Figure 1

Neighbor joining (NJ) trees of HERV-K(HML-2) sequences in the proviral reference sequence dataset for gag -derived cDNAs. The NJ-trees depict absolute numbers of nucleotide differences between the various sequences, excluding indels for pairwise comparisons, thus demonstrating private nucleotide differences between HML-2 loci. The tree on the right depicts a subset of sequences, labeled "modern" in the tree on the left, at higher resolution. Only HML-2 loci having the amplified gag region were included in the tree. The investigated gag region also includes a 96 bp region that distinguishes evolutionarily modern HERV-K(HML-2) from evolutionarily old (HERV-K(OLD)) proviruses. An intermediary group between modern and old proviruses is evident. For better resolution, a separate NJ tree for the modern HML-2 proviruses is shown at the right. For the sake of simplicity, only branches of proviruses identified as transcriptionally active in this study are indicated in the tree, other branches are unlabelled. Scale bars represent 5 nt differences in the left tree and 1 nt difference in the right tree.