Size-Correction and Principal Components for Interspecific Comparative Studies

By Liam J. Revell. Evolution; international journal of organic evolution, 2009

805 citations recorded by the source corpus.

Subfields: Animal Science and Zoology, Genetics

View Paper: https://www.semanticscholar.org/paper/43882f0fd0c81739943d5b34f192fe30e8bec6cf

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Citations in the corpus

Root traits are multidimensional: specific root length is independent from root tissue density and the plant economic spectrum (2016, methodology): “Journal of Ecology © 2016 British Ecological Society, Journal of Ecology, 104, 1299–1310 Traits that aligned with the plant economic spectrum (i.e. axis 1 in the species-level PCA, Table 1, Fig.”
Phylogenetic signal and linear regression on species data (2010, methodology): “Finally, I repeat a maximum likelihood procedure using the k statistic of Pagel (1999) in which we simultaneously estimate phylogenetic signal and the regression parameters (e.g. Revell 2009), thus obviating the need for a priori estimation of phylogenetic signal in the regres- sion variables.”
Phylogenetic Principal Components Analysis and Geometric Morphometrics (2013, methodology): “Phylogenetic principal components analysis (pPCA) is similar to PCA, except that the covariance matrix is inversely weighted by phylogeny and the space is centered on the estimated phenotype of the root node of the tree instead of the mean of the tips (Revell, 2009).”
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi (2014, methodology): “To visualize the diversity of decay chemistries in basidiomycetes, we applied phylogenetically informed principal-components analysis (PCA) (71) to the set of predicted carbohydrate- and lignin-active enzymes (Dataset S1).”
Fast and accurate detection of evolutionary shifts in Ornstein–Uhlenbeck models (2016, methodology): “Revell (2009) demonstrated that PCA is misleading for phylogenetic data and proposed phylogenetic PCA (pPCA) instead, which assumes a BM covariance among taxa.”
Moving beyond the guild concept: developing a practical functional trait framework for terrestrial beetles (2015, methodology): “However, this method only returns phylogenetically independent scores for nodes of the phylogenetic tree used and not for species themselves (Revell, 2009).”
A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. (2014, methodology): “Other applications include phylogenetic principal component analysis (PCA; Revell 2009), phylogenetic discriminant analysis (Motani and Schmitz 2011) and phylogenetic prediction (Garland and Ives 2000).”
Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes (2019, methodology): “PC scores are then obtained for the extant species as well as for the estimated ancestral taxa, and these scores are used to generate the ordination plot (for details, see Revell 2009).”
SURFACE: detecting convergent evolution from comparative data by fitting Ornstein‐Uhlenbeck models with stepwise Akaike Information Criterion (2013, methodology): “…phylogenetic residuals of four log-transformed traits (cephalothorax length, chelicera length, leg spine length and abdomen depth/length ratio) against log (TL), then retained the first two axes of a phylogenetic principal components analysis (pPCA) of these four size-adjusted traits (Revell 2009).”
mvmorph: an r package for fitting multivariate evolutionary models to morphometric data (2015, methodology): “…through ordination methods such as PCA and a sub-set of the ﬁrst principal components is then treated as independent univariate traits, evolutionary model inferences from these transformed spaces can be severely biased (Revell 2009; Monteiro 2013; Polly et al. 2013; Uyeda, Caetano & Pennell 2015).”
Statistical Issues and Assumptions of Phylogenetic Generalized Least Squares (2014, background): “…covariates (for more about principal component and factor analysis, see, e.g., Budaev 2010, and for phylogenetic principal components analysis see Revell 2009 and Polly et al. 2013); and (3) exclude predictors based on collinearity (i.e., the variance inflation factors revealed for them; see…”
phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things) (2023, methodology): “As such, primarily in an effort to control for overall size, I’ll first run a phylogenetic principal components analysis (Revell 2009) using the phytools function phyl.pca.”
Risk-taking behavior, urbanization and the pace of life in birds (2018, methodology): “In our best PPCA, species with high scores (i.e., high adult survival elasticities) were slow-lived and those with low scores (i.e., high fecundity elasticities) were fast-lived.”
Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly (2017, methodology): “As species are not phylogenetically independent from each other, it is common practice to use methods ‘correcting’ this dependence (Pagel 1999; Revell 2009; Diniz-Filho et al. 2012; de Bello et al. 2015).”
phytools: an R package for phylogenetic comparative biology (and other things) (2012, methodology): “resid Conducts phylogenetic size-correction, using least-squares regression (Revell 2009) phyl.”
The role of frugivory in the diversification of bats in the Neotropics (2012, methodology): “Finally, we conducted a phylogenetic principal components analysis (PPCA) (Revell, 2009; see Appendix S3) on the mean values of the independent variables at the genus level (see below) to confront the multicollinearity problem previously detected with bivariate PGLS analyses.”