Figure 2

An overview of the Ortholuge method. (A) Flow-chart outlining the main steps of the method. (B) The three ratios computed by Ortholuge. The phylogenetic distances in the numerator (dark line) and denominator (dashed line) for each ratio is shown, overlaid on the phylogenetic tree (gray line) that relates the ingroups and outgroup. Note that the three ratios are related such that Ratio2 = Ratio1 × Ratio3. Therefore, ratio data is presented both in terms of frequency histograms for all three ratios (see Fig. 4) and also as Ratio1 × Ratio2 plots (see Fig. 5) for just two of the three ratios – the latter is simply another way to conveniently visualize the data.