Conversely, the evolution of domain combinations shows the opposite trend.
The origin and evolution of domain combinations are derived using the same procedure as that for single domains.
The threat of deliberate release of infectious agents in areas where they are not generally encountered, or the natural evolution of novel combinations of genetic material, exemplified by the H1N1 2009 pandemic variant [1], further stress the need for rapid identification of unexpected agents.
These constraints limit the variation of a species' vocal repertoire and may have played an important role in the evolution of meaningful combinations of calls [ 3, 4].
Thus, if we observe a strong linear relationship across genomes and even kingdoms, we conclude that there are intrinsic, domain-specific constraints that act on the evolution of domain combinations throughout the whole evolutionary history.
However, gene duplication is known to be a rare event in vertebrate genomes, and the recruitment of duplicated genes to a novel expression domain (neofunctionalization) is an even rarer process that requires the evolution of novel combinations of transcription factor binding sites in upstream regulatory regions.
Not only can the evolution of new combination types be inferred from domain trees, so can the divergence of two evolutionarily related domains.
Given these artifacts, the identity and evolution of individual domain combinations needs careful consideration, but the general trend in the evolution of domain combinations with respect to protein domains still holds.
In this study, two possible models were provided to explain the evolution of RNase H combinations in prokaryotic genomes.
In contrast, the primary structures of Rhs genes are evolutionarily conserved, indicating that rhs sequence diversity is driven, not by rapid mutation, but by the relatively slow evolution of novel core/tip combinations.
