1000-Character Data Sets with Missing Data

Publication: Wright AM and Hillis DM (2014). Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data. PLOS ONE. Contents: 1000-character data sets with missing data, and the phylogenetic trees estimated from these sets. Details: These data sets were simulated along the tree in Fig. 1 of the paper, and contain 1000 characters. To assess the effects of missing data on phylogenetic estimation, we used several schemes for character deletion. We sorted the characters by rate of change, and divided them into three categories: fast-, intermediate-, and slow-evolving sites. Within each class of sites, we created data sets in which we removed between 10% and 100% of sites to investigate the effects of underrepresentation of certain classes of characters. Missing data were concentrated in fossil taxa, as seen in Figure 2.