Chinese Journal of Zoology（Manuscript ID: 23108）-Patterns of Variation in Levels of Homoplasy of the Avian Morphological Characters-Electronic appendix

As one of the major groups of vertebrates, the evolutionary relationship of birds has been one of the main focuses of ornithological research. Morphological and molecular characters have been widely used to infer phylogenetic relationships in birds, but morphological characters have long been limited by homoplasy, making it difficult to draw consistent conclusions about phylogenetic relationships. However, benefiting from the molecular data and sophisticated analysis methods, we have gradually reached a consensus on the phylogenetic relationships of birds in recent years. On this basis, it is necessary to re-explore the research value of the neglected morphological data. The study is based on the family-level phylogenetic tree of birds published by Prum in 2015, and the set of morphological characters of birds published by Livezey & Zusi in 2006. We assessed the level of homoplasy of characters defined by Livezey & Zusi, compared the differences in the level of homoplasy of different morphological characters, and discussed the role of morphological characters in improving the phylogenetic signal of molecular characters and the support of molecular trees.The study is based on the family-level phylogenetic tree of birds published by Prum in 2015, and the set of morphological characters of birds published by Livezey & Zusi in 2006. We assessed the level of homoplasy of characters defined by Livezey & Zusi, compared the differences in the level of homoplasy of different morphological characters, and discussed the role of morphological characters in improving the phylogenetic signal of molecular characters and the support of molecular trees as well.This process was performed by using PAUP to calculate the fit scores generated by comparing the Prum reconstructed molecular tree and the Livezey & Zusi reconstructed morphological tree, separately, to the set of morphological characters, generating the tabular data in the “ Electronic Appendix 1 ” for subsequent comparison of the fit scores of the two sets. The topology of the Prum molecular tree was also Compared with the Livezey & Zusi morphology trees, generating the comparison plots in “ Electronic Appendix 2” to allow the reader to visualize the topological differences between the two trees.For comparing differences in levels of homogeneity of different morphological features, we executed the Kolmogorov-Smirnov test to assess whether the fit scores within the set of several morphological features conformed to a normal distribution, obtaining the results of the test in the “eAppendix 3” to make judgments about the subsequent parametric or nonparametric tests to be performed .When comparing the fit scores before and after the inclusion of morphological characters, we also performed the Kolmogorov-Smirnov test to assess whether the data before and after the inclusion of morphological characters conformed to a normal distribution, obtaining the results of the “ Electronic Appendix 4 ” to make a parametric or nonparametric test for subsequent judgment.Other specific research methods and results are described in the paper "Patterns of Variation in Levels of Homoplasy of the Avian Morphological Characters".