Supplementary MaterialsFigure S1: Pearson correlation of dN/dS ratios calculated using reads tiled using criteria of 70% similarity and 70% insurance coverage (70/70) vs. percentage of the gene included in at least 5-fold read insurance coverage (%min5Xcov) and the common depth of read insurance coverage (avg read depth) are also shown.(XLS) pone.0024249.s004.xls (21K) GUID:?356F3DF3-DEC0-4813-977B-575FD960A7B6 Table S3: dN/dS ratios based on metagenomic reads tiled to the CC9311 genome with 80% similarity and 80% coverage. dN, dS, the percentage of the gene covered by at least 5-fold read coverage (%min5Xcov) and 1-fold read coverage (%min1Xcov), the average depth of read coverage (avg read depth), dN/dS calculated relative to the CC9311 genome sequence rather than a population consensus sequence (dN/dS vs CC9311), dN/dS calculated using a metagenome tiling of 70% similarity and 70% coverage (dN/dS 70_70), and pair-wise dN/dS calculated using PAML are also shown. For all of the dN/dS columns except for the PAML analysis, NaN indicates a dN/dS of 0/0. Inf indicates that only non-synonymous polymorphisms were detected. For the PAML analysis, reads that had only non-synonymous polymorphisms relative to the consensus (dN/dS?=?infinite) were not included. Accessory genes are highlighted in blue.(XLS) pone.0024249.s005.xls (632K) GUID:?5098F9AC-7155-450B-9BEB-443B9545848D Table S4: dN/dS ratios based on metagenomic reads tiled to the CC9902 genome with 80% similarity and 80% coverage. dN, dS, the percentage of the gene covered by at least 5-fold read coverage (%min5Xcov) and 1-fold read coverage (%min1Xcov), the 3-Methyladenine biological activity average depth of read coverage (avg read depth), dN/dS calculated relative to the CC9902 HESX1 genome sequence rather than a population consensus sequence (dN/dS vs CC9902), dN/dS calculated with the metagenome tiled with 70% similarity and 70% 3-Methyladenine biological activity coverage (dN/dS 70_70), and pair-wise dN/dS calculated using PAML are also shown. For all of the dN/dS columns except for the PAML analysis, NaN indicates a dN/dS of 0/0. Inf indicates that only non-synonymous polymorphisms were detected. For the PAML analysis, reads that had only non-synonymous polymorphisms relative to the consensus (dN/dS?=?infinite) were not included. Accessory genes are highlighted in blue.(XLS) pone.0024249.s006.xls (520K) GUID:?01273958-234F-41D9-9A7F-53E78D80CA06 Table S5: dN/dS ratios from 201 bp sliding window of metagenomic reads tiled to the CC9311 genome. The position of the window start and end coordinates based on the CC9311 genome are provided. Inf indicates that only non-synonymous polymorphisms were observed. * genes with dN/dS 1 for the entire gene.(XLS) pone.0024249.s007.xls (39K) GUID:?0FA0D5A3-DB4A-4577-8D55-A3BDE15AA52D Table S6: 3-Methyladenine biological activity dN/dS ratios from 201 bp sliding window of metagenomic reads tiled to the CC9902 genome. The position of the window start and end coordinates based on the CC9902 genome are provided. Inf indicates that only non-synonymous polymorphisms were observed. * genes with dN/dS 1 for the entire gene.(XLS) pone.0024249.s008.xls (28K) GUID:?BB7C116B-FC8F-48B3-BBD6-5D187C189E22 Table S7: Complete list of genes with dN/dS ratios 1 based on polymorphisms from metagenomic sequences tiled to the CC9311 genome. (DOCX) pone.0024249.s009.docx (115K) GUID:?67450B9D-6ED0-49DD-BB34-05E47E2C087C Table S8: Genes with dN/dS ratios 1 based on polymorphisms from metagenomic sequences tiled to the CC9902 genome. (DOCX) pone.0024249.s010.docx (114K) GUID:?83775AB6-BDF5-4498-8D81-AB065B311126 Abstract Environmental metagenomics provides snippets of genomic sequences from all organisms in an environmental sample and are an unprecedented resource of information for investigating microbial population genetics. Current analytical methods, however, are poorly equipped to handle metagenomic data, particularly of short, unlinked sequences. A custom analytical pipeline was developed to calculate dN/dS ratios, a common metric to evaluate the role of selection in the evolution of a gene, from environmental metagenomes sequenced using 454 technology of flow-sorted populations of marine population. Other annotated genes, in particular a possible porin, a large-conductance mechanosensitive channel, an ATP binding component of an ABC transporter, and a homologue.