Figure 1: Retroposon evidence for the early branching events in the avian tree of life.

The tree topology is derived from our presence/absence matrix (Supplementary Table S1; Supplementary Software) utilizing maximum parsimony and considering representatives of the key avian lineages^13,14. Black filled circles (branch A) are bird-specific retroposon insertions (exhibiting a 6-nt deletion that is found in some avian CR1s, but absent in all other avian and reptilian CR1s), and dark grey balls represent retroposon presence/absence markers that are congruent with one another. Light grey balls on grey gradient (label F) are retroposon markers that were probably inserted at the very beginning of the neoavian radiation and were subjected to incomplete lineage sorting of retroposon dimorphisms, as they exhibit presence/absence patterns that are incongruent with one another and with some of the retroposon markers on the dashed branches. Nodes without retroposon support are not collapsed (but highlighted by asterisks) if they received very strong support in nucleotide sequence analyses^12,13,14. Higher-ranking taxa are in red letters (English terms in orange letters and parentheses), including the new taxa Eufalconimorphae (falcons+parrots+passerines) and Psittacopasserae (parrots+passerines), and some recently introduced superordinal groupings^14,53,54. Bird names in bold letters belong to the nearest bird icon.