Global Diversity

In ecological communities, global (gamma) diversity is the product of local (alpha) and beta diversity: $S_{\gamma} = S_{\alpha} S_{\beta}$. For our purposes, alpha diversity is the estimated number of distinct transcripts in a library, which represents a tissue type. In the case of mixed-culture libraries, we discount total diversity by the expected portion of plant genes, $P_{plant}$ as in Section 2.4. Beta diversity is the turnover of quasispecies as we change libraries. Putting these together, we compute total diversity as $S_{\gamma} = \sum_i \hat{S}_i P_{plant}(i) \overline{C}_i$, where i is an index variable to indicate a particular library and $\overline{C}_i$ is the average complementarity between a library and all others (indexed by j) [32], or $\overline{C}_i = 1/n \sum_{j \ne i} C_{ji}$, where $C_{ji}$ is the computed complementarity between libraries j and i, and n is the number of comparisons made.