Phylogenetic Diversity indicator
The Phylogenetic Diversity indicator monitors the overall status of the Tree of Life across taxonomic groups. The indicator ranges from 0% to 100%, indicating the percentage of ‘phylogenetic diversity’—or total evolutionary history—expected to be lost due to extinction.
The full methodology is available in the 2023 paper published in Conservation Biology.
Global Phylogenetic Diversity indicator
The Expected Loss of Phylogenetic Diversity indicator (PD indicator) allows us to track the extinction risk to the diversity of Earth’s evolutionary lineages, a component of biodiversity that provides the benefits that we experience today, and others that will emerge in the future.
The PD indicator has been calculated for a single time point (2023) for all major vertebrate groups, seed plants, flowering plants, and freshwater crayfish. Additionally, trends have been calculated for groups with available Red List Index data for more than one timepoint, namely amphibians, birds, cycads and mammals. We will update and recalculate the PD indicator as taxonomic coverage and number of assessment timepoints grow across the Tree of Life. The data to reproduce the global PD indicator plot for 2023 is available here. The underlying phylogenetic data is available here, and extinction risk data is derived from the IUCN Red List of Threatened Species and Red List Index. Code to calculate the indicator, along with example data, is available here.
*The 2023 timepoints are provisional, based on a combination of Red List Index data (amphibians) and IUCN Red List v2023.2 data (all other clades), and is expected to change with updates to the Red List Index.
PD indicator at the national level
National disaggregation of the global PD indicator
The global PD indicator has been disaggregated to the national level across taxonomic groups to aid reporting towards national and global policy targets and goals. The nationally disaggregated PD indicator calculates the extinction risk to the branches of the Tree of Life connecting the species present in a given country or territory, using global phylogenetic trees and Red List data. To download the nationally disaggregated PD indicator values, click here.
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(s)
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, seed plants, and flowering plants that can be filtered to national species of interest for indicator calculation.
Step 2: identify suitable extinction risk data
National Red List data is recommended for calculating the indicator at the national level. Published national Red List data can be found here. For monitoring trends in extinction risk, repeated assessments across multiple timepoints are required, and information on national Red List Indices are available here. Global Red List Index data, available here, can also be filtered to national species for use in the PD indicator calculation.
Step 3: 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. A threshold of >80% of species with both phylogenetic and extinction risk data is advised for robust reporting.
Step 4: 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 probabilities of extinction and multiplying each phylogenetic branch length by the product of extinction probabilities of all species descendent to that branch. 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. Code to calculate the indicator, with example data, are available here.
If any components of this calculation are not possible or you need support, please contact us here.