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Mitochondrial genomic divergence in coelacanths (Latimeria): slow rate of evolution or recent speciation?

Marine Biology volume 157, pages 2253–2262 (2010)Cite this article

Abstract

Dating the divergence between the two known living species of coelacanths has remained a difficult issue because of the very ancient origin of this lineage of fish, which is more closely related to tetrapods than to other fishes. We sequenced the complete mitochondrial genome of a recently captured individual of the Indonesian coelacanth in order to solve this issue. Using an approach based on loglinear models, we studied the molecular divergence between the two species of coelacanths and three other pairs of species, one that has diverged recently (Pan) and two that have diverged more distantly in the past. The loglinear models showed that the divergence between the two species of coelacanths is not significantly different from the two species of Pan. A detailed gene by gene analysis of the patterns of nucleotide and amino acid substitutions between these two pairs of species further supports the similarity of these divergences. On the other hand, a molecular dating analysis suggested a much older origin of the two coelacanth species (between 20 and 30 million years ago). We discuss the potential reasons for this discrepancy. The analysis of new individuals of the Indonesian coelacanth will certainly help to solve this issue.

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Acknowledgments

We are grateful to Thibaut Jombart and an anonymous reviewer for their constructive comments on a previous version of this paper. This research was financially supported by an Action Thématique Incitative of the Institut de Recherche pour le Développement.

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Authors and Affiliations

  1. Loka Riset Budidaya Ikan Hias Air Tawar, Jl. Perikanan No. 13 RT, 001 RW 02, Pancoranmas Depok, Jawa Barat, 16436, Indonesia

    Sudarto

  2. Dinas Kelautan dan Perikanan, Sulawesi Utara, Jl. Komp. Pertanian Kalasey, PO BOX 1039, Manado, 5013, Indonesia

    Xandramaya C. Lalu

  3. Centre of Research for Coastal Management, Small Islands and Pacific Affair, Sam Ratulangi University, Manado, North Sulawesi, Indonesia

    Janny D. Kosen

  4. Zoology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, 16911, Indonesia

    Agus H. Tjakrawidjaja

  5. Faculty of Fisheries and Marine Science, Bogor Agricultural University (IPB), Bogor, Jawa Barat, Indonesia

    Ruby Vidia Kusumah

  6. Pusat Riset Perikanan Tangkap, BRKP-DKP, Jl. Pasir Putih, Ancol Jakarta Utara, Indonesia

    Bambang Sadhotomo

  7. Akademi Perikanan Sorong (APSOR-BPSDM.KP), Jl. Kapitan Pattimura, Tanjung Kasuari, Kota Sorong, Papua Barat, Indonesia

    Kadarusman

  8. Institut de Recherche pour le Développement, UR175 CAVIAR, GAMET, 361 rue Jean-François Breton, BP 5095, 34196, Montpellier Cédex 5, France

    Laurent Pouyaud & Emmanuel Paradis

  9. Institut de Recherche pour le Développement, Wisma Anugraha, Jl. Taman Kemang 32B, Jakarta, 12730, Indonesia

    Jacques Slembrouck

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  1. Sudarto
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  2. Xandramaya C. Lalu
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  3. Janny D. Kosen
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  4. Agus H. Tjakrawidjaja
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  5. Ruby Vidia Kusumah
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  6. Bambang Sadhotomo
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  7. Kadarusman
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  8. Laurent Pouyaud
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  9. Jacques Slembrouck
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  10. Emmanuel Paradis
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Corresponding author

Correspondence to Emmanuel Paradis.

Additional information

Communicated by M. I. Taylor.

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Sudarto, Lalu, X.C., Kosen, J.D. et al. Mitochondrial genomic divergence in coelacanths (Latimeria): slow rate of evolution or recent speciation?. Mar Biol 157, 2253–2262 (2010). https://doi.org/10.1007/s00227-010-1492-7

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  • DOI: https://doi.org/10.1007/s00227-010-1492-7

Keywords

  • Markov Chain Monte Carlo
  • Effective Population Size
  • Amino Acid Change
  • Codon Position
  • Calibration Point