Extended Data Figure 2: Geographic, temporal, and biogeographic strain variation.
From: Strains, functions and dynamics in the expanded Human Microbiome Project
a, Mean distance (Kimura two-parameter) among strains from subjects either within or between three-digit zip codes (the finest degree of geographic information available). Data and sample sizes are in Supplementary Table 2. b, Mean strain divergences between different visits for the same subject and body site compared to the mean distance between the same visits for the same subject and body site (technical replicates) for each species. c–u, PCoA plots based on the Kimura two-parameter distance17 are shown for Escherichia coli (c), Actinomyces johnsonii (d), and all species (that is, those shown Fig. 1b ; e–u), sorted in descending order of their niche-association score (Methods). Distance matrices used to generate these PCoAs are publicly available (Extended Data Table 1b).
