1. PNAS 2012
Alpha diversity:
how many species are
in each sample?

2. shared between samples?
PNAS 2012
Beta diversity:
how many species are
shared between samples?
Ok, desert soils are different from other soils. But why? What are the specific environmental factors?

3. Alpha vs. Beta diversity
Alpha: how many species are in each sample?
result is a single number representing the richness of the sample
results are reported in a table or as a curve (e.g. rarefaction)
Beta: which species are shared between samples?
result is a matrix of whole-sample similarities
results are multivariate and are reported as scaled plots (e.g. MDS, PCA)
Taxonomic vs. Functional diversity
Taxonomic: typically a single (sometimes multiple) taxonomic markers (genes)
sequences are converted to taxonomic classification
taxonomic classifications are presumed to reflect evolutionary history
Functional: typically all other genes (all = those that have database matches)
sequences are converted to predicted functions (by comparison to database)
predicted functions are treated as “traits”

4. Comparing diversity
Slides from Rob Knight, MBL STAMPS lecture

5. Observed species
Slides from Rob Knight, MBL STAMPS lecture

6. Phylogenetic Diversity (PD)
Slides from Rob Knight, MBL STAMPS lecture

7. Phylogenetic Diversity (PD)
Slides from Rob Knight, MBL STAMPS lecture

8. Phylogenetic Diversity (PD)
Slides from Rob Knight, MBL STAMPS lecture

9. Phylogenetic Diversity (PD)
Slides from Rob Knight, MBL STAMPS lecture

10. Phylogenetic Diversity (PD)
Slides from Rob Knight, MBL STAMPS lecture

11. Phylogenetic Diversity (PD)
Slides from Rob Knight, MBL STAMPS lecture

12. Unifrac uses phylogenetic diversity to measure beta diversity
more overlap on the phylogenetic tree  more similar communities

13. Unifrac uses phylogenetic diversity to measure beta diversity
more overlap on the phylogenetic tree  more similar communities
(how a community similarity matrix is generated from the phylogenetic tree)