To determine ω these methods, in addition to previously used variables, consider two major features of DNA evolution: the transition/transversion bias and the base or codon frequency bias.
As a simple model of DNA evolution, the Jukes-Cantor formula [33] is applied to estimate a probability of change for each base pair, with a customizable transition rate α (0.001 by default) and time t based on the edge weights.
Interestingly enough we find again that the description of the SS at the model level resembles mechanisms of DNA evolution, where the process involved is of copy and mutation.
For ML analyses, the best model of DNA evolution for the concatenated dataset was chosen among 56 nested models with Modeltest 3.7 [ 32].
For this purpose, MrModeltest v 2.2 [ 62] was used to determine the optimal available models of DNA evolution under the AIC criterion [ 63].
With Acorus included (Figs. 2I and 2L), it also shows monocots as monophyletic, consistent with a large body of evidence [ 7, 35, 41- 43, 63], and depicts faster chloroplast DNA evolution on the monocot lineage leading to grasses than in the Acorus lineage, also consistent with a substantial body of evidence (e.g. [ 9, 44]).
Mitochondrial DNA evolution at the population level may be modulated for example by the climatic variables [ 4] or by the diet of individuals [ 29].
Complete mitochondrial genome sequencing from poorly investigated groups is needed to supplement a gap in our current understanding of mitochondrial DNA evolution in the metazoa.
Gene trees were reconstructed using PhyML (Phylogenetic estimation using Maximum Likelihood) [ 50, 51] with the General Time Reversible plus Gamma (GTR + G) substitution model of DNA evolution, and the Subtree Pruning-Regrafting (SPR) branch-swapping method.
To investigate the potential impact of RHE on early metazoan mt DNA evolution, we studied the IGRs in all available mt genomes from sponges, which form the basal divergence with Eumetazoa within the animal lineage [ 29].
In addition, Wolbachia can affect host mitochondrial DNA evolution, because of the linkage between Wolbachia and associated mitochondrial haplotypes, and thus confound host phylogeny based on mtDNA.
