A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome

摘要

a Empirical (dashed) and surrogate phylodiversity accumulation curves. Surrogate curves are colored according to D^ value (Eq. (1)). New species that have a previously detected close relative contribute little phylodiversity and cause slow phylodiversity accumulation (blue). New species that do not have a close relative contribute more phylodiversity and cause faster accumulation (green). The empirical model (dashed) is below the neutral model (teal), signifying underdispersion in the order of first-time species detections. The times of sampling points are shown as vertical blue lines below the X-axis. Curves are rescaled from 0 to 1 in this figure. b How empirical and surrogate data are compared with generate an estimate for D. Differences between empirical and surrogate data at time m are shown on the Y-axis, and the D^ values used to generate surrogate datasets are shown on the X-axis. Color-coded points correspond to surrogate datasets are shown in a. Values shown in gray result from using extreme values of D^, which help the logistic error model (black line) fit to the data, and are not shown in a. The red arrows show the process of error minimization, yielding a D estimate. A figure showing significance testing for these data is available as Fig. S1.