Science 6 April 2012:
Vol. 336 no. 6077 pp. 48-51
DOI:10.1126/science.1218198
Research Article

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

B. Jesse Shapiro, Jonathan Friedman, Otto X. Cordero, Sarah P. Preheim, Sonia C. Timberlake, Gitta Szabó, Martin F. Polz, Eric J. Alm | 2 Comments

Ecologically separated Vibrio populations diverge by gene-specific rather than genome-wide selective sweeps.

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Shapiro et al. have shown that ecologically distinct, closely related populations of marine Vibrio can be nearly identical in a single gene while they are much more divergent elsewhere in the genome. They conclude that single-gene sweeps, not genomic sweeps, are responsible for regions of high identity in Vibrio genomes. They thus claim evidence against periodic selection, where selection favoring an adaptive mutation purges variation genome-wide (1), owing to extremely low recombination rates (2). However, periodic selection theory applies only to the diversity within a single, ecologically homogeneous population (ecotype) (1), while the single-gene sweeps observed involve transfer of an adaptive gene across ecotypes; these sweeps are therefore outside of periodic selection theory. Instead, single-gene sweeps across ecotypes are predicted by the widely accepted model of speciation by horizontal genetic transfer (HGT) (3-5). Here a niche-specifying gene from one (donor) ecotype transfers on a small segment to a recipient organism in another pre-existing ecotype; the recipient cell thereby founds a new ecotype. Only one HGT event is needed to homogenize the donor and new ecotypes at the niche-specifying gene while they maintain pre-existing divergence elsewhere in the genome. A related explanation for single-gene sweeps is that a generally-adaptive gene may transfer across ecotypes and without creating new ecotypes, the transferred gene confers benefit to each recipient ecotype (1). Receipt of the adaptive mutation in a given ecotype then causes a periodic selection event within the ecotype. The populations thereby become identical for the transferred sequence but retain their pre-existing divergence everywhere else on the genome. We conclude that Shapiro’s results do not contradict either empirical estimates of low recombination rates in bacteria or periodic selection theory. Two models of inter-ecotype transfer of adaptive genes explain the single-gene sweeps observed, and are consistent with periodic selection occurring within ecotypes. Sarah M. Kopac and Frederick M. Cohan, Wesleyan University

References 1. F. M. Cohan, E. B. Perry, Current Biology 17, R373 (2007). 2. M. Vos, X. Didelot, ISME J 3, 199 (Feb, 2009). 3. J. G. Lawrence, Curr Opin Microbiol 2, 519 (1999). 4. H. Ochman, E. Lerat, V. Daubin, Proc Natl Acad Sci U S A 102 Suppl 1, 6595 (May 3, 2005). 5. W. F. Doolittle, O. Zhaxybayeva, Genome Res 19, 744 (May, 2009).

Submitted on Thu, 06/14/2012 - 16:32

Isn't it most likely that nutrient chemicals establish the ecological niche of different bacterial species and that nutrient calibrated receptor-mediated events link the metabolism of nutrients to pheromones that standardize and control speciation (e.g., via changes in intracellular signaling and stochastic gene expression)? This would link microbes to man via the origins of the olfactory and immune systems with a clear evolutionary trail that can be followed by the development of olfaction and odor receptors.

Submitted on Fri, 04/06/2012 - 10:40