By combining structural and sequence analysis, and phylogenetic inference, we have explored the evolutionary history of classes A, B, E, F, and G and demonstrate that their multidomain architectures reflect their phylogenetic relationships, suggesting that the main evolutionary steps in their divergence are likely to have arisen from the recruitment of different domains.
Generally, gene duplications are thought to be an important precursor to the functional divergence of genes, and selection is the main evolutionary force driving gene function diversification [ 22, 52, 55– 55].
There is also a turning point after this early diversification (around 20 Mya), when observed disparity within lineages is smaller than expected under neutral evolution, suggesting that stabilising selection was the main evolutionary force constraining diversification within lineages after the main ecological divergence had taken place.
Overall, our results in rice support the findings in human and Arabidopsis that purifying selection is one of the main evolutionary forces acting on rice MIRNA genes, maintaining lower levels of sequence divergence in mature miRNAs than in their flanking regions.
Within such an ortholog group, the general expectation is that the main evolutionary force is purifying selection, which is reflected as sequence conservation, with most divergence between the orthologs arising from neutral substitutions.
While this representation is interesting to understand the effectiveness of JSD as a genetic divergence measure, it also confirms the findings of [11] regarding the main evolutionary scenario for CN.
In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions.
Two main evolutionary scenarios have been proposed.
These developmental patterns allow understanding of evolutionary divergences in metazoans and of the relationships among phyla.
What factors explain the extent to which divergent selection drives evolutionary divergence?
