In order to make a direct link between function and the molecular evolution rate we labeled each pair with only their most specific shared functions from GO terms.
To further verify the selection pressure, we compared the evolution rates that we obtained with those of the four-fold degenerate sites that were suggested as neutral references in yeast [ 60]. 1,952,398 four-fold degenerate sites were identified in 6,392 yeast genes.
Consistent with other tissue-specific elements whose evolution occurs at higher rates,, we have shown that muscle-specific enhancers are strongly- but not ultra-conserved.
By combining transcription analysis, evolution rates and comparative genomics, we were able to define new candidates for the essential gene set of Buchnera.
Moreover, because of the variable evolution rate among species we observed, the clock model with independent rates among lineages specified by a log-normal probability distribution was adopted [ 29].
Based on competition among subpopulations with different mutation rates, we investigated the evolution of mutation rates in finite asexual populations.
We calculated the evolution rates of TFBSs in NRs and NDRs based on the method proposed by Moses et al. [ 37].
In the absence of relevant fossil evidence for Melanohalea, we used molecular evolution rates for RPB1, nuLSU, and mtSSU loci recently reported for Parmeliaceae [ 12].
In this study, we estimated gene evolution rates from the GC content of genes instead of from the non-synonymous substitution rates (Ka) as the two parameters are highly correlated in the AT-rich genome of Buchnera, and because the GC content allows for estimations of the two orphan genes of Buchnera.
Strikingly, we also found differences in molecular evolution rates among all three groups.
