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This route of evolution plainly violates the Central Dogma.
This would be a typical case of subfunctionalization that is thought to be the preferred route of evolution of genes after duplication in modern genomes [ 136, 137].
This route of evolution conceivably was enabled by the virtual sequestration of intracellular parasites and symbionts from HGT and by the ensuing reduction of the effective population size 61, 62.
The MutS [ 71] and DAM [ 72] genes might have been acquired by mitochondrial genomes via horizontal gene transfer but in the case of RPS16 this route of evolution appears unlikely.
Clearly, under the « primordial eukaryotic lineage » scenario, viral hallmark genes in the NCLDV could plausibly originate from the primordial virus world, and transfer of genes from these viruses to the eukaryotic hosts potentially could be a major route of evolution.
The diversification of hydra-TRP-N4 (resp. its ancestor) may have been essential for the success of developing the cnidocyst weaponry and thus the success of this cnidarian-specific route of evolution.
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Alternative routes of evolution, such as duplication and subsequent inactivation of the ancestral poxvirus DNAP, cannot be formally ruled out but appear much less likely.
In Crenarchaeota, the DHH domain has partially deteriorated, losing the nuclease activity, and the RecJ-homolog apparently became a dedicated replication system component; the subsequent routes of evolution were notably different between the three major crenarchaeal branches (Sulfolobales, Desulforococcales and Thermoproteales), resulting in extreme sequence divergence.
The other example is the route of the evolution of NtdR (a regulator of the nitrotoluene degradation pathway) from NagR (a regulator of the naphthalene degradation pathway) (Ju et al. [2009]).
In addition to gene duplication, another route of gene evolution is the fusion of independent cistrons leading to bi- or multifunctional proteins (Brilli and Fani 2004b; Xie et al. 2003).
As shown in Figure 3, proteins in pattern 2 achieve the functional integration through combination with different domains, which is a predominant route of protein evolution.
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