The existence of large amounts of within-species genome content variability is puzzling. Population genetics tells us that fitness effects of new variants—either deleterious, neutral or advantageous—combined with the long-term effective population size of the species determines the likelihood of a new variant being removed, spreading to fixation or remaining polymorphic. Consequently, we expect that selection and drift will reduce genetic variation, which makes large amounts of gene content variation in some species so puzzling. Here, we amalgamate population genetic theory with models of horizontal gene transfer and assert that pangenomes most easily arise in organisms with large long-term effective population sizes, as a consequence of acquiring advantageous genes, and that the focal species has the ability to migrate to new niches. Therefore, we suggest that pangenomes are the result of adaptive, not neutral, evolution.
McInerney, J. O., McNally, A., & O'Connell, M. J. (2017). Why prokaryotes have pangenomes. Nature Microbiology, 2(4), https://doi.org/10.1038/nmicrobiol.2017.40