Trends in Genetics
ReviewHorizontal gene transfer and the evolution of bacterial and archaeal population structure
Section snippets
Genotypic clustering
Plants and animals are organized into phenotypic and genotypic clusters, and this forms the vernacular notion of a species. For bacteria and archaea the identification of natural clusters was difficult before sequencing became widely available because phenotypic traits used for traditional taxonomy were arbitrarily defined. Although traditional classification allowed reliable identification [7], it is clear that many taxonomic species do not necessarily represent natural units. Hence it was an
Formation of genotypic clusters
Recent population genomic data allow a synthesis of past theories and observations that were seemingly at odds in explaining cluster formation. In presenting this new evidence, we first pose the important question of whether genotypic clusters can originate among sympatric microbes in the absence of selection. The focus on sympatric differentiation is because geographic isolation, although thought to be an important factor in animals and plants, appears to be the exception in microbes having
A habitat-specific gene pool?
The above model shows how genotypic clusters in the core genome might arise, but has yet to consider fully the intricacies of the flexible genome – which has very high turnover, can contribute a large portion of the total genes, and makes up the bulk of the vast pan-genome. In fact, one of the puzzles of microbial biology is that genomes can be highly optimized energetically and functionally while tolerating the disruptive effect of horizontally acquired genes that are both phylogenetically and
Concluding remarks
Although we are only beginning to understand the intricacies of gene flow in the wild, it is becoming clear that gene-transfer networks need to be analyzed in the context of ecology. The recent results reviewed here add an evolutionary dimension to this ecological structure by showing how clusters may arise as a consequence of ecological specialization. The gradual mechanism by which this happens (Figure 1) is unexpected because theoretical considerations have suggested genome-wide selective
Acknowledgments
Funding was provided by grants from the Moore Foundation (M.F.P.), the National Science Foundation (DEB 0821391 to E.J.A. and M.F.P.), the National Institutes of Health (NIH)/National Institute of General Medical Sciences (NIGMS) (GM088558-01 to W.P.H.), and the MIDAS Center for Communicable Disease Dynamics at the Harvard School of Public Health (W.P.H.). We also thank James McInerney for helpful discussions.
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