Marine Biodiversity

, Volume 49, Issue 1, pp 521–526 | Cite as

Phylogeography of Noah’s giant clam

  • Cécile FauvelotEmail author
  • Serge Andréfouët
  • Daphné Grulois
  • Josina Tiavouane
  • Colette C. C. Wabnitz
  • Hélène Magalon
  • Philippe Borsa
Short Communication


Noah’s giant clam (Tridacna noae), recently resurrected from synonymy with T. maxima, occurs from Christmas Island to the Northern Line Islands and from the Ryukyu Islands to New Caledonia. We used mitochondrial and microsatellite markers to investigate the phylogeographic structure and demographic history of T. noae over most of its geographical range. Results from the two types of markers reveal a consistent population structure, partitioning T. noae into three distinct lineages: (1) eastern half of the Indo-Malay archipelago and Western Australia, (2) Melanesia and Micronesia, and (3) Central Polynesia. Demographic expansion initiated between 300,000 and 400,000 years ago, as was detected for each haplogroup. This pattern, which is congruent with other co-occurring Tridacna species, indicates a shared evolutionary history with expansion from past refuges following late-Pleistocene sea-level changes.


Tridacna Evolutionary history Mitochondrial DNA Microsatellite Indo-Pacific 



We thank P. Bosserelle (Wallis), J. Butscher (New Caledonia), P. Dor (Yap), C. Payri (Madang), M. Sapatu (Samoa), M. Savins (Kiribati), M. Selch (Kosrae) and B.-W. Su (Dongsha) for assistance in obtaining giant clam biopsies. Sampling in New Caledonia was carried out during the BIBELOT cruise (doi: Local communities, Ian Bertram (SPC) and staff from fisheries offices and relevant government institutions in SPC member countries are acknowledged for their kind support and cooperation in obtaining samples and required permits. Sample collection and/or shipment was in part facilitated by a grant from the Australian Government (DFAT) to SPC’s FAME division. Genetic analyses were co-funded by the BeN-Co project (ZoNéCo Program, New Caledonia) and the TriMax project (Laboratoire d’excellence CORAIL, Agence nationale de la recherche, France). Raw microsatellite data can be found at This is ENTROPIE contribution #181.

Supplementary material

12526_2017_794_MOESM1_ESM.pdf (823 kb)
ESM 1 (PDF 823 kb)
12526_2017_794_MOESM2_ESM.pdf (576 kb)
ESM 2 (PDF 576 kb)
12526_2017_794_MOESM3_ESM.pdf (753 kb)
ESM 3 (PDF 753 kb)


