Figure 5. Existing estimators underestimate diversity in HTLV-1 infection.

For HTLV-1 Patient D, three samples are pooled. Rarefaction curves from the pooled sample (black circles) and a subsample (red circles) are shown. Chao1bc, ACE, Bootstrap, Good-Turing and negative exponential estimates (blue, grey, green, black, and orange lines respectively) from the subsample, and DivE estimates (red cross) from the same subsample are plotted. Existing estimators produce a single estimate of diversity, and so their estimates are shown as lines. The diversity in the blood must be at least as great as that observed by pooling the samples. All existing estimators estimate the total diversity to be less than that observed. Given that the observed diversity is likely to be a small fraction of the total diversity this represents a considerable error. We used DivE to produce two estimates: the diversity in the pooled sample (i.e. in 15000 cells, red cross) and the total diversity of the blood. DivE accurately estimates the pooled sample species richness from the subsample, but also predicts higher values of species richness in the blood, consistent with the unseen clones implied by the pooled rarefaction curve. See Figure S3 for further examples.