| With the gradual decline of the neutralist-selectionist debate and the favoring of the selectionist's argument, the amount and type of natural selection acting at the molecular level is a major focus in genomics. Despite the ever-expanding amount of genes found with the footprint of positive selection, the majority falls into two categories, reproduction and immune/defense. This result is unsurprising given the strong selection pressure that is typically focused on specific amino acid sites within a gene from these categories. Because such strong selective pressure is needed to effect the measure of molecular selection, genes under weaker selection, yet still important for adaptation, may be undetectable. This work offers two methods, one previously derived, to detecting adaptation when selective forces are weak.; The measure of adaptive evolution, the rate ratio of nonsynonymous to synonymous substitutions (o) is notably conservative because positive selection (o > 1) is difficult to attain because protein structure is constrained. To compensate for the conservative nature, the first method identifies genes with significantly different o between lineages indicating shifts in selection. These shifts indicate changes in the selection acting on a gene, resulting from adaptation (higher o), decreased constraint (higher o), or increased constraint (lower o). The second method identifies positive selection acting on amino acid sites within a gene, so the constraint acting on the majority of the sites does not interfere with detecting adaptation. Each method was applied to a subset of genes comprising the four genomes of the bacterial plant pathogen, Xylella fastidiosa.; All methods performed better than the o > 1 measure, and found evidence of natural selection. While the site-specific model only found selection in pathogenic genes, differential selection was detected in both housekeeping and pathogenic genes. This suggests that the bacteria have adopted a generalized pathogenic response to different host environments, but adapt to the specific environment through selection shifts in housekeeping genes. |
