Abstract: Facing a major extinction crisis and constrained resources, conservation planning often involves difficult choices about which species to protect. Phylogenetic trees, i.e., leaf-labeled directed acyclic graphs, play an important role in this regard as they can be used to estimate how much “evolutionary heritage" is captured by each species and thus may be lost due to the current high rates of species extinction. Mathematically, this is formalized by the concepts of phylogenetic diversity (PD), a metric quantifying the biodiversity of sets of species based on their evolutionary relatedness, and phylogenetic diversity indices, measures that quantify the importance of species to overall biodiversity and provide prioritization criteria for conservation decisions.
In this talk, I will give a general introduction to phylogenetics and its use in biodiversity conservation. In particular, I will define the concept of phylogenetic diversity and introduce the Fair Proportion (FP) index, a popular PD index. I will then discuss two recent developments and challenges arising in conservation phylogenetics. First, I will consider the scenario of gene and species tree discordance, a scenario where phylogenetic trees obtained from individual genes differ from each other and the species tree, and analyze its effects on phylogenetic diversity conservation. Using the probabilistic multispecies coalescent model, I will show how prioritization decisions based on the FP index are affected by the phenomenon of gene and species tree discordance. Second, I will discuss the challenge of non-tree-like evolution and present some recent approaches towards defining and optimizing variants of PD on phylogenetic networks. In particular, I will explore the computational complexity of determining the maximum PD score over all subsets of species of fixed size under these variants and for different types of phylogenetic networks.