Journal of Molecular Evolution

, Volume 68, Issue 5, pp 516–527

Investigation of Heteroplasmy in the Human Mitochondrial DNA Control Region: A Synthesis of Observations from More Than 5000 Global Population Samples


    • Research DepartmentArmed Forces DNA Identification Laboratory
  • Jessica L. Saunier
    • Research DepartmentArmed Forces DNA Identification Laboratory
  • Harald Niederstätter
    • Institute of Legal MedicineInnsbruck Medical University
  • Katharine M. Strouss
    • Seattle Biomedical Research Institute
  • Kimberly A. Sturk
    • Research DepartmentArmed Forces DNA Identification Laboratory
  • Toni M. Diegoli
    • Research DepartmentArmed Forces DNA Identification Laboratory
  • Anita Brandstätter
    • Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical PharmacologyInnsbruck Medical University
  • Walther Parson
    • Institute of Legal MedicineInnsbruck Medical University
  • Thomas J. Parsons
    • International Commission on Missing Persons

DOI: 10.1007/s00239-009-9227-4

Cite this article as:
Irwin, J.A., Saunier, J.L., Niederstätter, H. et al. J Mol Evol (2009) 68: 516. doi:10.1007/s00239-009-9227-4


Instances of point and length heteroplasmy in the mitochondrial DNA control region were compiled and analyzed from over 5,000 global human population samples. These data represent observations from a large and broad population sample, representing nearly 20 global populations. As expected, length heteroplasmy was frequently observed in the HVI, HVII and HVIII C-stretches. Length heteroplasmy was also observed in the AC dinucleotide repeat region, as well as other locations. Point heteroplasmy was detected in approximately 6% of all samples, and while the vast majority of heteroplasmic samples comprised two molecules differing at a single position, samples exhibiting two and three mixed positions were also observed in this data set. In general, the sites at which heteroplasmy was most commonly observed correlated with reported control region mutational hotspots. However, for some sites, observations of heteroplasmy did not mirror established mutation rate data, suggesting the action of other mechanisms, both selective and neutral. Interestingly, these data indicate that the frequency of heteroplasmy differs between particular populations, perhaps reflecting variable mutation rates among different mtDNA lineages and/or artifacts of particular population groups. The results presented here contribute to our general understanding of mitochondrial DNA control region heteroplasmy and provide additional empirical information on the mechanisms contributing to mtDNA control region mutation and evolution.


Control regionHeteroplasmyMitochondrial DNAMutation rate

Supplementary material

239_2009_9227_MOESM1_ESM.doc (436 kb)
Supplementary Table S1 is available online. Haplotype data are available on request. Sequences from this data set may also be found at or under the following GenBank accession numbers: DQ906346-DQ906708; FJ026015-FJ026391; DQ418040-DQ418130; EU718790-EU719066; DQ418131-DQ418449; EU014897-EU015024; DQ359273-DQ359688; AY632902-AY633004; and DQ535903-DQ536089. 1 (DOC 436 kb)

Copyright information

© Springer Science+Business Media, LLC 2009