The hologenome theory of evolution proposes that evolutionary forces acting at the level of an individual organism (e.g., a single plant or animal) are instead acting on the "holobiont" - the inherent community of a host plus all of its symbiotic microbes. As selection operates on phenotypes, classic individual selection is effectively selection on the holobiont. Consequently, the collective genomes of the holobiont form a "hologenome". Variation in the hologenome encodes variation in phenotypes upon which evolutionary forces such as selection or neutrality can operate. Although there is a rich literature on binary host–microbe symbioses, the hologenome theory distinguishes itself by including the vast symbiotic complexity inherent in macroscopic individuals. The development of the theory and current expansions are summarized in an open access platform.
