International Journal of Legal Medicine

, Volume 120, Issue 5, pp 310–314 | Cite as

Application of a quasi-median network analysis for the visualization of character conflicts to a population sample of mitochondrial DNA control region sequences from southern Germany (Ulm)

  • Anita Brandstätter
  • Rachel Klein
  • Nina Duftner
  • Peter Wiegand
  • Walther ParsonEmail author
Short Communication


Entire mtDNA control region sequences from 100 individuals in a west Eurasian population sample from southern Germany (around the city of Ulm) were generated and analyzed. The control region was amplified in one piece and sequenced with ten different sequencing primers. Sequence evaluation was performed independently. Phylogenetic analyses were used for quality assurance purposes and for the determination of the haplogroup affiliation of the samples. The sequences were scrutinized performing a quasi-median network analysis. To visualize character conflicts, frequent mutations were filtered, and the reduced data were represented by the torso of their quasi-median network. Character incompatibilities were found to be based on real biological patterns of homoplasy. The population data will be incorporated in the EMPOP database (


West Eurasian population mtDNA polymorphisms Phylogenetic analyses Haplogroups assignment Forensic 

Supplementary material

414_2006_114_MOESM1_ESM.doc (36 kb)
Table S1 (DOC 36 kb)


  1. 1.
    Parson W, Parsons TJ, Scheithauer R, Holland MM (1998) Population data for 101 Austrian Caucasian mitochondrial DNA d-loop sequences: application of mtDNA sequence analysis to a forensic case. Int J Legal Med 111:124–132PubMedCrossRefGoogle Scholar
  2. 2.
    Imaizumi K, Parsons TJ, Yoshino M, Holland MM (2002) A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals. Int J Legal Med 116:68–73PubMedCrossRefGoogle Scholar
  3. 3.
    Imaizumi K, Parsons TJ (2005) A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals (vol 116, p 68, 2001). Int J Legal Med 119:183CrossRefGoogle Scholar
  4. 4.
    Lutz S, Weisser H-J, Heizmann J, Pollak S (1998) Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany. Int J Legal Med 111:67–77. Errata in Int J Legal Med 111 (1998) 286 and Int J Legal Med 112 (1999) 145–150PubMedCrossRefGoogle Scholar
  5. 5.
    Brandstätter A, Peterson CT, Irwin JA et al (2004) Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database. Int J Legal Med 118:294–306PubMedCrossRefGoogle Scholar
  6. 6.
    Vanecek T, Vorel F, Sip M (2004) Mitochondrial DNA D-loop hypervariable regions: Czech population data. Int J Legal Med 118:14–18PubMedCrossRefGoogle Scholar
  7. 7.
    Brandstätter A, Niederstätter H, Pavlic M et al (2006) Generating population data for the EMPOP database—an overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example. Forensic Sci Int (in press)Google Scholar
  8. 8.
    Parson W, Brandstätter A, Alonso A et al (2004) The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives. Forensic Sci Int 139:215–226PubMedCrossRefGoogle Scholar
  9. 9.
    Salas A, Prieto L, Montesino M et al (2005) Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP’02-03 proficiency testing trial. Forensic Sci Int 148:191–198PubMedCrossRefGoogle Scholar
  10. 10.
    Bandelt H-J, Quintana-Murci L, Salas A, Macaulay V (2002) The fingerprint of phantom mutations in mitochondrial DNA data. Am J Hum Genet 71:1150–1160PubMedCrossRefGoogle Scholar
  11. 11.
    Brandstätter A, Sänger T, Lutz-Bonengel S et al (2005) Phantom mutation hotspots in human mitochondrial DNA. Electrophoresis 26:3414–3429PubMedCrossRefGoogle Scholar
  12. 12.
    Parson W, Brandstätter A, Pircher M et al (2004) EMPOP—the EDNAP mtDNA population database concept for a new generation, high-quality mtDNA database. Int Congress Series 1261:106–108CrossRefGoogle Scholar
  13. 13.
    Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48PubMedGoogle Scholar
  14. 14.
    Bandelt H-J, Macaulay V, Richards M (2000) Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Mol Phylogenet Evol 16:8–28PubMedCrossRefGoogle Scholar
  15. 15.
    Ambach E, Parson W, Niederstätter H, Budowle B (1997) Austrian Caucasian population data for the quadruplex plus amelogenin: refined mutation rate for HumvWFA31/A. J Forensic Sci 42:1136–1139PubMedGoogle Scholar
  16. 16.
    Anderson S, Bankier AT, Barrell BG et al (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465PubMedCrossRefGoogle Scholar
  17. 17.
    Andrews RM, Kubacka I, Chinnery PF et al (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147PubMedCrossRefGoogle Scholar
  18. 18.
