Biodiversity Assessment using the Fair Proportion Index for Species Trees

Phylogenetic diversity indices are often used as a means of ranking species for conservation priority. A crucial issue in this process is the selection of an appropriate phylogenetic tree for application of these indices. We use the Fair Proportion Index to explore the range of outcomes that result from using gene-level vs. species-level phylogenies. We show both theoretically and by application to empirical data that the choice of phylogeny plays a key role in ranking species. We discuss the broad implications of our work to other measures applied to fixed phylogenies.