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Table 1 Different options in UniFrac allow different hypotheses to be tested.

From: UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context

Option Hypothesis
P-test There have been fewer transfers of lineages between environments than would be expected by chance, as measured by counting the number of transfers in a sample of trees in which sequences are randomly assigned to environments.
UniFrac There is less evolutionary history shared between a pair of environments than would be expected by chance, as measured by adding up the unique branch length (that leads to only one particular environment) in a sample of trees in which sequences are randomly assigned to environments.
Each environment individually When each environment is compared against all other environments taken together (i.e. all other environments are given the same label), the sequences from that environment alone are nonrandomly distributed on the tree when only changes to/from that environment are considered.
Each pair of environments When each environment is compared against each otherenvironment (removing all other environments except that pair from the tree), changes between that pair of environments occur less frequently than would be expected by chance.
All environments together When all environments are included in the same comparison, the total number of changes between environments is less than would be expected by chance, counting any change between different environments as a change.