Table 1. A priori predictions: Processes that may shift upon transition to an obligately host-dependent lifestyle.

Process	Rationale for predicted shift	Potential consequence for genome evolution
Reduced Ne and increased genetic drift	Population bottlenecks occur upon transmission to host offspring.	Accelerated fixation of slightly deleterious mutations under drift.
Shifts in selection coefficients	Selection may be relaxed on functions redundant in the intracellular niche. Host- level selection will favor nutritional functions and other host-beneficial traits.	Shifts in selective constraint across functions encoded.
Shifts in mutation rates	Stable intracellular niche may favor reduced mutation rates. However, interaction with host immune system may favor higher rates.	Shifts in rates of DNA sequence evolution.
	Small Ne may lead to higher mutation rate, due to reduced efficacy of selection favoring a low mutation rate.
Constrained gene exchange	Cellular sequestration may constrain gene exchange with genetically distinct bacteria.	Asexuality may exacerbate effects of genetic drift. Strong linkage implies that selective sweeps will purge diversity and possibly drive deleterious changes via genetic draft.