Beneficial mutations can arise within individuals neutral to the mutation's utility; variants demonstrating the change can then be selectively sorted from the progenitor population by the environment. This observation alone does not exclude the possibility that selective forces can also influence either the generation of genetic alterations, beneficial or otherwise, or the retention of alterations. Inheritable changes can be of at least two types: those that alter the genome by changing its DNA sequence (genetic), and those that establish a self- perpetuating physiological state (epigenetic) in individuals within an otherwise isogeneic population. Both genetic and epigenetic changes that favor a cell's survival may occur in organisms after exposure to an environment. I have demonstrated the existence of mechanisms that allow eukaryotes to adapt to growth-halting environments after exposure of the organism to the environment. The mechanisms result in the change of genomic DNA sequence at specific (selected) loci nonrandomly. These changes are the result of recombination and require only some of the components of the homologous recombination machinery. Environmentally induced changes in microbes could compromise the efficacy of vaccine- based therapies.
