Figure 2 |

a, Lineage-by-distance analysis of 16S rRNA gene-sequence data from human microbial communities in specific habitats. The x axis shows the percentage difference threshold (Olsen correction), over 1,241 unambiguously aligned positions of near full-length 16S rRNA gene sequences, for delineating separate lineages. The y axis shows the number of distinct lineages that exist at the distance threshold. If speciation and extinction occur with constant probabilities as 16S rRNA gene sequences diverge, this would result in an exponentially increasing number of lineages with diminishing evolutionary distances between them (a straight line on a semi logarithmic plot). Such a pattern seems to hold from the phylum level (largest distances between lineages) to approximately the species level. However, relative to this trend, all sites have an excess of recently diverged lineages. The excess lineages accumulate in the range of 16S rRNA gene divergence that is typically associated with species and strains. The inset depicts a portion of the same data at a larger scale. Samples were taken from 3–11 individuals, depending on the site. Data taken from refs ^1–5. b, When displayed as a dendrogram, 16S rRNA gene-based patterns of microbial diversity in soil and aquatic environments generally resemble the tree shape on the left, with new branches arising at all distances from the root. Patterns of diversity in vertebrate-associated communities resemble the tree shape on the right, with few branches arising close to the root and many branches arising close to the branch tips.