Perovskite-type La2Ti2O7 (LTO), having a layered structure and the separated H2 and O2 evolution sites, is attractive as an efficient photocatalyst.
However during the course of evolution some sites are strictly conserved (for correct folding) whereas others could be subject to positive selection [15].
Hence, under the neutral theory of molecular evolution, conserved sites are assumed to indicate functional or structural importance, while variable sites may be regarded as evolving free from, or under weak, selective constraints.
But coevolution may also be defined in a broader sense, as correlated evolution: two sites are said to be non-independent if they tend to undergo substitution events in the same branches of the tree.
Covarion models implemented in PROCOV may be especially useful for phylogenetic estimation when ancient divergences between sequences have occurred and rates of evolution at sites are likely to have changed over the tree.
PROCOV is a phylogenetic program to infer phylogeny under covarion models, which may be especially useful for problems involving estimates of deep divergences in the tree of life, where rates of evolution at sites are likely to have changed over the tree.
The BX3, BX5 and BX4 clades in our phylogeny are under strong adaptive evolution and some sites are under positive selection.
It is also interesting that coding fRNAs have a relatively greater influence on synonymous site evolution because synonymous sites are traditionally considered to evolve at a neutral rate, and we show that predicted coding fRNAs may be a significant source of non-neutral evolution at synonymous sites.
This was considered necessary as positively selected sites undergo convergent evolution whereas other sites are subject to neutral or nearly neutral drift, and different evolutionary mechanisms inevitably violate assumptions of the SRD06 evolutionary model [59].
The overall trends in the evolution of alternative sites are the same as in the case of cassette exons.
