Our genomic analysis further grouped the clusters into 286 highly diversified cluster families (CF) of pathways.
On the opposite, several poorly diversified clusters (SDR52E, 73C, 152C, 87D, 357C) that contain highly conserved sequences participate in primary metabolism such as chlorophyll synthesis or degradation, lipid metabolism or vitamin synthesis.
To explore whether pathogen antagonism could provide an explanation, we analyzed IL4 sequences from multiple mammalian lineages and found a strong signature of diversifying selection, clustered at interfaces that interact not only with IL4Rα but also with IL13α1.
Just as purifying selection acts to cluster substitutions along the sequence of a protein, there is evidence that diversifying selection leads to clustering as well.
The Dadaab GA2 strains diversified into 2 main clusters (branches on the tree) that met our clade definition, and were named clade GA2 (2.1) and GA2 (2.2) (see Figure 3).
The second hypothesis is that following cluster assembly, these gene clusters diverged over time as ascomycetes diversified, creating the subclade relationships now observed (Fig. 6b).
Sequences obtained early after infection (12 wpi) from these SMs were closely related but subsequently diversified, forming animal and time-point-specific clusters.
As for the tandem duplicated clusters with two genes, their expression patterns diversified significantly, indicative of substantial neofunctionalization during subsequent evolution processes.
It is possible that this clustering indicates diversifying selection acting on PPR genes from that region as a result of plants adapting to newly emerging sterility inducing genes.
Synthesizing the above, there is evidence that both negative purifying selection and positive diversifying selection promote the clustering of amino acid differences in a pairwise comparison of protein sequences.
