Abstract
The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low‐dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group‐specific consensus phylogenies. treespace also provides a user‐friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results.
Highlights
Genetic sequence data are becoming an increasingly common and informative resource in a variety of fields including evolutionary biology (Wolfe & Li, 2003), ecology (Hudson, 2008), medicine (Weinshilboum, 2002) and infectious disease epidemiology (Holden et al, 2013; Pybus & Rambaut, 2009)
We introduce TREESPACE, an R package providing a comprehensive toolkit for the analysis of phylogenetic incongruence
TREESPACE provides a simple framework for exploring landscapes of phylogenetic trees and investigating phylogenetic incongruence using tree–tree distances
Summary
Genetic sequence data are becoming an increasingly common and informative resource in a variety of fields including evolutionary biology (Wolfe & Li, 2003), ecology (Hudson, 2008), medicine (Weinshilboum, 2002) and infectious disease epidemiology (Holden et al, 2013; Pybus & Rambaut, 2009). Several metrics and measures of dissimilarity between trees have been developed (Table 1), each of which directly compares trees to each other according to certain biological or mathematical properties (Critchlow, Pearl, & Qian, 1996; Estabrook, McMorris, & Meacham, 1985; Hein, Jiang, Wang, & Zhang, 1996; Kendall & Colijn, 2015; Pavoine, Ollier, Pontier, & Chessel, 2008; Robinson & Foulds, 1979, 1981; Williams & Clifford, 1971) These methods of pairwise tree comparison can form the basis of further analyses aiming to visualize and characterize relationships in a whole set of phylogenies. It is fully integrated alongside existing standards for phylogenetics (Jombart, Balloux, & Dray, 2010; Popescu et al, 2012; Schliep, 2011) in the R software (R Core Team 2016)
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