Phylogenetic utility and evolution of indels: A study in neognathous birds

► Combined substitution and indel data yield a topology that cannot be obtained from either data set alone. ► The nucleotide insertion-to-deletion ratios indicate a rapid decrease of intron length. ► Indel fixation rate in neognathous birds is much faster than that in therian (placental) mammals. ► Indel fixation rates vary substantially among avian taxa and correlate with lineage-specific evolutionary rates.