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• W2078785469 abstract "•Mathematical models and genomic data provide new insights into microbial speciation. •Adaptive genes can either spread within populations or trigger genome-wide sweeps. •Formation of new genotypic clusters in sympatry requires (microgeographic) gene flow barriers. •If arisen in sympatry, genotypic clusters represent congruent ecological and genetic units. 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. 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. a set of sampled isolates or genomes from different geographic areas, where barriers to migration and gene flow are significant. the portion of the genome transmitted by vertical (clonal) evolution, unimpacted by HGT. Mutations in the clonal frame should all fall parsimoniously on a single phylogenetic tree. the portion of the genome that is present (or in practice, that can be aligned) in all of a given set of sequenced isolates or metagenomes. the set of genes or DNA that is present in only a fraction of a given set of sequenced isolates or metagenomes. the process in which an adaptive gene or allele (possibly a niche-specifying variant) spreads in a population by recombination faster than by clonal expansion. The result is that the adaptive variant is present in more than a single clonal background, and that diversity is not purged genome-wide. a technique commonly used in eukaryotic genetics to identify genomic variants that are associated with a phenotype of interest. In highly structured populations (e.g., clonal microbes), it is essential to correct for false associations due to phylogenetic structure. the process in which an adaptive gene or allele (possibly a niche-specifying variant) spreads in a population by clonal expansion of the genome that first acquired it. The result is that diversity is purged genome-wide, and that the adaptive variant is linked in the same clonal frame as the rest of the genome. the incorporation of foreign DNA into a genome. Incorporation can be mediated by either homologous recombination or nonhomologous recombination of DNA that enters a cell via transformation, transduction, or conjugation. In bacteria and archaea, all gene transfer is horizontal (i.e., always unidirectional). a mechanism of DNA integration requiring at least short tracts of identity between the genome and the foreign DNA, mediated by RecA (protein necessary for DNA repair, recombination, and maintenance) and mismatch repair machinery. The integrated DNA can result in single nucleotide changes and, in some cases, addition or loss of relatively long stretches of DNA including entire genes. the total set of all genomic DNA in a particular environment or sample. a type of natural selection that favors rare phenotypes in a population. a specific set of ecological parameters (environments, resources, physical and chemical characteristics, biotic interactions, etc.) to which an organism is adapted. This does not necessarily imply (but does not exclude) physical separation between niches. a mutation, gene, or allele that allows a cell to be part of a particular niche. These variants are under positive selection within the particular niche, but not outside it. integration of DNA with no homologous allele already present in the genome, often mediated by phage and integrative elements. This results in the acquisition of entirely new genes. a group of individuals sharing genetic and ecological similarity, and coexisting in a sympatric setting. a type of natural selection that favors variants conferring a fitness advantage, causing them to increase in frequency in a population. a set of sampled isolates or genomes from the same geographic area, where barriers to migration and gene flow are low or nonexistent." @default.
• W2078785469 created "2016-06-24" @default.
• W2078785469 creator A5029276946 @default.
• W2078785469 creator A5067717492 @default.
• W2078785469 date "2014-05-01" @default.
• W2078785469 modified "2023-10-02" @default.
• W2078785469 title "Ordering microbial diversity into ecologically and genetically cohesive units" @default.
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• W2078785469 doi "https://doi.org/10.1016/j.tim.2014.02.006" @default.
• W2078785469 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4103024" @default.
• W2078785469 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24630527" @default.
• W2078785469 hasPublicationYear "2014" @default.
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