An evaluation of the usefulness of morphological characters to infer higher-level relationships in birds by mapping them to a molecular phylogeny

The considerable morphological variation observed among birds was codified into phylogenetic characters by Livezey and Zusi (2006). Herein we have evaluated the phylogenetic signal of 1,860 of these characters by mapping them to a molecular phylogeny including 102 taxa that represent all extant birds (with the underlying assumption that this tree topology is a good estimate of the evolutionary relationships among birds). The characters fit the molecular tree with a mean consistency index (CI) of 0.38. Muscle characters are the most homoplasious (CI 0.32), while characters related to integument, feathers, intestinal, respiratory, syrinx, urogenital, nervous, and reproductive organs show a considerably better fit (mean CI 0.49). We also explored what characters may unambiguously support certain basal clades that are well-supported by molecular data. We found only a few clades (e.g., Galloanserae, Procellarimorphae) being supported by unambiguous apomorphies, while many well-established clades (e.g., Pelecaniformes, Charadriiformes, Accipitriformes, Coraciiformes) lack such support entirely.

Methods
The dataset consists of a PAUP-file used to analyse the fit of the morphological variation among birds described by Livezey & Zusi (Livezey BC, Zusi RL. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy: I. – Methods and characters. Bulletin of the Carnegie Museum of Natural History 2006; 37; 1-556) to different molecular-based higher-level avian phylogenies published by Prum et al. (Prum RO, Berv JS, Dornburg A, et al., A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 2015; 526; 569-573) and Hackett et al. (Hackett SJ, Kimball RT, Reddy S, et al., A phylogenomic study of birds reveals their evolutionary history. Science 2008; 320; 1763-1768).