Phylogenetics and Comparative Methods

by

Nathan G. Swenson

• LAST REVIEWED: 04 January 2022
• LAST MODIFIED: 30 June 2014
• DOI: 10.1093/obo/9780199830060-0087

Introduction

Ecologists and evolutionary biologists alike are frequently concerned with whether two characters or traits are correlated. Whether one is interested in the evolutionary correlation of two traits per se or simply interested in not violating the assumption of independent data points in their statistical analyses, phylogenetically informed comparative analyses are essential. Specifically, species are non-independent entities, and closely related species often have the tendency to be similar in their form, function, and niches: this non-independence must be considered when making ecological and evolutionary inferences. The literature on this topic is rather extensive, contentious, and methods laden, generally making it difficult to navigate. This article is an attempt to boil down this literature and to compile a series of key readings that range from the fundamentals of phylogenetics and comparative methods to more advanced analytical approaches for studying trait evolution and correlated trait evolution, as well as a few analytical resources that have been developed to facilitate phylogenetically informed analyses of comparative data sets.

General Overviews of Phylogenetics

Phylogenetic information largely permeates the comparative analysis literature. Without a basic understanding of phylogenetic information and how phylogenetic trees are inferred it is difficult to understand the various comparative methodologies employed. Felsenstein 2004 is a comprehensive text spanning tree inferences to trait evolution and comparative methods written by a central authority on these topics. For a general overview regarding inferring phylogenetic trees, the edited volume Lemey, et al. 2009 is a useful resource. A briefer introduction to molecular evolution and its consequences for how biologists infer phylogenetic trees, Nei and Kumar 2000 provides an accessible entryway. Lastly, Baum and Smith 2013 is a delightful text on not only how phylogenetic trees are constructed but also on how they can be used in ecological and evolutionary biology.

• Baum, D. A., and S. D. Smith. 2013. Tree thinking: An introduction to phylogenetic biology. Greenwood Village, CO: Roberts.

  NNNA contemporary text focusing on the generation and interpretation of phylogenetic data in biology. Written and designed to be accessible to a broad audience.

• Felsenstein, J. 2004. Inferring phylogenies. Sunderland, MA: Sinauer Associates.

  NNNThis is the essential and authoritative text on inferring and analyzing phylogenetic trees. Provides a detailed coverage of the historical development and implementation of phylogenetic analyses.

• Lemey, P., M. Salemi, and A. M. Vandamme, eds. 2009. The phylogenetic handbook. Cambridge, UK: Cambridge Univ. Press.

  DOI: 10.1017/CBO9780511819049

  NNNThis edited volume provides a treatment of nucleotide- and protein-based phylogenetic inference. The work primarily focuses on phylogenetic inference itself and has less information regarding comparative analyses.

• Nei, M., and S. Kumar. 2000. Molecular evolution and phylogenetics. Oxford: Oxford Univ. Press.

  NNNBegins with a useful background regarding molecular evolution before diving into phylogenetic tree inference. The book provides one of the more seamless integrations of molecular evolution and phylogenetics.