COMMUNITY ECOLOGY / SEQUENCING FIELD STATION
Microbe Mosaic
More kinds is not the same as more diversity.
Two questions. One sequencing budget.
Spend 300 reads across three samples. Find the community with the most taxa and the one with the highest effective Shannon diversity. A dominant taxon can hide many rare kinds, while an even community scores highly on effective diversity.
Sequence at least 60 reads per sample before submitting. The comparison table uses the first equal number of reads from each sample; unequal raw counts can mislead. Watch the rarefaction curves and allocate extra reads where richness is still rising.
Start by sampling all three communities. Compare at equal depth before deciding.
Compare at matched depth
| Sample | Taxa observed | Effective diversity | Gini–Simpson |
|---|
Read the measures · source & limitations
Observed richness counts nonzero taxa. Effective Shannon diversity is exp(−Σ p log p), the number of equally abundant taxa with the same entropy. Gini–Simpson is 1−Σ p²; Good’s coverage is 1−singletons/reads. These calculations are scalar adaptations of scikit-bio (BSD-3-Clause). Rarefaction shows expected observed richness under subsampling without replacement.
Synthetic, seeded reads omit sequencing errors, taxonomic uncertainty and extraction bias. A high coverage estimate does not prove every rare taxon was discovered. Expedition profiles change between rounds; these are puzzles, not claims about real forest, tidepool or leaf communities.
License · scikit-bio source