  Phylogenetic diversity indices such as the Fair Proportion (FP) index are
frequently discussed as prioritization criteria in biodiversity conservation.
They rank species according to their contribution to overall diversity by
taking into account the unique and shared evolutionary history of each species
as indicated by its placement in an underlying phylogenetic tree.
Traditionally, phylogenetic trees were inferred from single genes and the
resulting gene trees were assumed to be a valid estimate for the species tree,
i.e., the "true" evolutionary history of the species under consideration.
However, nowadays it is common to sequence whole genomes of hundreds or
thousands of genes, and it is often the case that conflicting genealogical
histories exist in different genes throughout the genome, resulting in
discordance between individual gene trees and the species tree. Here, we
analyze the effects of gene and species tree discordance on prioritization
decisions based on the FP index. In particular, we consider the ranking order
of taxa induced by (i) the FP index on a species tree, and (ii) the expected FP
index across all gene tree histories associated with the species tree. On one
hand, we show that for particular tree shapes, the two rankings always
coincide. On the other hand, we show that for all leaf numbers greater than or
equal to five, there exist species trees for which the two rankings differ.
Finally, we illustrate the variability in the rankings obtained from the FP
index across different gene tree and species tree estimates for an empirical
multilocus mammal data set.
