Blount, Z. D., Barrick, J. E., Davidson, C. J. & Lenski, R. E. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489, 513–8 (2012). Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of…
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Olivier Tenaillon, et al. Science 335, 457 (2012); DOI: 10.1126/science.1212986 To estimate the number and diversity of beneficial mutations, we experimentally evolved 115 populations of Escherichia coli to 42.2°C for 2000 generations and sequenced one genome from each population. We identified 1331 total mutations, affecting more than 600 different sites. Few mutations were shared…
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Second-Order Selection for Evolvability in a Large Escherichia coli Population. Robert J. Woods, et al. Science 331, 1433 (2011); In theory, competition between asexual lineages can lead to second-order selection for greate revolutionary potential. To test this hypothesis, we revived a frozen population of Escherichia coli from a long-term evolution experiment and compared the fitness…
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Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli. Wielgoss, Sébastien; Barrick, Jeffrey E; Tenaillon, Olivier; Cruveiller, Stéphane; Chane-Woon-Ming, Béatrice et al. (2011) G3 (Bethesda, Md.) vol. 1 (3) p. 183-186 ABSTRACT The quantification of spontaneous mutation rates is crucial for a mechanistic understanding of the evolutionary process. In…
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Herron MD, Doebeli M (2013) Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli. PLoS Biol 11(2): e1001490. doi:10.1371/journal.pbio.1001490 Abstract The causes and mechanisms of evolutionary diversification are central issues in biology. Geographic isolation is the traditional explanation for diversification, but recent theoretical and empirical studies have shown that frequency-dependent selection can drive diversification without…
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Trends Microbiol. 2011 Jan;19(1):1-7. doi: 10.1016/j.tim.2010.10.003. Epub 2010 Nov 9. Abstract Bacterial strains are currently grouped into species based on overall genomic similarity and sharing of phenotypes deemed ecologically important. Many believe this polyphasic taxonomy is in need of revision because it lacks grounding in evolutionary theory, and boundaries between species are arbitrary. Recent taxonomy…
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Chan, J., & Halachev, M. (2012). Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC microbiology, 0(758), 3–11. Retrieved from http://www.biomedcentral.com/1471-2180/12/302/ Abstract Background Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared…
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Peña, A., Teeling, H., Huerta-Cepas, J., Santos, F., Yarza, P., Brito-Echeverría, J., Lucio, M., et al. (2010). Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. The ISME journal, 4(7), 882–95. doi:10.1038/ismej.2010.6 Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive…
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Retchless, A. C., & Lawrence, J. G. (2007). Temporal fragmentation of speciation in bacteria. Science (New York, N.Y.), 317(5841), 1093–6. doi:10.1126/science.1144876 Because bacterial recombination involves the occasional transfer of small DNA fragments between strains, different sets of niche-specific genes may be maintained in populations that freely recombine at other loci. Therefore, genetic isolation may be…
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Zhaxybayeva, O., Swithers, K. S., Lapierre, P., Fournier, G. P., Bickhart, D. M., DeBoy, R. T., Nelson, K. E., et al. (2009). On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proceedings of the National Academy of Sciences of the United States of America, 106(14), 5865–70. doi:10.1073/pnas.0901260106 Since publication of the first…
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McDaniel, L. D., Young, E., Delaney, J., Ruhnau, F., Ritchie, K. B., & Paul, J. H. (2010). High frequency of horizontal gene transfer in the oceans. Science (New York, N.Y.), 330(6000), 50. doi:10.1126/science.1192243 Oceanic bacteria perform many environmental functions, including biogeochemical cycling of many elements, metabolizing of greenhouse gases, functioning in oceanic food webs (microbial…
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Cadillo-Quiroz, H., Didelot, X., Held, N. L., Herrera, A., Darling, A., Reno, M. L., Krause, D. J., et al. (2012). Patterns of gene flow define species of thermophilic Archaea. PLoS biology, 10(2), e1001265. doi:10.1371/journal.pbio.1001265 Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here…
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Barraclough, T. G., Balbi, K. J., & Ellis, R. J. (2012). Evolving Concepts of Bacterial Species. Evolutionary Biology, 39(2), 148–157. doi:10.1007/s11692-012-9181-8 The same evolutionary forces that cause diversification in sexual eukaryotes are expected to cause diversification in bacteria. However, in bacteria, the wider variety of mechanisms for gene exchange (or lack thereof) increases the range…
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Cohan, F. M., & Perry, E. B. (2007). A systematics for discovering the fundamental units of bacterial diversity. Current biology : CB, 17(10), R373–86. doi:10.1016/j.cub.2007.03.032 Bacterial systematists face unique challenges when trying to identify ecologically meaningful units of biological diversity. Whereas plant and animal systematists are guided by a theory-based concept of species, microbiologists have…
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