Building trees of algae: Some advances in phylogenetic and evolutionary analysis

Abstract

Molecular phylogenetics has become a prominent aspect of algal systematics. The field of phylogenetic reconstruction is fast-evolving and novel techniques take time to penetrate taxonomic research. We highlight a selection of advances in phylogenetic inference and evolutionary analysis methods that could, in our opinion, benefit algal systematic studies. The focus of the paper is on model-based techniques. Following a brief introduction to maximum likelihood and Bayesian phylogenetic inference methods, we address model selection and partitioning strategies, and illustrate some issues concerning systematic error (phylogenetic bias), data saturation and tree rooting. We discuss the importance ..