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Forty Million Years of Independent Evolution: A Mitochondrial Gene and Its Corresponding Nuclear Pseudogene in Primates

Journal of Molecular Evolution volume 61, pages 1–11 (2005)Cite this article

Abstract

Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-nt-long numt of the rRNA specifying mitochondrial DNA residing on human chromosome 3 and its corresponding mitochondrial gene in 18 anthropoid primates, we were able to retrace about 40 MY of primate rDNA evolutionary history. The results illustrate strengths and weaknesses of mtDNA data sets in reconstructing and dating the phylogenetic history of primates. We were able to show the following. In contrast to numt-DNA, (1) the nucleotide composition of mtDNA changed dramatically in the different primate lineages. This is assumed to lead to significant misinterpretations of the mitochondrial evolutionary history. (2) Due to the nucleotide compositional plasticity of primate mtDNA, the phylogenetic reconstruction combining mitochondrial and nuclear sequences is unlikely to yield reliable information for either tree topologies or branch lengths. This is because a major part of the underlying sequence evolution model — the nucleotide composition — is undergoing dramatic change in different mitochondrial lineages. We propose that this problem is also expressed in the occasional unexpected long branches leading to the “common ancestor” of orthologous numt sequences of different primate taxa. (3) The heterogeneous and lineage-specific evolution of mitochondrial sequences in primates renders molecular dating based on primate mtDNA problematic, whereas the numt sequences provide a much more reliable base for dating.

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Acknowledgments

We acknowledge the excellent technical assistance of Martina Ohme and Claudia Schwiegk. Thanks go to Christian Roos for primate DNA and to Kira Gee for editorial assistance. Two anonymous reviewers are gratefully acknowledged for their helpful comments.

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Authors and Affiliations

  1. Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56,, D-48149 , Münster, Germany

    Jürgen Schmitz

  2. Faculty of Bioscience & Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan

    Oliver Piskurek

  3. Institute of Anthropology, Johannes Gutenberg-University, D-55099 , Mainz, Germany

    Hans Zischler

Authors
  1. Jürgen Schmitz
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  2. Oliver Piskurek
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  3. Hans Zischler
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Correspondence to Jürgen Schmitz.

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[Reviewing Editor: Dr. Rafael Zardoya]

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Schmitz, J., Piskurek, O. & Zischler, H. Forty Million Years of Independent Evolution: A Mitochondrial Gene and Its Corresponding Nuclear Pseudogene in Primates. J Mol Evol 61, 1–11 (2005). https://doi.org/10.1007/s00239-004-0293-3

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  • DOI: https://doi.org/10.1007/s00239-004-0293-3

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