Figure 1 illustrates three possible scenarios that we consider for the change in transposition probabilities.
The step change in transposition rates is shown as a vertical line at the 5000 t h generation.
In the second scenario (burst, no regulation), we introduce a 100-fold step change in transposition probability at the 5000 t h generation.
To check for changes in the transposition rate, we fit models in which transposition rates vary exponentially with time.
At least two TE families show clear changes in their transposition dynamics: in Fot2 and Fot6, the transposition rate tends to decrease with time.
Departure from this linear pattern denotes deletions or changes in the transposition rate and can be used as a basis for parameter estimation.
Unfortunately, empirical insights remain scarce and information about TE dynamics in genomes, such as changes in the transposition rate or correlations between different TE families, do not cover enough species nor enough TE families to provide broad and general inference about genome evolution.
Many of these changes are either in Ty1 transposons, where copy number changes can be explained by differences in transposition rates, or in tandemly-repeated genes, where gene copy number changes can be explained by unequal cross-overs [ 35, 36].
In addition to point mutations, other mutations were generally shown as the changes in genomic structure: inversion, transposition, translocation and duplication, gene gain and gene lost, gene fusion and gene split, gene fragmentation (pseudogene) or insertion and deletion (indel).
However, inversions might be not the only mutational events causing gene order changes in chlorophytes cpDNAs, as transpositions have been proposed to account for some of the rearrangements observed in Campanulaceae [ 30] and in subclover [ 31] cpDNAs.
