Figure 3.

Distribution of apparent homoplasies. Position along the genome is shown on the x axis and homoplasy degree, the number of times a particular mutation has occurred in excess in the tree as inferred by maximum likelihood, is shown on the y axis (left). Individual mutations are marked by vertical lines, synonymous ones in green and non-synonymous in red. The ratio of apparent homoplasy over synapomorphy kernel density estimates (bandwidth = 0.1) is shown in blue for synonymous (dashed) and non-synonymous (solid) sites separately. Arrows at the top indicate the positions and names of coding sequences within the MERS-CoV genome.