Second, since MTs are multifunctional proteins, their structures may have been subjected to a constant evolutionary "push and pull" by competing functional pressures which could have resulted in some convergent evolution of particular structural subunits.
It is well known that NJ have better properties than UPGMA when reconstructing evolutionary trees because it does not assume a constant evolutionary rate [ 20].
The majority of plant miRNAs are evolutionarily young and are only present in one to few species and it is likely that MIR loci in plant genomes are in a constant dynamic evolutionary state [ 15, 16].
Thus, these genes may be in a constant process of evolutionary updating between species.
This observation reminds us a classic concept of molecular clock, which claims an approximately constant evolutionary rate over time for any given protein or DNA sequence in all lineages [ 35].
This obvious contradiction, however, may be resolved by interpreting it in light of the constant evolutionary struggle between host and pathogen: DDX3X may have evolved as an antiviral protein, but viruses then, in turn, developed strategies to hijack DDX3X function and use it for their own benefit, thereby counteracting the antiviral effect of DDX3X.
Indeed, our results imply that, in general, loops are under constant evolutionary constraints which, apparently, are weaker than those for a protein core but still strong enough to preserve the loop overall structure.
These results can explain phenotypic divergence in a constant environment and also how evolutionary jumps and adaptive radiations involve altered gene regulation.
The fourth data set was simulated using the same tree topology as in the primary example but with constant evolutionary rate (see Materials and Methods).
