As a grad student in anthropological genetics, one of the more tedious tasks I had was aligning mtDNA sequences manually, noting the mutations (differences from the revised Cambridge Reference Sequence, which belongs to haplogroup H), and determining the haplogroup (or lineage). The difficulty was compounded by a lack of comprehensive definitions. I had a stack of references listing diagnostic mutations, but not for every haplogroup, not even for the subset of haplogroups found in Europe, which was the focus of my research. Part of the problem was that when I started whole genome sequencing wasn’t available. Whenever a new haplogroup was discovered, the authors would name it, and in some cases the same name was given to different sequences because there was no standardized nomenclature. What I needed was a phylogenetic tree, showing the relationships between lineages, and all diagnostic mutations for each haplogroup.
That’s what you can find at PhyloTree.org. The “updated comprehensive phylogenetic tree of global human mitochondrial DNA variation” lists all mitochondrial haplogroups, with diagnostic mutations from both the coding and control regions, based on full sequences deposited in GenBank. The figure below shows a portion of the tree for Haplogroup H1a:
Haplogroup H1a. Coding region mutations are in black, control region mutations in blue.
Coding region mutations are in black, control region mutations in blue. Established haplogroup names are in in black at the base of the branches, and proposed haplogroup labels are shown in red. GenBank accession numbers are provided at the tips of the branches. Assigning haplogroups to your samples is as easy as using the find function in your Internet brower. PhyloTree is continuously updated as new sequences are published; they’re currently on Build 7.0 as of November 2009.
PhyloTree is a valuable and much need resource for the anthropological genetics community, especially poor grad students.
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van Oven, M., & Kayser, M. (2009). Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation Human Mutation, 30 (2) DOI: 10.1002/humu.20921
