Se podrán analizar los siguientes metagenomas: a) Cuatro Ciénegas b) Microbioma humano Hay que elegir un sistema en cual se desee trabajar. 1. El trabajo puede se hará en equipos de trabajo de 2 a 3 personas. 2. Se tiene que elegir un problema de interés, previamente aprobado por los profesores, para analizar distintos metagenomas.…
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1. Sharon, I. et al. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome research 23, 111–20 (2013). The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed…
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1. Dorador, C., Vila, I., Witzel, K.-P. & Imhoff, J. F. Bacterial and archaeal diversity in high altitude wetlands of the Chilean Altiplano. Fundamental and Applied Limnology / Archiv für Hydrobiologie 182, 135–159 (2013). Abstract: The microbial diversity of five unconnected high altitude (≥ 3800 m a.s.l.) wetlands from the Chilean Altiplano was analyzed by…
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1. Beazley, M. J. et al. Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill. PloS one 7, e41305 (2012). Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of…
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1. Touchon, M., Hoede, C. & Tenaillon, O. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS genetics (2009).at Abstract The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change.…
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1. Friedman, J., Alm, E. & Shapiro, B. Sympatric speciation: when is it possible in bacteria? PloS one (2013).at Abstract According to theory, sympatric speciation in sexual eukaryotes is favored when relatively few loci in the genome are sufficient for reproductive isolation and adaptation to different niches. Here we show a similar result for clonally…
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Population Genomics of Early Events in the Ecological Differentiation of Bacteria DOI: 10.1126/science.1218198 Science 336, 48 (2012); B. Jesse Shapiro et al. Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in…
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Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton DOI: 10.1126/science.1157890 Science 320, 1081 (2008); Dana E. Hunt et al. Identifying ecologically differentiated populations within complex microbial communities remains challenging, yet is critical for interpreting the evolution and ecology of microbes in the wild. Here we describe spatial and temporal resource partitioning among Vibrionaceae strains…
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1. Wielgoss, S. & Barrick, J. Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. PNAS 3, (2013). Mutations are the ultimate source of heritable variation for evolu- tion. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should…
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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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