The availability of this comprehensive phylogenetic dataset serves as the foremost baseline of Tridacninae relationships to support future studies examining giant clam systematics, ecology and conservation.

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Acknowledgements

We thank the members of the Reef Ecology Laboratory for their support and assistance, especially Marc Chang and Sudhanshi Jain for help in the laboratory. Authors Neo ML and Fauvelot C acknowledge Gustav Paulay for sharing T. squamosina sample UF463401 and image from the Farasan Island, Saudi Arabia; Felix Lorenz and Jana Kratzsch for sharing T. rosewateri image from Cargados Carajos Archipelago, Mauritius Outlying Territories; and Serge Andréfouët for sharing T. elongatissima image from Juan de Nova Island. Author Neo ML also acknowledges National Research Foundation (NRF), Prime Minister’s Office, Singapore, for supporting her research endeavours at the St John’s Island National Marine Laboratory. This research is supported by the National Research Foundation, Prime Minister’s Office, Singapore, under its Marine Science R&D Programme (MSRDP-P03).

Author information

Authors and Affiliations

  1. Department of Biological Sciences, National University of Singapore, Singapore, Singapore

    Edwin Y. W. Tan, Quek Z. B. Randolph, Mei Lin Neo & Danwei Huang

  2. Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore

    Mei Lin Neo & Danwei Huang

  3. UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d’Excellence-CORAIL, Centre IRD de Nouméa, Noumea Cedex, New Caledonia, France

    Cécile Fauvelot

  4. UMR LOV (Sorbonne Université, CNRS), Laboratoire d’Océanographie de Villefranche, Villefranche-sur-Mer, France

    Cécile Fauvelot

Authors
  1. Edwin Y. W. Tan
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  2. Quek Z. B. Randolph
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  3. Mei Lin Neo
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  4. Cécile Fauvelot
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  5. Danwei Huang
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Correspondence to Mei Lin Neo or Danwei Huang.

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Tan, E.Y.W., Quek, Z.R., Neo, M.L. et al. Genome skimming resolves the giant clam (Bivalvia: Cardiidae: Tridacninae) tree of life. Coral Reefs 41, 497–510 (2022). https://doi.org/10.1007/s00338-020-02039-w

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