Fig. 5.—

Gene conversion between the plastid rpoC2 and mitochondrial ψrpoC2 genes of A. syriaca. (A) Plot of percent identity between homologous regions of the plastome and mitochondrial genomes of A. syriaca over a 20-bp sliding window. Green indicates 100% identity, brown <100% but at least 30% identity, and red <30% identity. Gap positions in the alignment were considered to have no identity. (B) ML phylogeny of plastid rpoC2 and mitochondrial ψrpoC2 sequences. The numbers above or below the branches are bootstrap support values. Plastid gene sequences are indicated in green and mitochondrial pseudogene sequences in black. In the absence of gene conversion or other confounding factors, both the plastid and mitochondrial sequences should produce monophyletic groups with identical branching orders; however, strongly supported placement of the A. syriaca mitochondrial pseudogene sequence in the plastid clade indicates sufficient gene conversion to affect the outcome of the phylogenetic analysis.