Computing Phylogenetic Diversity

Phylogenetic Diversity(PD)is a well-regarded measure of the overall biodiversity of a set of present-day species(taxa)that indicates its ecological significance.In the Maximize Phylogenetic Diversity(Max-PD)problem one is asked to find a small set of taxa in a phylogenetic tree for which this measure is maximized.Max-PD is particularly relevant in conservation planning,where limited resources necessitate prioritizing certain taxa to minimize biodiversity loss.Although Max-PD can be solved in polynomial time [Steel,SB,2005;Pardi&Goldman,PLoS,2005],its generalizations-which aim to model biological processes and other aspects in conservation planning with greater accuracy-often exhibit NP-hardness,making them computationally challenging.This thesis explores a selection of these generalized problems within the framework of parameterized complexity. In Generalized Noah's Ark Problem(GNAP),each taxon only survives at a certain survival probability,which can be increased by investing more money in the taxon.We show that GNAP is W[1]-hard with respect to the number of taxa but is XP with respect to the number of different costs and different survival probabilities. Additionally,we show that unit-cost-NAP,a special case of GNAP,is NP-hard. In Time Sensitive Maximization of Phylogenetic Diversity(Time-PD),different extinction times of taxa are considered after which they can no longer be saved.For Time-PD,we present color-coding algorithms that prove that Time-PD is fixed-parameter tractable(FPT)with respect to the threshold of diversity and the acceptable loss of diversity. In Optimizing PD with Dependencies(PDD),each saved taxon must be a source in the ecological system or a predator of another saved species.These dependencies are given in a food-web.We show that PDD is FPT when parameterized with the size of the solution plus the height of the phylogenetic tree. Further,we consider pa...