Neutrality in the Metaorganism
Fig 4
Impact of sample number on the goodness of fit of the neutral expectation.
For each sampling depth, communities were resampled 100 times with replacement at a rarefaction level of 1,000 reads/sample. The left panel shows the results for simulated neutral communities. The immigration parameter was fixed at m = 0.05, and neutral dynamics were simulated for 106 time steps in all cases. Generally, goodness of fit remained high over a large range of sample sizes, reflecting the underlying completely neutral community dynamics. Note that the goodness of fit did not reach 1.0 in finite and relatively small metacommunities, even if all communities were sampled. The right panel shows the effect of subsampling for several host-associated microbial communities. As for the simulated data, observed levels of neutrality were relatively robust, only dropping off at very low sample sizes. The C. elegans datasets showed a very poor fit at very low sampling depths but began to level off well below the neutrality values of the other datasets. Shaded areas indicate 95% bootstrap confidence intervals. The data used to generate this figure are available in S1 Data. OTU, operational taxonomic unit.