Phylogenetic trees of subfamily structure based on LTR nucleotide sequence data. LTRs from full, fragmented, and solo LTR elements were aligned via ClustalX 1.8 (Thompson et al. 1997), and the NJ method was used to construct trees. Insertions/deletions were ignored. Values on individual branches are bootstrap percentages based on 1000 bootstrap repetitions. Each LTR in the tree is named by the genomic clone in which it was found. For elements with two LTRs, the 3′ LTR is labeled by a lower case “b” following the clone number. Each tree is shown with a scale bar determined by the number of nucleotide substitutions per site between two sequences. (A) Phylogenetic tree displaying substructure within Cer8 and Cer9 families, with Cer7 as the outgroup. The tight branching of the tree demonstrates the high sequence identity shared amongCer9 family members. * indicates the presence of a ∼108 bp insert in the center of Cer9 LTR; ** indicates the presence of a ∼106 bp insert in the center of the Cer9 LTR. Both inserts are >85% identical. (B) Phylogenetic tree displaying substructure within Cer12 and Cer16 families, withCer7 as the outgroup. Cer12 consists of two subfamilies (Cer12 and 12-1); Cer16 has three subfamilies (Cer16, 16-1, and 16-2). The tight clustering seen in both families represents a high degree of nucleotide identity between elements within a subfamily.