YFull: FAQ↩ Back 

Q: Can you explain the mutation rate in the mitochondrial genome and how YFull addresses the challenges of building the MTree?

A: The mitochondrial genome consists of only 16,569 base pairs, and consequently, the number of mutations is significantly less compared to the Y-chromosome, with mutations occurring much less frequently, averaging once every 1,000 to 2,000 years.

One of the major challenges in constructing the MTree is the occurrence of back mutations, which happen quite often. To address this, YFull researches the relationships between individual mtDNA samples. This is necessary to identify back mutations that might otherwise be missed by the MTree algorithms.

Some mutations due to their high frequency of occurrence, are not used in tree construction at all, similar to how they are treated in PhyloTree.org. The mutations 309.1C(C), 315.1C, AC indels at 515-522, A16182c, A16183c, 16193.1C(C), and C16519T/T16519C are not considered for phylogenetic reconstruction and are therefore excluded from the tree.

Branches on the MTree have their trust rating, indicated by stars ranging from 1 to 5. For convenience, they are highlighted in different shades of green on the MTree. The rating is based on a set of criteria, with a 4-5 star rating corresponding to branches that match the PhyloTree or were formed by rare mutations. Subclades with a one-star rating may be removed from the tree as soon as conflicting information arises from new samples.

References:

For constructing the MTree YFull uses data from their customers and data from GenBank The initial version of MTree was based on the PhyloTree 17 of van Oven (18 Feb 2016). See van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. PhyloTree.org. doi:10.1002/humu.20921

Also, YFull used some information from Ian Logan's website.

The formula of calculation of the phylogenetic weight of mutation based on HaploGrep principes See Weissensteiner H., Pacher D., Kloss-Brandstätter A., Forer L., Specht G., Bandelt H.-J., Kronenberg F., Salas A., Schönherr S. 2016. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucl. Acids. Res. 2016 Apr 15; doi:10.1093/nar/gkw233

For the mtDNA haplogroup classification, YFull uses Kulczynski distance. See Kloss-Brandstätter A., Pacher D., Schönherr S., Weissensteiner H., Binna R., Specht G., Kronenberg F. 2011. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups< Hum Mutat. 2011 Jan;32(1):25-32. doi: 10.1002/humu.21382. Epub 2010 Nov 16.

Last updated May 29, 2024.