mitoTree

mitoTree

Background

Human mitochondrial DNA (mtDNA) is an essential marker in various scientific disciplines [1]. It has been key for understanding human evolution and movement across the globe and is still used to reveal human migration and settlement [2–4].

So far, the most widely accepted phylogenetic tree of worldwide human mitochondrial DNA variation was PhyloTree, introduced by van Oven and Kayser [5]. However, it is no longer actively maintained, and the last update was released in 2016. Due to the constantly growing amount of sequence data and additionally published data repositories [6], the last build of PhyloTree (PT17) is comparatively small and, more importantly, insufficient to describe the diversity of mtDNA data. A growing number of sequences do not truly fit into the provided haplogroup scheme of PT17 [7], leading to imprecise classification and unnecessary coarsening of haplogroup estimates. The higher resolution of mtDNA sequence data generated by NGS/MPS methods further amplifies this problem. The increased level of detail is simply not reflected in PhyloTree. In our last publication, we showed how additional sequence data can be used to increase haplogroup resolution. Based on 26,011 vetted full mitogenomes, we refined the haplogroup defining motifs for full mitogenomes, resulting in an increase of 18%. Applying our approach on a specific portion of the mtDNA – known as the control region - the increase was 30% [7].

Various fields of research require repositories and tools, including updated collections of mtDNA sequence data assigned to a developing haplogroup scheme.

Expected outcomes

The idea of mitoTree is to create an up-to-date and interactive phylogenetic tree of human mitochondrial DNA based on quality controlled full mitochondrial DNA sequences. Gathering already generated data and utilizing them in a modern, handy implementation is the next step in data modernization and harmonization. This update of the human phylogeny allows for improved haplogrouping and prevents the unregulated development of self-introduced haplogroups. Additionally, the improved knowledge of the human mtDNA phylogeny is applicable in various scientific disciplines and will push a variety of current research areas.

Funding

This project is funded by the FWF.

Collaborators

Contact

Any questions or interested in collaborating? E-mail me: nicole.huber@i-med.ac.at

Literature cited

  1. H.-J.J. Bandelt, M. van Oven, A. Salas, Haplogrouping mitochondrial DNA sequences in legal medicine/forensic genetics, Int. J. Legal Med. 126 (2012) 901–916. doi:10.1007/s00414-0120762-y

  2. M. Bodner, U.A. Perego, G. Huber, L. Fendt, A.W. Röck, B. Zimmermann, A. Olivieri, A. Gómez-Carballa, H. Lancioni, N. Angerhofer, M.C. Bobillo, D. Corach, S.R. Woodward, A. Salas, A. Achilli, A. Torroni, H.-J.Bandelt, W. Parson, Rapid coastal spread of First Americans: novel insights from South America’s Southern Cone mitochondrial genomes., Genome Res. 22 (2012) 811–820. doi:10.1101/gr.131722.111.

  3. M. de Saint Pierre, F. Gandini, U.A. Perego, M. Bodner, A. Gómez-Carballa, D. Corach, N. Angerhofer, S.R. Woodward, O. Semino, A. Salas, W. Parson, M. Moraga, A. Achilli, A. Torroni, A. Olivieri, Arrival of Paleo-Indians to the southern cone of South America: new clues from mitogenomes., PLoS One. 7 (2012) e51311. doi:10.1371/journal.pone.0051311.

  4. P. Soares, A. Achilli, O. Semino, W. Davies, V. Macaulay, H.-J. Bandelt, A. Torroni, M.B. Richards, The archaeogenetics of Europe., Curr. Biol. 20 (2010) R174-83. doi:10.1016/j.cub.2009.11.054.

  5. van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat. 2009 Feb;30(2):E386-94. doi: 10.1002/humu.20921.

  6. F. Rubino, R. Piredda, F.M. Calabrese, D. Simone, M. Lang, C. Calabrese, V. Petruzzella, M. Tommaseo-Ponzetta, G. Gasparre, M. Attimonelli, HmtDB, a genomic resource for mitochondrion-based human variability studies., Nucleic Acids Res. 40 (2011) D1150–D1159. doi:10.1093/nar/gkr1086

  7. Dür A, Huber N, Parson W. Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences. Int J Mol Sci. 2021 May 27;22(11):5747. doi: 10.3390/ijms22115747.