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Whether the evolution of functions is tree-like as the authors repeatedly claim could be tested by reconstructing a phylogenetic network based on the functional content of genomes.
Evolution in general is much more than the evolution of cells, or the evolution of functions (even if these two aspects are very important to understand evolution).
The evolution of functions that are associated with corresponding FFs along the timeline reveals that primordial metabolic domains evolved earlier than informational domains involved in translation and transcription, supporting the metabolism-first hypothesis rather than the RNA world scenario.
The tree of functions - if it can be reconstructed- would certainly be informative about the evolution of functions; the tree of cells divisions - if it can be reconstructed- will be informative about a part of cellular evolution.
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Cis transcriptional regulation is a powerful driving force in the evolution of function and form [1], [2].
The evolution of function is consistent with the evolution of network topologies.
Inferring the evolutionary histories of families is an important step in understanding the evolution of function.
Therefore the ability to infer the evolutionary histories of families is an important step in understanding the evolution of function.
These sequencing efforts delivered and continue to deliver valuable insights into the evolution of function and species.
Then, to examine the driving force for the evolution of function for genes in Groups 2a and 3, we further analyzed adaptive evolution at the amino acid level.
In short, our process represents homology inference in terms of a gene family-specific model of the evolution of function within that family.
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