First published 2 July 2012
Comparing Distance-Based Phylogenetic Tree Construction Methods Using An Individual-Based Ecosystem Simulation, EcoSim
Ryan Scott, Robin Gras
Phylogenetic trees are constructed frequently in biological research to provide an understanding of the evolutionary history of the organisms being studied. Often, the actual phylogenetic tree is unknown and the phylogenetic tree constructed is an estimate. There are many methods of phylogenetic tree construction which fall into two main categories: distance-based methods and character-based methods. To test the accuracy of these methods, it is necessary that the system being studied is one for which the actual phylogenetic tree is known. EcoSim is an ecosystem simulation in which predator and prey agents possessing a complex behavioral model can interact, evolve and speciate. In this experiment, we used EcoSim to test the accuracy of the three main distance-based phylogenetic tree construction methods, when constructing a single tree and when performing phylogenetic bootstrapping. Since EcoSim provides data regarding speciation events, we were able to construct the actual phylogenetic trees from this data. We then performed the UPGMA, Neighbor-Joining, and Fitch-Margoliash methods at various time-steps and used symmetric distance as a metric to compare the topologies of the actual and estimated trees. On average, trees contained nearly 30 taxa. We found that the Fitch-Margoliash method with bootstrapping performed slightly better than the other methods, however no method constructed trees in which more than 50% of the partitions were correct.