Figure 5

TEs became conserved after transforming or inserting into ANRIL exons. MEGA 5.1 was used to predict the most appropriate substitution models and to build ML (maximum likelihood) trees. Both trees were built using the Tamura three-parameter model. Numbers indicate bootstrap values, and the scale at the bottom measures genetic distances in nucleotide substitutions per site. (A) ML tree of exon 13 (E13TE13) and TE13 (the highest-scoring free TE13 located outside the ANRIL gene). All E13TE13 sequences are clustered together in a large subtree with a reasonable topology (marked by the large dashed square). In simians, the E13TE13 sequences are not only clustered together but also have short terminal branches (marked by the small dashed square). In contrast, the free TE13 sequences are clustered together in the remaining large subtree with a meaningless topology. A relative-rate test confirms that mammalian TE13 sequences have evolved more rapidly than simian E13TE13 sequences. Thus, the insertion of TE13 into ANRIL (not merely into an ANRIL exon) also constrained the evolution of TE13. (B) ML tree of E3TE3 (the TE3 in exon 3) and TE3 (the highest-scoring free TE3 located outside ANRIL). All E3TE3 sequences in simians are not only clustered together but also have short terminal branches. In agreement with Figure 4, this result indicates that TE3 became highly conserved after inserting into exon 3.