Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence

By R. Freckleton, P. Harvey, Mark Pagel. American Naturalist, 2002

2,583 citations recorded by the source corpus.

Subfields: Genetics, Nature and Landscape Conservation, Paleontology

View Paper: https://www.semanticscholar.org/paper/63ee8bce97f5b1fcfab382590701ccacc70771ae

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In Genetics

In Nature and Landscape Conservation

In Paleontology

Citations in the corpus

Can amphibians take the heat? Vulnerability to climate warming in subtropical and temperate larval amphibian communities (2012, background): “…under a Brownian model of trait evolution where variance in traits accumulates with time since divergence from a common ancestor, whereas values of k 1 indicate that the actual covariance between the traits is lower than would be expected under a Brownian model (Freckleton et al., 2002).”
Bergmann's rule in mammals: a cross-species interspecific pattern (2013, neutral): “…maximum likelihood in PGLS and can vary between 0 (no phylogenetic signal) and 1 (the observed pattern is predicted by the phylogeny; similarity among species scales in proportion to their shared evolutionary time, assuming a Brownian motion model of evolution) (Pagel 1999, Freckleton et al. 2002).”
Methods of assessing extinction risk in marine fishes. (2004, background): “Phylogenetically independent analyses can remove bias, noise and lack of statistical independence that occur in simple cross-species analyses by incorporating relatedness among taxa (Rickman et al. 2000; Reynolds et al. 2001; Freckleton 2002).”
Testosterone and melanin-based black plumage coloration: a comparative study (2008, methodology): “The method applies likelihood ratio statistics to test hypotheses of correlated trait evolution and also to estimate the importance of phylogenetic corrections in the models (Freckleton et al. 2002).”
Phylogenetic signal, evolutionary process, and rate. (2008, background): “This is because the likelihood equation for λ is usually not defined for values of λ > 1.0 (Freckleton et al., 2002).”
Diet predicts intestine length in Lake Tanganyika’s cichlid fishes (2009, methodology): “A k-value of 0AE0 indicates that trait variation is independent of the phylogeny, whereas a k-value of 1AE0 indicates that trait variation is as predicted by Brownian motion evolution along the phylogeny ( Freckleton, Harvey & Pagel 2002 ).”
The evolution of self-control (2014, methodology): “We incorporated the parameter λ in the PGLS models to estimate phylogenetic signal and regression parameters simultaneously, using a maximum likelihood procedure (200, 201).”
Influences on the transport and establishment of exotic bird species: an analysis of the parrots (Psittaciformes) of the world (2004, methodology): “While it is now almost standard practice to perform phylogenetic controls (Harvey & Pagel, 1991; Garland et al., 1999; Freckleton et al., 2002; but see Harvey & Rambaut, 2000), there is no phylogenetic association to control for in this case.”
Niche conservatism in non‐native birds in Europe: niche unfilling rather than niche expansion (2013, methodology): “To account for possible phylogenetic non-independence, we included a species-level phylogeny as a correlation structure in the model (Freckleton et al., 2002).”
SCALE AND HIERARCHY IN MACROEVOLUTION (2007, background): “…and waning of clades and the intrinsic biotic properties of their constituent organisms, populations or species (involving a huge range of traits from nectar spurs in angiosperms to geographical range sizes in birds) (see reviews in Freckleton et al. 2002, 2003; Coyne and Orr 2004; Paradis 2005).”