Analysis of Phylogenetics and Evolution with R

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Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing (2013, unknown): “ Frustratingly, DIVA, Python LAGRANGE, C++ LAGRANGE, and R’s ape package (Paradis 2012) each use a different numbering scheme for internal nodes.”
Two new graphical methods for mapping trait evolution on phylogenies (2013, background): “Most, including phytools, rely extensively on the important core phylogenetics package, 'ape' (Paradis, Claude & Strimmer 2004; Paradis 2012).”
PAPER Recent range shifts of European dragonflies provide support for an inverse relationship between habitat predictability and dispersal (2013, methodology): “These approaches were used because they provide a greater flexibility of data analysis than analyses based on phylogenetic contrasts and also allow the incorporation of categorical variables and calculations of complex models (Paradis, 2006).”
Functional trait and phylogenetic tests of community assembly across spatial scales in an Amazonian forest (2010, methodology): “The ‘‘ape’’ library was then used to import and manipulate the phylogeny as needed in R (Paradis 2006, R Development Core Team 2009).”