Review
Mitogenomics: digging deeper with complete mitochondrial genomes

https://doi.org/10.1016/S0169-5347(99)01660-2Get rights and content

Abstract

Mitochondrial genomes are being used to study increasingly ancient divergences among animal groups. Recent studies of complete mitochondrial DNA sequences have arrived at somewhat heretical conclusions, raising questions about the use of mitochondrial gene sequences for studying the relationships among highly divergent lineages. Other studies have documented convergent evolution of mitochondrial gene order, casting doubt on the use of these characters for phylogenetic analysis. The use of mitochondrial genomes for studying such deep divergences is coming under increased scrutiny, and these novel results need to be confirmed with data from nuclear genes.

Section snippets

Vertebrate relationships

An accurate phylogeny is the foundation for a complete understanding of vertebrate evolution. Therefore, questions of vertebrate relationships have been a primary focus in the field of molecular systematics. Although fossils provide evidence of morphological change, the genetic changes associated with evolution can only be discerned from comparisons among extant taxa. In Fig. 2, we present the traditional hypothesis of relationships of chordate taxa discussed in this review.

Digging deeper

Although the gene content of animal mtDNA is nearly constant, the relative position of these genes around the molecule varies among major taxonomic groups. The mechanisms responsible for these rearrangements are not well understood, but it is apparent that transfer RNA (tRNA) genes change position more frequently than either rRNAs or protein-coding genes17, 18, 19. It has been suggested that such rearrangements can be used as cladistic characters for studying relationships among higher-level

Conclusions

Mitochondrial sequences have resolved phylogenies deeper than originally expected, but their usefulness as a marker for highly divergent lineages is still controversial. Further studies of nuclear markers are required to confirm these mitochondrial phylogenies. If the hypotheses supported by paleontological data hold up, then slowly evolving nuclear genes will be more useful than complete mtDNA sequences28. If the non-traditional hypothesis is correct, then the utility of this widely used

Acknowledgements

We are grateful to Jessica Bolker, Sarah Cohen, Karen Carleton, Pat Danley, Jeff Markert, Todd Streelman, Ulfur Arnason and an anonymous reviewer for suggestions on the manuscript and to Ying Cao and Ann-Sofie Rasmussen for advance copies of their publications.

References (28)

  • A. Sidow et al.

    A molecular evolutionary framework for eukaryotic model organisms

    Curr. Biol.

    (1994)
  • J.C. Avise

    Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics

    Annu. Rev. Ecol. Syst.

    (1987)
  • T.D. Kocher

    Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

    Proc. Natl. Acad. Sci. U. S. A.

    (1989)
  • A. Meyer et al.

    Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish

    J. Mol. Evol.

    (1990)
  • S.B. Hedges et al.

    Relations of fish and tetrapods

    Nature

    (1993)
  • R. Zardoya et al.

    Evolutionary relationships of the coelacanth, lungfishes, and tetrapods based on the 28S ribosomal RNA gene

    Proc. Natl. Acad. Sci. U. S. A.

    (1996)
  • R. Zardoya et al.

    The complete nucleotide sequence of the mitochondrial genome of the lungfish (Protopterus dolloi) supports its phylogenetic position as a close relative of land vertebrates

    Genetics

    (1996)
  • R. Zardoya et al.

    The complete DNA sequence of the mitochondrial genome of a ‘living fossil’, the coelacanth (Latimeria chalumnae)

    Genetics

    (1997)
  • R. Zardoya

    Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data

    Mol. Biol. Evol.

    (1998)
  • A-S. Rasmussen et al.

    The mitochondrial DNA molecule of the hagfish (Myxine glutinosa) and vertebrate phylogeny

    J. Mol. Evol.

    (1998)
  • Y. Cao

    The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates

    Mol. Biol. Evol.

    (1998)
  • A-S. Rasmussen et al.

    Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fish within the tree of bony fish

    J. Mol. Evol.

    (1999)
  • C. Delarbre

    The complete nucleotide sequence of the mitochondrial DNA of the dogfish, Scyliorhinus canicula

    Genetics

    (1998)
  • G.J.P. Naylor et al.

    Structural biology and phylogenetic estimation

    Nature

    (1997)
  • Cited by (313)

    View all citing articles on Scopus
    View full text