Systematic biology: advances and directions in theory and methods of phylogenetic reconstruction

Abstract

We examine the concepts of parsimony, likelihood and posterior probability, which are central to alternative methods for selecting optimal topologies in phylogenetic reconstruction. Complexity and mathematical sophistication of the description of the space of trees and of exploration methods based on parsimony, likelihoods and Bayesian posterior probabilities points to educational requirements demanding an unavoidable knowledge base in the philosophy of science, statistical theory and methods, and molecular biology. Such higher education becomes necessary in order to understand the operation of diverse available methods, but most importantly, to be able to discern their theoretical basis and to critically decide which option to use in different aspects of taxonomic research. Importance of the need of an informed use of methods becomes evident in the tendency to use either parsimony or probabilistic methods (likelihood and Bayesian) without exploring epistemological implications of such approaches in phylogenetic reconstruction. Undoubtedly, interest in methods of phylogenetic reconstruction is expanding. Therefore, it is important that phylogenetic biologists consider carefully the epistemological basis and relevance of methods they use in the selection of optimal topologies.