Fig. 6

Nucleotide diversity (π) across the plastid genome of Campanula americana. A, Upper panel shows the sliding window analysis of π obtained from a whole-genome alignment including all Western, Eastern and Appalachian lineages. Lower panel shows the π analysis within-lineage (Western, purple; Eastern, orange; Appalachian, green). B, Dispersed repeats across the Western lineage and Appalachian lineage plastid genome. Gray links represent shared repeats between genomes, while purple and green represent repeats with different nucleotide sequence for Western and Appalachian lineages, respectively. The π hotspots shown in panel A match the regions with divergent repetitive DNA sequences between lineages. C, Nucleotide diversity of individual gene alignments. The genes involved in replication show higher π values compared to genes involved in photosynthesis