The L2 lineage tree given is under construction and has not been subjected to complete statistical analysis. Of particular uncertainty are the inclusion of the two sequences at the top (Igkwnp1, Ac3949#1) and the substitutions above them. This lineage joins the main lineage below ftenode and at about the same time as M lineage. Since M lineage is poorly defined, the arrangement of that 3-way split is undefined rendering the top of the L2 lineage into this state of uncertainty.
This is a preliminary apomorphies list and is not complete.
Several well defined parallel and back mutations come to light particularly well between this lineage and the main lineage. They are neither clustered in positions on the tree nor in coordinates along the L1 sequence. Thus, in constrast to the usual assumption of gene conversion for homoplasy in these sequences, the patterns are more consistent with hypervariability of individual bases, perhaps as RT hotspots.
All of the sequences indicated have extensive private divergence.
In addition to the L2 lineage sequences, the alignment contains for context outside sequence: L1MdA2, L1Md17, L1Md6, L1Md1, DAC, R5, L1FTE. Some sequences in the alignment belong in L2, but are too short to place reliably within the tree.