Speciation in the shadow of recombination and lateral gene transfer

Advances in population genetics and genomics driven by more efficient and affordable DNA sequencing and analyses have uncovered large variety in the patterns of microbial genetic diversity. The fact that genes can be horizontally transmitted at unexpectedly high rates within and between related asexually reproducing lineages radically changed our understanding of prokaryotic evolution and ecology. Consequently, we have had to change the view of species as monolithic discrete units and acknowledge that most data actually support much fuzzier distinctions. Here, we review population genetics, genomics, and experimental genetics findings that convey a complex picture of microbial speciation processes and highlight some underappreciated forces of microbial speciation including biogeography.