Inferring Phylogenies from RAD Sequence Data
Figure 3
Accuracy of the RAD method for inferring Drosophila phylogeny.
Proportions are indicated on the left axis. The x-axis shows the percent similarity used for clustering, the three rows show each minimum cluster size, and the read lengths and restriction sites used are indicated by column. Gray bars represent total matrix length as represented on the right axis. Black points are the mean proportion of correct nodes in a tree (out of a total of 9), blue points are the mean proportion of correct nodes with bootstrap support greater than 70%, and red points are the mean proportion of incorrect nodes with bootstrap support greater than 70%. Purple points are the proportion of clusters that are orthologous and yellow points are the proportion of invariant sites within clusters. Results from every set of parameters are shown. Points represent the mean ± SE of the five replicates of clustering, filtering, and tree inference for each set of parameters with randomized input order of sequences into UCLUST. However, not all parameters produced five usable matrices (one or more taxa with all empty sequence). The number of successful replicates is shown in Table S2.