Figure 4

Allelic gene conversion between within array Tb62 (adenylate cyclase, Tb927.7.6080), identified by compatibility criterion. A. SISCAN output, showing the changes in phylogenetic signal along a multiple alignment of gene copies 2, 3 and 4. Genetic distances were calculated to identify the closest relatives from three sequences using a sliding window approach. Coloured lines represent the three phylogenetic resolutions: copies 2 and 3 as closest relatives (red), 2 and 4 (blue) and 3 and 4 (green). The significance of observed similarity is assessed through randomisation of the sequences within a given window and expressed as a Z-score; if the similarity persists over many replicates, outweighing the contribution of any compositional bias, the observation is significant (where the Z-score exceeds 1.96). B. Diagram of the chromosomal position of Tb62. Dashed lines link gene copies to putative breakpoints. C. RETICULATE output. The multiple alignment of all copies is represented by both axes and shaded areas identify where there is incompatibility between the phylogenetic signal of two different regions.