Figure 3.

Gene conversion between the native and foreign copies of atp1. (A) Sections of the atp1 alignment that demonstrate three examples of gene conversion of the foreign pseudogene copies by functional native copies from Plantago. Regions of putative gene conversion are highlighted in blue when the converting and converted sequences are from the same individual and in green when the interacting sequences are from apparently different species (see text). The full atp1 alignment is available in Additional File 1a. (B) Maximum likelihood (ML) phylogenetic analysis of the mosaic evolutionary history of the foreign atp1 copy from Plantago macrorhiza line B (green). For this analysis, the sequence spanning nt 582-738 was separated from the rest of the P. macrorhiza B foreign atp1 sequence and both regions were included in the data set as independent sequences. All other converted regions, including the two other regions shown in (A) and the region converted by plastid atpA (Additional File 1a; [71]), were excluded prior to phylogenetic analysis. The final alignment contained 1185 bp. Bootstrap values >80% from 100 ML replicates are shown.