The history of life unfolds within a phylogenetic context. Comparative phylogenetic methods are statistical approaches for analyzing historical patterns along phylogenetic trees. This task view describes R packages that implement a variety of different comparative phylogenetic methods. This is an active research area and much of the information is subject to change.

Ancestral state reconstruction : Continuous characters can be reconstructed using maximum likelihood, generalised least squares or independent contrasts in ape. Root ancestral character states under Brownian motion or Ornstein-Uhlenbeck models can be reconstructed in ouch, though ancestral states at the internal nodes are not. Discrete characters can be reconstructed using a variety of Markovian models that parameterize the transition rates among states using ape.

Diversification Analysis: Lineage through time plots can be done in ape and laser. A simple birth-death model for when you have extant species only (sensu Nee et al. 1994) can be fitted in ape as can survival models and goodness-of-fit tests (as applied to testing of models of diversification). laser implements likelihood methods using a model testing approach for inferring temporal shifts in diversification rates based on a birth-death or pure-birth process. The gamma statistic (Pybus and Harvey 2000) is also available in laser. Net rates of diversification (sensu Magellon and Sanderson) can be calculated in geiger. diversitree implements the BiSSE method (Maddison et al. 1997) and later improvements (FitzJohn et al. 2009). apTreeshape also has tests for differential diversification (see description ).

Divergence Times: Non-parametric rate smoothing (NPRS) and penalized likelihood can be implemented in ape.

Phylogenetic Inference: Maximum likelihood, UPGMA, neighbour joining, bio-nj and fast ME methods of phylogenetic reconstruction are all implemented in the package ape. phangorn can estimate trees using distance, parsimony, and likelihood. phyclust can cluster sequences. scaleboot can perform the Shimodaira-Hasegawa test for comparing trees.For more information on importing sequence data, see the Genetics task view.

Time series: Paleontological time series data can be analyzed using a likelihood-based framework for fitting and comparing models (using a model testing approach) of phyletic evolution (based on the random walk or stasis model) using paleoTS.

Tree Simulations: Trees can be simulated using constant-rate birth-death with various constraints in TreeSim, a birth-death process in geiger, and PhySim. Random trees can be generated in ape by random splitting of edges (for non-parametric trees) or random clustering of tips (for coalescent trees). phybase can simulate coalescent trees as well.

Trait evolution: Independent contrasts for continuous characters can be calculated using ape or picante. Analyses of discrete trait evolution, including models of unequal rates or rates changing at a given instant of time, as well as Pagel's transformations, can be performed in Geiger. geiger. Brownian motion models can be fit in geiger and ape. Ornstein-Uhlenbeck (OU) models can be fitted in geiger, ape and ouch. matticce uses ouch to search for where a regime transition occurs. In its current implementation, geiger fits only single-optimum models. Other continuous models, including Pagel's transforms and models with trends, can be fit with geiger. ANOVA's and MANOVA's in a phylogenetic context can also be implemented in geiger. A GLS linear model (sensu Garland and Ives 2000) can be fitted using PHYLOGR; the more traditional GLS methods (senu Grafen or Martins) can be implemented in ape. Phylogenetic autoregression (sensu Cheverud et al) and Phylogenetic autocorrelation (Moran's I) can be implemented in ape or--if you wish the significance test of Moran's I to be calculated via a randomization procedure--in ade4 or adephylo (ade4 has been deprecated in favor of adephylo). Correlation between traits using a GLMM can also be investigated using MCMCglmm.

Trait Simulations : Continuous traits can be simulated using brownian motion in ouch, geiger, ape, and picante, the Hansen model (a form of the OU) in ouch and a speciational model in geiger. Discrete traits can be simulated using a continuous time Markov model in geiger. phangorn can also simulate discrete traits, especially DNA or AA. Both discrete and continuous traits can be simulated under models where rates change through time in geiger.

Tree Manipulation : Branch length scaling using ACDC; Pagel's (1999) lambda, delta and kappa parameters; and the Ornstein-Uhlenbeck alpha parameter (for ultrametric trees only) are available in geiger. Rooting, resolving polytomies, dropping of tips, setting of branch lengths including Grafen's method can all be done using ape. Extinct taxa can be pruned using geiger. phylobase offers numerous functions for querying and using trees (S4), as does phybase. Tree rearrangements (NNI and SPR) can be performed with phangorn.

Community Ecology : picante and vegan integrate several tools for using phylogenetics with community ecology.

Phyloclimatic Modeling : phyloclim integrates several new tools in this area.

Tree Plotting and Visualization: User inputted trees can be plotted using ape, ade4, adephylo, phylobase and ouch. paleoPhylo is specialized for drawing paleobiological phylogenies. Trees can also be examined (zoomed) and viewed as correlograms using ape. Ancestral state reconstructions can be visualized along branches using ape.

Miscellaneous: rmesquite offers a way to call headless Mesquite from R, useful for many kinds of analyses. To do the reverse, use R.Mesquite .

References

• Butler MA, King AA 2004 Phylogenetic comparative analysis: A modeling approach for adaptive evolution. American Naturalist 164, 683-695.
• Cheverud JM, Dow MM, Leutenegger W 1985 The quantitative assessment of phylogenetic constraints in comparative analyses: Sexual dimorphism in body weight among primates. Evolution 39, 1335-1351.
• FitzJohn RG, Maddison WP, and Otto SP 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Systematic Biology 58: 595-611.
• Garland T, Harvey PH, Ives AR 1992 Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41, 18-32.
• Hansen TF 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51: 1341-1351.
• Maddison WP, Midford PE, and Otto SP 2007. Estimating a binary character's effect on speciation and extinction. Systematic Biology 56: 701–710.
• Magallon S, Sanderson, M.J. 2001. Absolute Diversification Rates in Angiosperm Clades. Evolution 55(9):1762-1780.
• Moore, BR, Chan, KMA, Donoghue, MJ (2004) Detecting diversification rate variation in supertrees. In Bininda-Emonds ORP (ed) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Kluwer Academic pgs 487-533.
• Nee S, May RM, Harvey PH 1994. The reconstructed evolutionary process. Philosophical Transactions of the Royal Society of London Series B Biological Sciences 344: 305-311.
• Pagel M 1999 Inferring the historical patterns of biological evolution. Nature 401, 877-884
• Pybus OG, Harvey PH 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society of London Series B Biological Sciences 267, 2267-2272.