Discovering complete quasispecies in bacterial genomes

ABSTRACT Mobile genetic elements can be found in almost all genomes. Possibly the most common non-autonomous mobile genetic elements in bacteria are REPINs that can occur hundreds of times within a genome. The sum of all REPINs within a genome are an evolving populations because they replicate and mutate. We know the exact composition of this population and the sequence of each member of a REPIN population, in contrast to most other biological populations. Here, we model the evolution of REPINs as quasispecies. We fit our quasispecies model to ten different REPIN populations from ten different bacterial strains and estimate duplication rates. We find that our estimated duplication rates range from about 5 × 10 −9 to 37 × 10 −9 duplications per generation per genome. The small range and the low level of the REPIN duplication rates suggest a universal trade-off between the survival of the REPIN population and the reduction of the mutational load for the host genome. The REPIN populations we investigated also possess features typical of other natural populations. One population shows hallmarks of a population that is going extinct, another population seems to be growing in size and we also see an example of competition between two REPIN populations.