Fig. 3

Histograms showing the distribution of synonymous substitution rates calculated using codeml in PAML, dashed lines were placed at local maxima detected using scipy.signal.find_peaks_cwt with a range of 10 to 15. a and b taken together clearly show the division between the A and B subgenomes of Eleusine coracana and Oropetium thomaeum. a 23,975 synonymous substitution rates between the A subgenome and O. thomaeum with local maxima found at − 1.27, and 4.1. b 20,834 synonymous substitution rates between the B subgenome and O. thomaeum with local maxima found at − 1.26, and 4.12. c shows the split between Eleusine indica. c 14,443 synonymous substitution rates between the A subgenome and E. indica with local maxima found at − 9.07,-4.84, − 0.201, and 4.12. d 13,923 synonymous substitution rates between the B subgenome and E. indica with local maxima found at − 8.85, − 2.64, − 0.063, and 4.11. e closely mirrors d because the A subgenome is closely related to E. indica. e 22,052 synonymous substitution rates between the A subgenome and the B subgenome with local maxima found at − 8.88, − 2.68, − 0.001, and 4.15. They also show the signature of the A and B subgenome split. A number of these likely represent gene conversions events that would have been invisible to our homeolog calling method and some number could be the result of error that can occur at regions of homeologous crossover leading to miscategorization at the extreme bounds of a crossover. f 4037 synonymous substitution rates between A and a with local maxima found at − 9.1, − 2.96, and − 0.173. g 2530 synonymous substitution rates between B and B with local maxima found at − 3.04, and − 0.16