The Slow:Fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes

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Different microbial species are thought to occupy distinct ecological niches, subjecting each species to unique selective constraints, which may leave a recognizable signal in their genomes. Thus, it may be possible to extract insight into the genetic basis of ecological differences among lineages by identifying unusual patterns of substitutions in orthologous gene or protein sequences. We use the ratio of substitutions in slow versus fast-evolving sites (nucleotides in DNA, or amino acids in protein sequence) to quantify deviations from the typical pattern of selective constraint observed across bacterial lineages. We propose that elevated S:F in one branch (an excess of ... continued below

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Alm, Eric & Shapiro, B. Jesse April 15, 2009.

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Different microbial species are thought to occupy distinct ecological niches, subjecting each species to unique selective constraints, which may leave a recognizable signal in their genomes. Thus, it may be possible to extract insight into the genetic basis of ecological differences among lineages by identifying unusual patterns of substitutions in orthologous gene or protein sequences. We use the ratio of substitutions in slow versus fast-evolving sites (nucleotides in DNA, or amino acids in protein sequence) to quantify deviations from the typical pattern of selective constraint observed across bacterial lineages. We propose that elevated S:F in one branch (an excess of slow-site substitutions) can indicate a functionally-relevant change, due to either positive selection or relaxed evolutionary constraint. In a genome-wide comparative study of gamma-proteobacterial proteins, we find that cell-surface proteins involved with motility and secretion functions often have high S:F ratios, while information-processing genes do not. Change in evolutionary constraints in some species is evidenced by increased S:F ratios within functionally-related sets of genes (e.g., energy production in Pseudomonas fluorescens), while other species apparently evolve mostly by drift (e.g., uniformly elevated S:F across most genes in Buchnera spp.). Overall, S:F reveals several species-specific, protein-level changes with potential functional/ecological importance. As microbial genome projects yield more species-rich gene-trees, the S:F ratio will become an increasingly powerful tool for uncovering functional genetic differences among species.

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  • Journal Name: ISME Journal

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  • Report No.: LBNL-1887E
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 957408
  • Archival Resource Key: ark:/67531/metadc927812

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  • April 15, 2009

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  • Nov. 13, 2016, 7:26 p.m.

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  • Nov. 18, 2016, 4:18 p.m.

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Alm, Eric & Shapiro, B. Jesse. The Slow:Fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes, article, April 15, 2009; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc927812/: accessed May 22, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.