Evolutionary history of telomeric TE families. (A) Phylogeny of telomeric TE families inferred from ORF2 peptide sequences. Six major telomeric retrotransposon (TR) clades were identified, each with 100% bootstrap support (see Supplemental Fig. S6). The naming scheme is based on TR clades originally described by Villasante et al. (2007), with the addition of the novel TR5 and TR6 clades identified here. The tree branches are colored by TR clade, and the outer circle colors correspond to the host species clades shown in B. The tree is rooted using ORF2 sequences from nontelomeric Jockey clade TEs (data not shown) (see Supplemental Fig. S6). (B) Dated species tree showing major events in the diversification of Drosophila telomeric TEs based on species tree/TE tree reconciliation (see Methods). Rectangles are colored based on the TR clades shown in A. TR clade origins are indicated by filled rectangles, and losses are indicated by an “X.” Horizontal transfer events are summarized by circular (transfers within subgenera) and vertical (transfers between subgenera) arrows. Both types of arrows are colored based on TR clade. Two additional transfer events are shown by curved arrows: one giving rise to the origin of the TR2 clade (black arrow) and the other showing the transfer of a TR2 clade TE to the outgroup species Leucophenga varia (blue arrow). For additional descriptions of TR clade evolution, see Supplemental Text in the Supplemental Materials. Parentheses next to the major Drosophila species clades indicate the number of species harboring the corresponding TR clade over the total number of species within each species clade. (C) Rates of horizontal transfer for nontelomeric versus telomeric Jockey clade TEs.