Phylogenetic signal and linear regression on species data

By Liam J. Revell. 2010

824 citations recorded by the source corpus.

Subfields: Ecology, Paleontology, Social Psychology

View Paper: https://www.semanticscholar.org/paper/a9db52339a81d6f798bf6b9a01e72830afb1003e

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Citations in the corpus

Untangling the influence of phylogeny, soil and climate on leaf element concentrations in a biodiversity hotspot (2015, methodology): “Under such a scenario, phylogenetic correction becomes redundant in the analysis of trait correlations (Revell 2010).”
Measurement errors should always be incorporated in phylogenetic comparative analysis (2015, methodology): “We rescaled the tree height of all trees to one to have comparable rates across trees (Revell 2010).”
Niche differentiation and expansion of plant species are associated with mycorrhizal symbiosis (2018, methodology): “incorporate it into the model with an appropriate strength (Freckleton et al., 2002; Revell, 2010).”
Bergmann's rule in mammals: a cross-species interspecific pattern (2013, neutral): “For PGLS, we set λ , the character describing the phylogenetic signal (Pagel 1999, Revell 2010), ﬁ xed at 1 (for the series of the analyses with shifting latitude thresholds), and we additionally calculated λ for the whole dataset and the various taxonomic subsets. λ is calculated by maximum…”
phytools: an R package for phylogenetic comparative biology (and other things) (2012, methodology): “In this package, I have focused primarily on implementing several phylogenetic comparative methods from my own work (Revell 2008, 2009, 2010; Revell, Harmon & Collar 2008; Revell & Harrison 2008; Revell & Collar 2009; Lindenfors, Revell & Nunn 2010; Mahler et al. 2010; Revell et al. in press);…”
Trait‐related responses to habitat fragmentation in Amazonian bats (2015, methodology): “PGLS models were fit using the ‘pgls’ function in the R package caper (Orme et al. 2013), following the recommendation of Revell (2010) in simultaneously estimating phylogenetic signal (quantified using Pagel’s k, Pagel 1999) and the regression model.”
Continuous traits and speciation rates: Alternatives to state‐dependent diversification models (2017, result): “Note that PGLS and the simulation approach need not yield identical results: PGLS assumes that the residuals of the relationship between traits and speciation rates can be modelled as a Brownian motion on the phylogeny (Revell, 2010); the simulation approach assumes Brownian motion in the trait only”
Supporting Online Material for Evolutionary Conservation of Species' Roles in Food Webs (2012, result): “To do so, we compared the results of an ordinary least squares (OLS) and a phylogenetic generalized least squares (PGLS) regression with species’ benef t bi as the response variable and species trophic level li as the predictor variable (64).”
mvmorph: an r package for fitting multivariate evolutionary models to morphometric data (2015, background): “Nevertheless, such an approach implicitly assumes that one trait is evolutionarily responding to the other (Hansen, Pienaar & Orzack 2008; Revell 2010; Hansen & Bartoszek 2012), a critical assumption of biological causality which is actually relaxed in a multivariate setting focused on mere…”
Generalized linear mixed models for phylogenetic analyses of community structure (2011, neutral): “In a phylogenetic context, these would be similar to phylogenetic regressions with phylogenetic signal in the residuals (Gage and Freckleton 2003, Duncan et al. 2007, Lavin et al. 2008, Revell 2010).”
Of mice and mammoths: generality and antiquity of the island rule (2013, background): “…squares regressions even when independent variables have a strong phylogenetic signal (Revell, 2010) or when the rate of anagenetic variation exceeds that of cladogenesis (see Ricklefs & Starck, 1996; Bj€orklund, 1997; Losos, 2003, 2011; McNab, 2003; Carvalho et al., 2006; Sibly et al., 2012).”
Phylogenetic Regression for Binary Dependent Variables (2014, methodology): “This type of behavior— sensitivity of a statistical regression method to the distribution of the independent variable—is also found in phylogenetic regression with continuous dependent variables (Revell 2010).”
Correlates of extinction risk in squamate reptiles: the relative importance of biology, geography, threat and range size (2016, positive): “We followed 196 Revell (2010) and simultaneously estimated phylogenetic signal (Pagel’s λ, using maximum 197 likelihood) and regression model, an approach which has been shown to outperform 198 equivalent non-phylogenetic approaches.”
Which intrinsic traits predict vulnerability to extinction depends on the actual threatening processes (2013, methodology): “0.62) indicating phylogenetic correction was not necessary (Revell 2010).”