Before microbes or any of their component molecules ever had direct contact with cells of the innate immune system, they could be detected by proteins that were retained in evolution for this express purpose.
To investigate this, and gain further insight into why these three duplicate genes have been retained in evolution, we carried out gene disruption followed by RNA-seq gene expression profiling.
This indicates that ATP-requiring enzymes, respectively the genes encoding their catalysts, have a higher propensity to be retained in the course of network evolution and that the retention of ATP-requiring reactions may be one of the selective forces acting on network evolution.
In fact, the percentage of ATP-consuming reactions in a given organism negatively correlated with that organism's total number of core metabolic reactions (Spearman coefficient -0.95, p < 0.0001), indicating that ATP-consuming reactions have a higher propensity to be retained in the course of network evolution.
James Leebens-Mack, a plant geneticist at the University of Georgia in Athens, agrees: "We now need to determine whether certain types of genes tended to be retained in duplicate and investigate how functional evolution of these genes contributed to major innovations such as the origin of the seed".
One group of elements was identified as providing useful affordances that communicate important aspects of the theory of evolution that should be retained in the new visualization.
At some early stage during the evolution of viviparous mammals, eggs came to be retained in the oviducts of the mother.
At the early stages, genome duplication may increase evolutionary rates of duplicated genes21,22 and may facilitate the evolution of a new adaptive function because the original function can be retained in other copies (so-called neofunctionalization model)23,24.
In accord with these findings, we estimated that ancestral introns have a high probability to be retained in extant genomes, and conversely, that a substantial fraction of extant introns have retained their positions since the early stages of eukaryotic evolution.
Both of these patches are well conserved in aSelBL (green boxes, Figure 2), suggesting ribosome binding may also have been retained in aSelBL evolution.
