- The purpose of this tree to provide a framework of LINE-1 sequences separated by strong bootstrap values defining the known lineages prior to the A2/TF split. The apomorphies defined are then used in GenBank searches and library screenings to find additional sequences to populate and define the various segments of the LINE-1 history.
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Statistics
- Because the sequences were chosen to be widely spaced, and only a couple of representatives of known lineages are used, there are few homoplasies in evidence. Most ambiguities listed are due to the truncation patterns of the various sequences.
- As the tree is filled in, additional homoplasies appear. We see a distribution with the overall data where 1/3 of positions are homoplasic between different main stem locations, and most of those positions engage in more than one homoplasy. Many of these are CG columns. Others are suspected reverse transcriptional mutations hotspots. Some are just coincidental parallel and back mutation. Some of the positions that are known to be homoplasic due to information from outside this alignment are flagged in the apomorphies list.
- Homoplasy in LINE-1 is often assumed to be due to gene conversion. As branches are added that pack close together, there is an increased incidenceof homoplasy of the kind that a substitution appears to occur and then revert soon after. This may reflect gene conversion limited to pairs of very homologous sequences.
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Sources of sequence