Research data supporting "Revealing patterns of homoplasy in discrete phylogenetic datasets with a cross-comparable index"

Datasets include published phylogenetic matrices and trees that were used in analyses in the manuscript "Revealing patterns of homoplasy in discrete phylogenetic datasets with a cross-comparable index" in Zoological Journal of the Linnean Society. List of data files Empirical tree files These Newark format PHYLIP files represent the topologies derived from the empirical studies and were used in Analysis 1. Some are rooted and some are not fully bifurcating. • Telluraves (Ksepka et al., 2019): ‘Telluraves_tree.phy’. • Passeriformes a (Steell et al., 2023): ‘Passeriformes_a_tree.phy’. • Passeriformes b (Steell et al., 2023): ‘Passeriformes_b_tree.phy’. • Neornithes (Field et al., 2020): ‘Neornithes_tree.nex’. • Avialae a (Benito et al., 2022): ‘Avialae_a_tree.nex’. • Avialae b (Benito et al., 2022): ‘Avialae_b_tree.nex’. Dichotomous trees for simulations These Newark format PHYLIP files represent fully dichotomous trees where nodes were randomly resolved when populating branch lengths using the accelerated transformation algorithm (see extended methods above). Branch lengths represent morphological change. These trees were used in all simulations for this study (Analyses 2-5). • Telluraves (Ksepka et al., 2019): ‘Telluraves_tree_branchlengths_dichot.phy’. • Passeriformes a (Steell et al., 2023): ‘Passeriformes_tree_branchlengths_dichot.phy’. • Neornithes (Field et al., 2020): ‘Neornithes_tree_branchlengths_dichot.phy’. • Avialae a (Benito et al., 2022): ‘Avialae_tree_branchlengths_dichot.phy’. Empirical character taxon matrices NEXUS files of empirical character taxon matrices used in Analysis 1. • Telluraves (Ksepka et al., 2019): ‘Telluraves_matrix.nex’. • Passeriformes a (Steell et al., 2023): ‘Passeriformes_matrix_a.nex’. • Passeriformes b (Steell et al., 2023): ‘Passeriformes_matrix_b.nex’. • Neornithes (Field et al., 2020): ‘Neornithes_matrix.nex’. • Avialae a and b (Benito et al., 2022): ‘Avialae_matrix.nex’. Empirical datasets came from the following publications: Benito, J., Kuo, P. C., Widrig, K. E., Jagt, J. W. M., & Field, D. J. (2022). Cretaceous ornithurine supports a neognathous crown bird ancestor. Nature, 612(7938), 100–105. https://doi.org/10.1038/s41586-022-05445-y Field, D. J., Benito, J., Chen, A., Jagt, J. W. M., & Ksepka, D. T. (2020). Late Cretaceous neornithine from Europe illuminates the origins of crown birds. Nature, 579(7799), 397–401. https://doi.org/10.1038/s41586-020-2096-0 Steell, E. M., Nguyen, J. M. T., Benson, R. B. J., & Field, D. J. (2023). Comparative anatomy of the passerine carpometacarpus helps illuminate the early fossil record of crown Passeriformes. Journal of Anatomy, 242(3), 495–509. https://doi.org/10.1111/joa.13761 Ksepka, D. T., Grande, L., & Mayr, G. (2019). Oldest Finch-Beaked Birds Reveal Parallel Ecological Radiations in the Earliest Evolution of Passerines. Current Biology, 29(4), 657-663.e1. https://doi.org/10.1016/j.cub.2018.12.040