Hit or miss in phylogeographic analyses: the case of the cryptic NUMTs

Mol Ecol Resour. 2011 Nov;11(6):1056-9. doi: 10.1111/j.1755-0998.2011.03050.x. Epub 2011 Jul 27.


Phylogeographic studies call for attention as nuclear copies of mitochondrial DNA (NUMT) may generate erroneous results. Here, we report the presence of NUMTs differing only by 1-3 bp from authentic mitochondrial haplotypes, consequently named cryptic NUMTs. In contrast to traditional NUMTs, for which reliable tools for detection are established, cryptic NUMTs question the validity of phylogeographic analyses based solely on mitochondrial DNA, like the one presented here on the European bark beetle Ips typographus. Caution is called as cryptic NUMTs might be responsible for haplotype richness found in several species, and the necessity of refined methods for NUMT detection is highlighted.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cell Nucleus / genetics*
  • Coleoptera / genetics*
  • DNA, Mitochondrial / genetics*
  • Electron Transport Complex IV / genetics
  • Europe
  • Haplotypes / genetics
  • Molecular Sequence Data
  • Phylogeography / methods*
  • Research Design
  • Sequence Analysis, DNA


  • DNA, Mitochondrial
  • Electron Transport Complex IV