Fig. 6.

Clustering of hypermethylated LTR sequences in the phylogenetic trees. Neighbor-joining trees of members of (a) IAPLTR2a2, (b) IAPEY, and (c) IAPLTR2. Nucleotide sequences of the hypomethylated copies and randomly selected hypermethylated copies of the same subfamily were aligned using Clustal X [37] to generate a neighbor-joining tree on Mega5 [19]. Open and closed circles indicate hypomethylated and hypermethyated copies, respectively. In each panel, u1, u2, u3, etc. are locus names of hypomethylated copies, and m1, m2, m3, etc. are locus names of hypermethylated copies. The clade that includes the most hypomethylated copies (designated as hypomethylated clade) is indicated. The numbers on the nodes indicate bootstrap values (1000 replicates)