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Comparative Phylogenetic Analyses of the Adaptive Radiation of Lake Tanganyika Cichlid Fish: Nuclear Sequences Are Less Homoplasious But Also Less Informative Than Mitochondrial DNA

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Abstract

Over 200 described endemic species make up the adaptive radiation of cichlids in Lake Tanga-nyika. This species assemblage has been viewed as both an evolutionary reservoir of old cichlid lineages and an evolutionary hotspot from which the modern cichlid lineages arose, seeding the adaptive radiations in Lakes Victoria and Malawi. Here we report on a phylogenetic analysis of Lake Tanganyika cichlids combining the previously determined sequences of the mitochondrial ND2 gene (1047 bp) with newly derived sequences of the nuclear RAG1 gene (∼700 bp of intron 2 and ∼1100 bp of exon 3). The nuclear data—in agreement with mitochondrial DNA—suggest that Lake Tanganyika harbors several ancient lineages that did not undergo rampant speciation (e.g., Bathybatini, Trematocarini). We find strong support for the monophyly of the most species-rich Tanganyikan group, the Lamprologini, and we propose a new taxonomic group that we term the C-lineage. The Haplochromini and Tropheini both have an 11-bp deletion in the intron of RAG1, strongly supporting the monophyly of this clade and its derived position. Mapping the phylogenetically informative positions revealed that, for certain branches, there are six times fewer apomorphies in RAG1. However, the consistency index of these positions is higher compared to the mitochondrial ND2 gene. Nuclear data therefore provide, on a per–base pair basis, less but more reliable phylogenetic information. Even if in our case RAG1 has not provided as much phylogenetic information as we expected, we suggest that this marker might be useful in the resolution of the phylogeny of older groups.

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Acknowledgments

We thank S. Koblmüller, J. Snoeks, C. Sturmbauer, E. Verheyen, and L. De Vos for provision and identification of some of the specimens and R. Gueta, I. Eistetter, T. Mack, and the other members of the Meyer lab for technical assistance. We are grateful to M. Cummings and L. Rüber and the second anonymous reviewer for discussions and valuable comments on the manuscript. This study was supported by the Landesstiftung Baden-Württemberg, the Center for Junior Research Fellows (University Konstanz), and the EU (Marie Curie fellowship) to W.S. and grants from the Deutsche Forschungsgemeinschaft to A.M.

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  1. Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, 78457, Germany

    Céline Clabaut, Walter Salzburger & Axel Meyer

  2. Center for Junior Research Fellows, University of Konstanz, Konstanz, 78457, Germany

    Walter Salzburger

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  1. Céline Clabaut
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Clabaut, C., Salzburger, W. & Meyer, A. Comparative Phylogenetic Analyses of the Adaptive Radiation of Lake Tanganyika Cichlid Fish: Nuclear Sequences Are Less Homoplasious But Also Less Informative Than Mitochondrial DNA. J Mol Evol 61, 666–681 (2005). https://doi.org/10.1007/s00239-004-0217-2

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