As we observe the 200th anniversary of Charles Darwin's birth, microbiologists interested in the application of Darwin's ideas to the microscopic world have a lot to celebrate: an emerging picture of the (mostly microbial) Tree of Life at ever-increasing resolution, an understanding of horizontal gene transfer as a driving force in the evolution of microbes, and thousands of complete genome sequences to help formulate and refine our theories. At the same time, quantitative models of the microevolutionary processes shaping microbial populations remain just out of reach, a point that is perhaps most dramatically illustrated by the lack of consensus on how (or even whether) to define bacterial species. Here, we summarize progress and prospects in bacterial population genetics, with an emphasis on detecting the footprint of positive Darwinian selection in microbial genomes.
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This work was part of the Virtual Institute for Microbial Stress and Survival ( http://VIMSS.lbl.gov ) supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics:GTL program through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and US Department of Energy. B.J.S. was funded by a Natural Sciences and Engineering Research Council of Canada, Canada Graduate Scholarship.