FIG. 2.—

Neighbor joining phylogeny of autonomous hobo_AC elements based on 3 kb of the transposase domain. The boxed sequences indicate elements that are complete in the genome assembly we used. The presence of nested TE in complete hobo_AC elements was determined by running Repeatmasker with a library of repetitive sequences found in the anole genome. Seven different patterns of nested elements were recovered and are schematically presented on the right of each sequence (structure 3 corresponds to elements 93, 13, 10, and 253). Though all 45 elements are very similar to each other, they differ in their length and structure. The arrows on the right indicate the recombination of elements 3 and 4 resulting in element 1.