Plant Systematics and Evolution

, Volume 282, Issue 3–4, pp 257–280 | Cite as

Non-coding nuclear DNA markers in phylogenetic reconstruction

  • Miriam Calonje
  • Santiago Martín-Bravo
  • Christoph Dobeš
  • Wei Gong
  • Ingrid Jordon-Thaden
  • Christiane Kiefer
  • Markus Kiefer
  • Juraj Paule
  • Roswitha Schmickl
  • Marcus A. Koch


Molecular DNA based data sets are the most important resource for phylogenetic reconstruction. Among the various marker systems, which were introduced and optimized within the last decade, coding sequences played an important role, especially when molecular clock approaches and multi-gene datasets were assembled. However, non-coding DNA sequences do not only play a quantitatively dominant role, as demonstrated by the two examples nuclear ITS (Internal transcribed spacer regions of nuclear ribosomal DNA) and plastidic trnL-F region, but there is also a wide range of different marker systems that can be applied in different ways. Herein, we review the application of several non-coding nuclear DNA marker systems for phylogenetic reconstructions and summarize valuable information for future research.


ETS Intron ITS Molecular marker Phylogenetic reconstruction Promoter SSR Transposon 

Supplementary material

606_2008_31_MOESM1_ESM.doc (62 kb)
Supplementary References (ETS phylogenetic studies) (doc 61 kb)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Miriam Calonje
    • 1
  • Santiago Martín-Bravo
    • 1
  • Christoph Dobeš
    • 1
  • Wei Gong
    • 1
  • Ingrid Jordon-Thaden
    • 1
  • Christiane Kiefer
    • 1
  • Markus Kiefer
    • 1
  • Juraj Paule
    • 1
  • Roswitha Schmickl
    • 1
  • Marcus A. Koch
    • 1
  1. 1.Heidelberg Institute of Plant Science, Biodiversity and Plant SystematicsHeidelberg UniversityHeidelbergGermany

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