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).
Institute of Legal Medicine, Innsbruck Medical University, Austria.
Bettina
B
Zimmermann
Alexander
A
Röck
Gabriela
G
Huber
Tanja
T
Krämer
Peter M
PM
Schneider
Walther
W
Parson
D001208:Asia; D004272:DNA, Mitochondrial / Q000235:genetics*; D030561:Databases, Nucleic Acid; D005060:Europe; D005828:Genetics, Population; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
D004272:DNA, Mitochondrial