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Trends Microbiol. 2014 May;22(5):235-47. doi: 10.1016/j.tim.2014.02.006. Epub 2014 Mar 13.

Ordering microbial diversity into ecologically and genetically cohesive units.

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Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada. Electronic address:
Parsons Laboratory for Environmental Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:


We propose that microbial diversity must be viewed in light of gene flow and selection, which define units of genetic similarity, and of phenotype and ecological function, respectively. We discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and on evidence from some of the first microbial populations studied with genomics. These show that if recombination is frequent and selection moderate, ecologically adaptive mutations or genes can spread within populations independently of their original genomic background (gene-specific sweeps). Alternatively, if the effect of recombination is smaller than selection, genome-wide selective sweeps should occur. In both cases, however, distinct units of overlapping ecological and genotypic similarity will form if microgeographic separation, likely involving ecological tradeoffs, induces barriers to gene flow. These predictions are supported by (meta)genomic data, which suggest that a 'reverse ecology' approach, in which genomic and gene flow information is used to make predictions about the nature of ecological units, is a powerful approach to ordering microbial diversity.


ecological differentiation; gene flow; mosaic sympatric speciation; population genomics; reverse ecology; selective sweeps

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