Disentangling the effects of selection and loss bias on gene dynamics

Significance Evolution of microbes is dominated by horizontal gene transfer and the incessant host–parasite arms race that promotes the evolution of diverse antiparasite defense systems. The evolutionary factors governing these processes are complex and difficult to disentangle, but rapidly growing genome databases provide ample material for testing evolutionary models. Rigorous mathematical modeling of evolutionary processes, combined with computer simulation and comparative genomics, allowed us to elucidate the evolutionary regimes of different classes of microbial genes. Only genes involved in key informational and metabolic pathways are subject to strong selection, whereas most of the others are effectively neutral or even burdensome. Mobile genetic elements and defense systems are costly, supporting the understanding that their evolution is governed by the same factors.