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Supplementary Figure 1. Genome coverage for some of the most represented viruses
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and plasmids. Data were obtained by metagenome read mapping against the specified
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genomes using GS Reference Mapper with a minimum overlap length of 20 bp and a
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minimum overlap identity of 95%.
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Supplementary Figure 2. Phylogeny of several ORFs found on the longest contigs from
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each metagenome. Values on branches represent bootstrap values. A. Phylogenetic
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reconstruction for ORF 34 on contig 942 of El Berbera, which encodes a hypothetical protein;
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B. Phylogenetic reconstruction for ORF 7 on contig 439 of Hamdoun, which encodes a
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possible DNA helicase C. Phylogenetic reconstruction for ORF 41 on contig 353 of
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Hamdoun, which encodes a bacteriophage protein.
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Supplementary Figure 3. Community structure predicted by PHACCS. Rank-abundance
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curves representing the community structure and estimates of diversity (R: richness; E:
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evenness; H’: Shannon-Wiener index of diversity). The abundance of each genotype is plotted
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versus its abundance rank, with the genotype of rank one being the most abundant.
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Supplementary Figure 4. First two principal coordinates from the principal coordinate
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analysis of the four samples. The PCA was run by FastUniFrac to visualize the overall
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patterns of variation between the four samples.
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