Supplementary Text

This document comtains supplementary material to H.-J. Sun et al. (2018b).

It describes the morphological dataset and the results of tree searches using Fitch parsimony and a Bayesian method: approaches that are subject to errors resulting from logically incoherent treatment of inapplicable data (Maddison, 1993). We also present the results of tree searches with the algorithm described by Brazeau, Guillerme, & Smith (2018), which reduces error due to inapplicable data in a parsimony setting. Finally, we document how each character is parsimoniously reconstructed on optimal trees.

Supplementary figures and tables appear after the text.

References

Sun, H.-J., Smith, M. R., Zeng, H., Zhao, F.-C., Li, G.-X., & Zhu, M.-Y. (2018b). Hyoliths with pedicles illuminate the origin of the brachiopod body plan. Proceedings of the Royal Society B: Biological Sciences, 285(1887), 20181780. doi:10.1098/rspb.2018.1780

Maddison, W. P. (1993). Missing data versus missing characters in phylogenetic analysis. Systematic Biology, 42(4), 576–581. doi:10.1093/sysbio/42.4.576

Brazeau, M. D., Guillerme, T., & Smith, M. R. (2018). An algorithm for morphological phylogenetic analysis with inapplicable data. Systematic Biology. doi:10.1101/209775