Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences

In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.

Automated summary

A new algorithm for alignment and haplogroup estimation of mitochondrial DNA sequences was proposed in this study, which led to a significant increase in haplogroup defining motifs for both full mitogenomes and the mtDNA control region. The algorithm has been implemented in the EMPOP mtDNA database and is freely accessible, benefiting various scientific disciplines such as medical, population and forensic genetics.