Supplementary Figure 2

The impact of missing data on quartet informativeness for simulated data (a-f) and the empirical Viburnum data set (g). This is an extension of Fig. 1. Data were simulated on three topologies, a balanced tree, an imbalanced tree, and the Viburnum topology with branch lengths scaled by penalized likelihood, and the outgroup removed. The number of loci that are quartet informative for each split is shown under each tree. In the absence of missing data all 1,000 simulated loci are informative about every edge (a-f; black circles). Under mutation-disruption (a-c) quartet information is lost faster in double-digest data (light grey) than in single-digest data (dark grey), and its effect varies depending on tree shape (see description in Fig. 1). Data simulated at low sequencing coverage (d-f) had either 50% (dark grey) or 80% (light grey)
of data randomly missing. Here the effect of tree shape is more pronounced. Nearly all information is recovered across the deepest splits in the balanced topology (d) due to its hierarchical redundancy, but no data is recovered in the imbalanced topology (e) which does not increase in hierarchical redundancy across deeper edges. The empiricalViburnum topology is relatively balanced, and data simulated on this topology (c, f) appears similar to that simulated on the balanced topology (a, d). The true distribution of quartet informativeness recovered in the Viburnum RAD-seq data set (g) is similar to the expectation when data were simulated on this topology under low sequencing coverage (f).