Fig. 3

Emergence and timing of CR1-mobilized SINE activity during early passerine evolution. a Phylogenomic analysis of early passerine relationships using retroposon presence/absence markers (colored balls) mapped on a maximum likelihood phylogeny of concatenated retroposon-flanking sequences (GTRCAT model, 1000 bootstrap replicates; Additional file 5). The single conflicting marker on the Eupasseres branch (Tgu10, cf. Additional file 1: Table S2) is indicated by a red ball with black circle and was likely affected by incomplete lineage sorting within Suboscines. Our sampling consists of the major deep passerine lineages sensu Barker et al. [23]. The later additions of two genome assemblies (Corvus cornix and Manacus vitellinus) were only included in the presence/absence table (Additional file 1: Table S2). Red and green asterisks indicate emergence of TguSINE1 and PittSINE, respectively. The black asterisk indicates that for some loci (Additional file 1: Table S2), Malurus cyaneus was sampled instead of Myzomela eques to represent the Maluridae/Meliphagidae clade [23]. Only bootstrap values <100% are shown and the names of pictured birds are emphasized in bold. b A scenario for the emergence of PittSINE. Template switching from TguSINE1 RNA (red, tRNA^Ile head; orange, CR1 tail) to tRNA^Asp (green) during target-primed reverse transcription by CR1 reverse transcriptase (blue). The resultant tRNA^Asp-CR1 chimaera was flanked by a target site duplication (grey) and transcriptional activation gave rise to the PittSINE family