    Bär W, Brinkmann B, Budowle B et al (2000) DNA Commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing. Int J Legal Med 113:193–196PubMedCrossRefGoogle Scholar
  19. 19.
    Carracedo A, Bär W, Lincoln P et al (2000) DNA Commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing. Forensic Sci Int 110:79–85PubMedCrossRefGoogle Scholar
  20. 20.
    Steinlechner M, Parson W (2001) Automation and high through-put for a DNA database laboratory: development of a laboratory information management system. Croat Med J 42:252–255PubMedGoogle Scholar
  21. 21.
    Helgason A, Sigureth aS, Gulcher JR et al (2000) mtDNA and the origin of the Icelanders: deciphering signals of recent population history. Am J Hum Genet 66:999–1016PubMedCrossRefGoogle Scholar
  22. 22.
    Malyarchuk BA, Grzybowski T, Derenko MV et al (2002) Mitochondrial DNA variability in Poles and Russians. Ann Hum Genet 66:261–283PubMedCrossRefGoogle Scholar
  23. 23.
    Derenko MV, Malyarchuk BA, Dambueva IK, Zakharov IA (2003) Structure and diversity of the mitochondrial gene pools of south Siberians. Dokl Biol Sci 393:557–561PubMedCrossRefGoogle Scholar
  24. 24.
    Derenko MV, Grzybowski T, Malyarchuk BA et al (2003) Diversity of mitochondrial DNA lineages in south Siberia. Ann Hum Genet 67:391–411PubMedCrossRefGoogle Scholar
  25. 25.
    Malyarchuk BA, Grzybowski T, Derenko MV et al (2003) Mitochondrial DNA variability in Bosnians and Slovenians. Ann Hum Genet 67:412–425PubMedCrossRefGoogle Scholar
  26. 26.
    Reidla M, Kivisild T, Metspalu E et al (2003) Origin and diffusion of mtDNA haplogroup X. Am J Hum Genet 73:1178–1190PubMedCrossRefGoogle Scholar
  27. 27.
    Achilli A, Rengo C, Magri C et al (2004) The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet 75:910–918PubMedCrossRefGoogle Scholar
  28. 28.
    Loogväli E-L, Roostalu U, Malyarchuk BA et al (2004) Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol Biol Evol 21:2012–2021PubMedCrossRefGoogle Scholar
  29. 29.
    Palanichamy MG, Sun C, Agrawal S et al (2004) Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am J Hum Genet 75:966–978PubMedCrossRefGoogle Scholar
  30. 30.
    Achilli A, Rengo C, Battaglia V et al (2005) Saami and Berbers—an unexpected mitochondrial DNA link. Am J Hum Genet 76:883–886PubMedCrossRefGoogle Scholar
  31. 31.
    Bandelt H-J, Achilli A, Kong Q-P et al (2005) Low “penetrance” of phylogenetic knowledge in mitochondrial disease studies. Biochem Biophys Res Commun 333:122–130PubMedCrossRefGoogle Scholar
  32. 32.
    Torroni A, Achilli A, Macaulay V et al (2006) Harvesting the fruit of the human mtDNA tree. Trends Genet 22:339–345PubMedCrossRefGoogle Scholar
  33. 33.
    Allard MW, Miller K, Wilson M et al (2002) Characterization of the Caucasian haplogroups present in the SWGDAM forensic mtDNA dataset for 1771 human control region sequences. Scientific Working Group on DNA Analysis Methods. J Forensic Sci 47:1215–1223PubMedGoogle Scholar
  34. 34.
    Malyarchuk BA, Rogozin IB, Berikov VB, Derenko MV (2002) Analysis of phylogenetically reconstructed mutational spectra in human mitochondrial DNA control region. Hum Genet 111:46–53PubMedCrossRefGoogle Scholar
  35. 35.
    Allard MW, Wilson MR, Monson KL, Budowle B (2004) Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA data set. Leg Med 6:11–24CrossRefGoogle Scholar
  36. 36.
    Allard MW, Polanskey D, Miller K et al (2005) Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set. Forensic Sci Int 148:169–179PubMedCrossRefGoogle Scholar
  37. 37.
    Lutz S, Weisser H-J, Heizmann J, Pollak S (1997) A third hypervariable region in the human mitochondrial D-loop. Hum Genet 101:384PubMedGoogle Scholar
  38. 38.
    Tambets K, Rootsi S, Kivisild T et al (2004) The western and eastern roots of the Saami—the story of genetic “outliers” told by mitochondrial DNA and Y chromosomes. Am J Hum Genet 74:661–682PubMedCrossRefGoogle Scholar
  39. 39.
    Brandstätter A, Parsons TJ, Parson W (2003) Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups. Int J Legal Med 117:291–298PubMedCrossRefGoogle Scholar
  40. 40.
    Poetsch M, Wittig H, Krause D, Lignitz E (2003) Mitochondrial diversity of a northeast German population sample. Forensic Sci Int 137:125–132PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Anita Brandstätter
    • 1
  • Rachel Klein
    • 2
  • Nina Duftner
    • 1
    • 3
  • Peter Wiegand
    • 2
  • Walther Parson
    • 1
    Email author
  1. 1.Institute of Legal MedicineInnsbruck Medical UniversityInnsbruckAustria
  2. 2.Institute of Legal MedicineUniversity Clinics UlmUlmGermany
  3. 3.Bauer Center for Genomics ResearchHarvard UniversityCambridgeUSA

Personalised recommendations