Application of a west Eurasian-specific filter for quasi-median network analysis: Sharpening the blade for mtDNA error detection

The application of quasi-median networks provides an effective tool to check the quality of mtDNA data. Filtering of highly recurrent mutations prior to network analysis is required to simplify the data set and reduce the complexity of the network. The phylogenetic background determines those mutations that need to be filtered. While the traditional EMPOPspeedy filter was based on the worldwide mtDNA phylogeny, haplogroup-specific filters can more effectively highlight potential errors in data of the respective (sub)-continental region. In this study we demonstrate the performance of a new, west Eurasian filter EMPOPspeedyWE for the fine-tuned examination of data sets belonging to macrohaplogroup N that constitutes the main portion of mtDNA lineages in Europe. The effects on the resulting network of different database sizes, high-quality and flawed data, as well as the examination of a phylogenetically distant data set, are presented by examples. The analyses are based on a west Eurasian etalon data set that was carefully compiled from more than 3500 control region sequences for network purposes. Both, etalon data and the new filter file, are provided through the EMPOP database (www.empop.org).

[1]  Manfred Kayser,et al.  Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation , 2009, Human mutation.

[2]  M. Stoneking,et al.  Mitochondrial DNA variation and language replacements in the Caucasus , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[3]  Walther Parson,et al.  EMPOP--a forensic mtDNA database. , 2007, Forensic science international. Genetics.

[4]  H. Bandelt,et al.  Human Mitochondrial DNA and the Evolution of Homo sapiens , 2006 .

[5]  Hans-Jürgen Bandelt,et al.  Phantom mutation hotspots in human mitochondrial DNA , 2005, Electrophoresis.

[6]  W. Parson,et al.  Mitochondrial DNA population data of HVS-I and HVS-II sequences from a northeast German sample. , 2007, Forensic science international.

[7]  W. Parson,et al.  Forensic and phylogeographic characterization of mtDNA lineages from northern Thailand (Chiang Mai) , 2009, International Journal of Legal Medicine.

[8]  T. Kivisild,et al.  Quality Assessment of DNA Sequence Data: Autopsy of A Mis‐Sequenced mtDNA Population Sample , 2006, Annals of human genetics.

[9]  Q. Kong,et al.  Estimation of Mutation Rates and Coalescence Times: Some Caveats , 2006 .

[10]  W. Parson.  The Art of Reading Sequence Electropherograms , 2007, Annals of human genetics.

[11]  Hans-Jürgen Bandelt,et al.  Translating DNA data tables into quasi-median networks for parsimony analysis and error detection. , 2007, Molecular phylogenetics and evolution.

[12]  Hans-Jürgen Bandelt,et al.  A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. , 2005, Biochemical and biophysical research communications.

[13]  Anita Brandstätter,et al.  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. , 2007, Forensic science international.

[14]  Peter Wiegand,et al.  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) , 2006, International Journal of Legal Medicine.