International Journal of Legal Medicine

, Volume 126, Issue 6, pp 901–916 | Cite as

Haplogrouping mitochondrial DNA sequences in Legal Medicine/Forensic Genetics

  • Hans-Jürgen BandeltEmail author
  • Mannis van Oven
  • Antonio Salas
Original Article


Haplogrouping refers to the classification of (partial) mitochondrial DNA (mtDNA) sequences into haplogroups using the current knowledge of the worldwide mtDNA phylogeny. Haplogroup assignment of mtDNA control-region sequences assists in the focused comparison with closely related complete mtDNA sequences and thus serves two main goals in forensic genetics: first is the a posteriori quality analysis of sequencing results and second is the prediction of relevant coding-region sites for confirmation or further refinement of haplogroup status. The latter may be important in forensic casework where discrimination power needs to be as high as possible. However, most articles published in forensic genetics perform haplogrouping only in a rudimentary or incorrect way. The present study features PhyloTree as the key tool for assigning control-region sequences to haplogroups and elaborates on additional Web-based searches for finding near-matches with complete mtDNA genomes in the databases. In contrast, none of the automated haplogrouping tools available can yet compete with manual haplogrouping using PhyloTree plus additional Web-based searches, especially when confronted with artificial recombinants still present in forensic mtDNA datasets. We review and classify the various attempts at haplogrouping by using a multiplex approach or relying on automated haplogrouping. Furthermore, we re-examine a few articles in forensic journals providing mtDNA population data where appropriate haplogrouping following PhyloTree immediately highlights several kinds of sequence errors.


Mitochondrial DNA Forensics mtDNA database Haplogroup PhyloTree Multiplex genotyping mtDNAmanager MitoTool HaploGrep Sequence error Quality control 



The Ministerio de Ciencia e Innovación (SAF2008-02971 and SAF2011-26983) and the European project “A European Initial Training Network on the history, archaeology, and new genetics of the Trans-Atlantic slave trade (EUROTAST)” (EU project: 290344) gave support to AS. MvO was supported in part by the Netherlands Forensic Institute (NFI) and by a grant from the Netherlands Genomics Initiative (NGI)/Netherlands Organization for Scientific Research (NWO) within the framework of the Forensic Genomics Consortium Netherlands (FGCN).

Supplementary material

414_2012_762_MOESM1_ESM.doc (157 kb)
ESM 1 (DOC 157 kb)
414_2012_762_MOESM2_ESM.xlsx (79 kb)
ESM 2 (XLSX 78 kb)


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Hans-Jürgen Bandelt
    • 1
    Email author
  • Mannis van Oven
    • 2
  • Antonio Salas
    • 3
  1. 1.Department of MathematicsUniversity of HamburgHamburgGermany
  2. 2.Department of Forensic Molecular Biology, Erasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
  3. 3.Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultade de MedicinaUniversidade de Santiago de CompostelaGaliciaSpain

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