Thanks to visit codestin.com
Credit goes to www.nature.com

Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

A unified classification system for eukaryotic transposable elements should reflect their phylogeny

Nature Reviews Genetics volume 10, page 276 (2009)Cite this article

Access through your institution
Buy or subscribe

To assist genome annotators in naming transposable elements (TEs), Wicker et al. propose in their Guidelines article (A unified classification system for eukaryotic transposable elements. Nature Rev. Genet. 8, 973–982 (2007))1 a classification and nomenclatural system aimed at simplifying annotation to assist future detailed structural, functional and evolutionary analyses1. However, even though the proposed classification system mimics organismal phylogenetic classification, it fails to do so consistently.

Classifications are a necessary prerequisite for human communication, and most biological classifications are hierarchical. The relationships between entities in any hierarchical system are of two kinds only: either one entity is included in another or they are mutually exclusive. The only rule that applies to the ranks in biological nomenclature is their sequence — a class includes one or more orders, an order one or more families and so on. Most biologists agree that classifications should reflect phylogeny (see Ref. 2 for one exception), although how phylogeny is reconstructed is controversial. This aside, the majority of organismal phylogenies are inherently hierarchical, and thus either a clade is included in another clade or two clades are mutually exclusive. Hence, as long as the groups remain monophyletic3 (for an alternative point of view see Refs 4, 5), a hierarchical classification is ideally suited to reflect phylogeny6.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

References

  1. Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nature Rev. Genet. 8, 973–982 (2007).

    Article  CAS  Google Scholar 

  2. Felsenstein, J. Inferring Phylogenies (Sinauer Associates, Sunderland, Massachusetts, 2004).

    Google Scholar 

  3. Nelson, G., Murphy, D. J. & Ladiges, P. Y. Brummitt on paraphyly: a response. Taxon 52, 295–298 (2003).

    Article  Google Scholar 

  4. Brummitt, R. K. Further dogged defense of paraphyletic taxa. Taxon 52, 803–804 (2003).

    Article  Google Scholar 

  5. Nordal, I. & Stedje, B. Paraphyletic taxa should be accepted. Taxon 54, 5–8 (2005).

    Article  Google Scholar 

  6. Sober, E. Philosophy of Biology (Oxford Univ. Press, Oxford, 1993).

    Google Scholar 

  7. Petersen, G. & Seberg, O. Stowaway MITEs in Hordeum (Poaceae): evolutionary history, ancestral elements, and classification. Cladistics (in the press).

  8. Patterson, C. Homology in classical and molecular biology. Mol. Biol. Evol. 5, 603–625 (1988).

    CAS  Google Scholar 

  9. Swofford, D. L., Olsen, G. J., Waddell, P. J. & Hillis, D. M. in Molecular Systematics (eds Hillis, D. M., Moritz, C. & Mable, B. K.) 407–514 (Sinauer Associates Inc., Sunderland, Massachusetts, 1996).

    Google Scholar 

  10. de Pinna, M. C. C. Concepts and tests of homology in the cladistic paradigm. Cladistics 7, 367–394 (1991).

    Article  Google Scholar 

  11. Brower, A. V. Z. & Schawaroch, V. Three steps of homology assessment. Cladistics 12, 265–272 (1996).

    Google Scholar 

  12. Williams, D. M. in Milestones in Systematics (eds Williams, D. M. & Forey, P. L.) 191–224 (CRC, Boca Raton, Florida 2004).

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Ole Seberg and Gitte Petersen are at the Laboratory of Molecular Systematics, Natural History Museum of Denmark, Sølvgade 83, opg. S, DK-1307 Copenhagen K, Denmark.,

    Ole Seberg & Gitte Petersen

Authors
  1. Ole Seberg
    View author publications

    Search author on:PubMed Google Scholar

  2. Gitte Petersen
    View author publications

    Search author on:PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Seberg, O., Petersen, G. A unified classification system for eukaryotic transposable elements should reflect their phylogeny. Nat Rev Genet 10, 276 (2009). https://doi.org/10.1038/nrg2165-c3

Download citation

  • Issue date:

  • DOI: https://doi.org/10.1038/nrg2165-c3

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing