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

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

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?

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”

Comparing diversity Slides from Rob Knight, MBL STAMPS lecture

Observed species Slides from Rob Knight, MBL STAMPS lecture

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

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

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

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

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

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

Unifrac uses phylogenetic diversity to measure beta diversity more overlap on the phylogenetic tree  more similar communities http://unifrac.colorado.edu

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) http://unifrac.colorado.edu