Phylogenetics and systematics in a nutshell

Abstract

During the last 50 years, phylogenetic systematics has suffered a substantial transformation in philosophy and methods. Systematics has gone from been a merely descriptive discipline to a scientific theory encompassing solid evolutionary principles capable of inferring robust and replicable historical hypothesis about the interrelationships of taxa. This chapter provides the basic concepts in the field of systematic biology (e.g., terminology, characters codification, tree description) and phylogenetic reconstructions (e.g., alignments, reconstruction methods, support measurements). A particular emphasis is given to nucleotide data. It will provide a guide on how sequences can be used to detect natural selection, adaptation, recombination, and to evaluate substitution saturation. In particular, this chapter seeks to provide the novice with all basic concepts necessary to understand and interpret phylogenetic hypotheses: for instance, to understand nucleotide substitution models, what a molecular clock is, tree selection methods (e.g., Maximum Parsimony, Maximum Likelihood, Bayesian), how to interpret node support values, and testing tree topologies (e.g., Kishino-Hasegawa). Finally, a short review is presented on the current phylogenetic knowledge of avian Haemosporida.