We consider a set of species S and are interested in the assessment of the subsets of S from a phylogenetic diversity viewpoint. Several measures can be used for this assessment. Here we have retained phylogenetic diversity (PD) in the sense of Faith, a measure widely used to reflect the evolutionary history accumulated by a group of species. The PD of a group of species X included in S is easy to calculate when the phylogenetic tree associated with S is perfectly known but this situation is rarely verified. We are interested here in cases where uncertainty regarding the length of branches and the topology of the tree is reflected in the fact that several phylogenetic trees are considered to be plausible for the set S. We propose several measures of the phylogenetic diversity to take account of the uncertainty arising from this situation. A natural problem in the field of biological conservation is to select the best subset of species to protect from a group of threatened species. Here, the best subset is the one that optimizes the proposed measures. We show how to solve these optimal selection problems by integer linear programming. The approach is illustrated by several examples.