Follow these steps to calculate the Phylogenetic Diversity (PD) indicator at the national level for a given taxonomic group.

Data needed:

• Time-calibrated phylogenetic tree

• National or global IUCN Red List or equivalent data

R code and example data to calculate this indicator are available here.

Step 1: select a time-calibrated phylogenetic tree

First, a time-calibrated phylogeny is needed, from which the PD indicator will be calculated. There are several options for phylogenetic trees. Countries can produce phylogenetic trees to encompass their national biodiversity. Alternatively, publicly available phylogenetic trees can be acquired in numerous ways, but we advise contacting us here for available phylogenetic trees for vertebrates, crayfish and seed plants.

Step 2: match the species

National taxonomies can vary from global taxonomies for a variety of reasons. Match the species in your national taxonomy to those in the phylogenetic tree as best as possible, removing those that do not match. >80% congruence is advised for robust reporting.

Step 3: calculate the PD indicator

Once the species are matched across national extinction risk data and the phylogeny, the PD indicator can be calculated. This is done by converting the extinction risk categories to probabilties of extinction and multiplying each phylogenetic branch by the product of extinction probabilities of all descendant species. The sum of these calculations, divided by the overall phylogenetic diversity of the taxonomic group, gives the proportion of phylogenetic diversity expected to be lost for a given group at a given time point.

If any components of this calculation are not possible or you need support, please contact us here.