Table 3 A hypothetical illustration of how HaploGrep3 output could be updated to include information about predefined and standardized micro-, meso-, and macro- haplogroups, as well as the mtHg-address unique to each haplotype. TreeCluster results based on the full PhyloTree phylogeny used for mtDNA haplogroup nomenclature could be used to define standardized sets of micro-, meso-, and macro-haplogroups, as well as mtHg-address. Certain TreeCluster thresholds informative about human migrations and population histories could be used to determine secondary haplogroup groupings (here indicated with red, blue, and green colors). For illustration purposes, we focus on nine hypothetical TreeCluster levels (TreeCluster runs with thresholds from 0 to 0.008). In reality, one can decide on any number of thresholds to be included in the mtHg-address. For the mtHg-address that distinguishes each haplotype, one would need to incorporate a TreeCluster run with a threshold of 0. Note that the names of micro-, meso-, and macro-Hg are determined based on the MRCA-haplogroup of all haplogroups belonging to the same group for the appropriate TreeCluster threshold. In the above example, tc_0.004 is used to define micro-haplogroups. Both B4a1a1b and J2b1a belong to the same tc_0.004 group, and thus R is determined as the most recent parent haplogroup for both of them. Please note that this table is completely fictional, and its sole purpose is to illustrate the concept of mtHg-address, how to achieve it, and how it could be integrated into HaploGrep3 output. As such, this table is not a proposal for actual standardization

From: mtDNA “nomenclutter” and its consequences on the interpretation of genetic data