Fig. 3.

A non-adaptationist model for consequences of codiversification in microbiomes. In Step 1, a host lineage evolves permissive but variable filters for a gut microbiome, allowing diverse microbes to colonize its gut. In Step 2, a subset of microbes (dark outline) specialize in the host lineage, losing genes necessary to colonize diverse environments in favor of specialization on the particular host niche. As host genes creating this specific niche drift, the specialized microbes follow. In Step 3, the codiversifying microbes are now reliable environmental stimuli, and serve as developmental cues, reducing constraint on the host genome for essential processes. Mutations in the host genome arise that are neutral in the presence of these microbes, but deleterious in their absence. For example, an essential host-encoded developmental molecule X is required to signal Y. Microbial product Z elicits a similar downstream effect as X. At some point, a mutation in the host genome results in the loss of function of X, which is neutral when microbially encoded Z is present. In Step 4, in the absence of the codiversifying microbe, neither X nor Z is present to signal to Y, resulting in reduced fitness of the host