Mitochondrial genomic divergence in coelacanths (Latimeria): slow rate of evolution or recent speciation?
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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.
KeywordsMarkov Chain Monte Carlo Effective Population Size Amino Acid Change Codon Position Calibration Point
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.
- Akaike H (1973) Information theory and an extension of the maximum likelihood principle. In: Petrov BN, Csaki F (eds) Proceedings of the second international symposium on information theory, Akadémia Kiado, Budapest, pp 267–281Google Scholar
- Charif D, Lobry J (2007) SeqinR 1.0-2: A contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. In: Bastolla U, Porto HRM, Vendruscolo M (eds) Structural approaches to sequence evolution: molecules, networks, populations. Springer, New York, pp 207–232Google Scholar
- Heibl C (2010) LAGOPUS: R-package for Bayesian relaxed-clock molecular dating. http://www.christophheibl.de
- Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, OxfordGoogle Scholar
- Nelson JS (2006) Fishes of the world, 4th edn. Wiley, HobokenGoogle Scholar
- R Development Core Team (2009) R: a language and environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org
- Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876–4882Google Scholar
- Yee TW (2009) VGAM: vector generalized linear and additive models. R package version 0.7-8. http://www.stat.auckland.ac.nz/~yee/VGAM
- Zardoya R, Meyer A (1997) The complete DNA sequence of the mitochondrial genome of a “living fossil,” the coelacanth (Latimeria chalumnae). Genetics 146:995–1010Google Scholar