  1. Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48CrossRefGoogle Scholar
  2. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier (France)Google Scholar
  3. Borsa P, Fauvelot C, Tiavouane J et al (2015) Distribution of Noah’s giant clam, Tridacna noae. Mar Biodivers 45:339–344. CrossRefGoogle Scholar
  4. Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631. CrossRefGoogle Scholar
  5. Davies SW, Treml EA, Kenkel CD, Matz MV (2015) Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean. Mol Ecol 24:70–82. CrossRefGoogle Scholar
  6. DeBoer TS, Naguit MRA, Erdmann MV et al (2014) Concordance between phylogeographic and biogeographic boundaries in the coral triangle: conservation implications based on comparative analyses of multiple giant clam species. Bull Mar Sci 90:277–300. CrossRefGoogle Scholar
  7. Delrieu-Trottin E, Mona S, Maynard J et al (2017) Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes. Sci Rep 7:40519. CrossRefGoogle Scholar
  8. Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Ser B 39:1–38Google Scholar
  9. Dreyer H, Steiner G (2006) The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica – and the first record for a putative Atpase subunit 8 gene in marine bivalves. Front Zool 3:13. CrossRefGoogle Scholar
  10. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973. CrossRefGoogle Scholar
  11. Evans SM, McKenna C, Simpson SD et al (2016) Patterns of species range evolution in indo-Pacific reef assemblages reveal the coral triangle as a net source of transoceanic diversity. Biol Lett 12:20160090. CrossRefGoogle Scholar
  12. Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol 13:853–864. CrossRefGoogle Scholar
  13. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and windows. Mol Ecol Resour 10:564–567. CrossRefGoogle Scholar
  14. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925Google Scholar
  15. Gardner JPA, Boesche C, Meyer JM, Wood AR (2012) Analyses of DNA obtained from shells and brine-preserved meat of the giant clam Tridacna maxima from the central Pacific Ocean. Mar Ecol Prog Ser 453:297–301. CrossRefGoogle Scholar
  16. Grulois D, Tiavouane J, Dumas PP, Fauvelot C (2015) Isolation and characterization of fifteen microsatellite loci for the giant clam Tridacna maxima. Conserv Genet Resour 7:73–75. CrossRefGoogle Scholar
  17. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  18. Huelsken T, Keyse J, Liggins L et al (2013) A novel widespread cryptic species and phylogeographic patterns within several giant clam species (Cardiidae: Tridacna) from the indo-Pacific Ocean. PLoS One 8:e80858. CrossRefGoogle Scholar
  19. Hui M, Kraemer WE, Seidel C et al (2016) Comparative genetic population structure of three endangered giant clams (Cardiidae: Tridacna species) throughout the indo-West Pacific: implications for divergence, connectivity and conservation. J Molluscan Stud 82:403–414. CrossRefGoogle Scholar
  20. Johnson MS, Prince J, Brearley A et al (2016) Is Tridacna maxima (Bivalvia: Tridacnidae) at Ningaloo reef, Western Australia? Molluscan Res:1–7.
  21. Kochzius M, Nuryanto A (2008) Strong genetic population structure in the boring giant clam, Tridacna crocea, across the indo-Malay archipelago: implications related to evolutionary processes and connectivity. Mol Ecol 17:3775–3787. CrossRefGoogle Scholar
  22. Lambeck K, Chappell J (2001) Sea level change through the last glacial cycle. Science 292:679–686. CrossRefGoogle Scholar
  23. Lizano AMD, Santos MD (2014) Updates on the status of giant clams Tridacna spp. and Hippopus hippopus in the Philippines using mitochondrial CO1 and 16S rRNA genes. Philipp Sci Lett 7:187–200Google Scholar
  24. Ludt WB, Bernal MA, Bowen BW, Rocha LA (2012) Living in the past: Phylogeography and population histories of indo-Pacific wrasses (genus Halichoeres) in shallow lagoons versus outer reef slopes. PLoS One.
  25. Neo ML, Low JKY (2017) First observations of Tridacna noae (Röding, 1798) (Bivalvia: Heterodonta: Cardiidae) in Christmas Island (Indian Ocean). Mar Biodivers 1–3. doi:
  26. Pellissier L, Leprieur F, Parravicini V et al (2014) Quaternary coral reef refugia preserved fish diversity. Science 344:1016–1019. CrossRefGoogle Scholar
  27. Rambaut A, Suchard MA, Xie D, Drummond AJ (2014) Molecular evolution, phylogenetics and epidemiology. Available from
  28. Raymond M, Rousset F (1995) GENEPOP: a population genetic software for exact tests and ecumenicism. J Hered 86:248–249Google Scholar
  29. Rogers AR (1995) Genetic evidence for a Pleistocene population explosion. Evolution 49:608–615Google Scholar
  30. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569Google Scholar
  31. Su Y, Hung JH, Kubo H, Liu LL (2014) Tridacna noae (Röding, 1798)–a valid giant clam species separated from T. Maxima (Röding, 1798) by morphological and genetic data. Raffles Bull Zool 62:124–135Google Scholar
  32. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595Google Scholar
  33. Tamura K (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 9:678–687Google Scholar
  34. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599. CrossRefGoogle Scholar
  35. Weir BS (1996) Genetic data analysis II. Sinauer Associates, SunderlandGoogle Scholar
  36. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370. Google Scholar

Copyright information

© Senckenberg Gesellschaft für Naturforschung and Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d’excellence CORAIL, Centre IRD de NouméaNoumea CedexNew Caledonia
  2. 2.Université Côte d’Azur, CNRS, FRE 3729 ECOMERSNiceFrance
  3. 3.Secretariat of the Pacific CommunityNouméaNew Caledonia
  4. 4.Changing Ocean Research Unit, Institute for the Oceans and FisheriesUniversity of British Columbia, Aquatic Ecosystems Research LaboratoryVancouverCanada
  5. 5.UMR ENTROPIE (Université de La Réunion, CNRS, IRD), Laboratoire d’excellence CORAILUniversité de La RéunionLa RéunionFrance

Personalised recommendations