With the release of PhyloTree Build 14, and the simultaneous introduction of the RSRS as a new reference sequence (Behar et al. 2012), some changes were made in the way of denoting mutations in the mtDNA tree. In particular, ancestral and descendant bases (from an evolutionary point of view) are now included for all substitutions (whether transitions or transversions), and exclamation marks are now used to indicate back-mutations to an evolutionary ancestral state.
As this change caused some inconvenience for those used to the ‘old’ notation style, we hereby offer, in parallel to the new notation, an rCRS-oriented version of PhyloTree, in a format that is similar to that of previous Builds. In this rCRS-oriented version, exact base changes are only specified for transversions (e.g. “3516A”), whereas transitions are indicated merely by their nucleotide position number (e.g. “16172”). Furthermore, the @ symbol is used as a prefix for mutations toward an rCRS state (e.g. “@263”). Note that the rCRS represents the nodal haplogroup H2a2a1 sequence, and therefore H2a2a1 should serve as the starting point in this tree for reading off rCRS-based mutation lists.
The following persons are thanked for suggestions and help in preparing this rCRS-oriented version: Walther Parson, Alexander Röck, Antonio Salas, Hans Bandelt, Antonio Torroni, Alessandro Achilli, Anna Olivieri, Oscar Lao.