Graphical Methods for Visualizing Comparative Data on Phylogenies
Phylogenies have emerged as central in evolutionary biology over the past three decades or more, and an extraordinary expansion in the breadth and sophistication of phylogenetic comparative methods has played a large role in this growth. In this chapter, I focus on a somewhat neglected area: the use of graphical methods to simultaneously represent comparative data and trees. As this research area is theoretically very broad, I have concentrated on new methods developed by me, or techniques devised by others and implemented by me as part of my R phylogenetics package, phytools. I describe a variety of methods in this chapter, including approaches that can be used to map reconstructed discrete or continuous character evolution on trees; techniques for projecting phylogenetic trees into morphospace; and methods for visualizing phylogenies in the context of a global or regional geographic map. In this chapter, my intention is not merely to showcase new methods that I have developed. Rather, I have also dedicated considerable attention to detailing the algorithms and computational techniques required for these approaches with the hope that this chapter will become a resource or jumping-off point for researchers interested in building new, more advanced approaches and methods in this area.
Thanks to L. Z. Garamszegi for inviting me to contribute this chapter. Thanks are also due to D. Collar, L. Mahler, and R. Mehta for contributing the data and trees that I used for some of these visualizations; to D. Collar, L. Harmon, and L. Mahler for lots of discussion of these methods; to D. Bapst, L. Mahler, E. Miller, and M. Pie for suggesting (in one way or another) methods that appear in this chapter; and to L. Mahler, R. Maia, and an anonymous reviewer for reading and commenting on an earlier version of this chapter. This research was funded in part by a grant from the National Science Foundation (DEB 1350474).
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