Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation

By Mark Pagel, F. Lutzoni. 2002

102 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Plant Science

View Paper: https://www.semanticscholar.org/paper/eace298d96ed1ce61385ae40c4b37874c2cd975b

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In Ecology, Evolution, Behavior and Systematics

In Plant Science

Citations in the corpus

Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible‐Jump Markov Chain Monte Carlo (2006, methodology): “Markov chain Monte Carlo methods are now widely used in phylogenetic inference (e.g., Rannala and Yang 1996; Wilson and Balding 1998; Larget and Simon 1999; Huelsenbeck et al. 2001; Lutzoni et al. 2001; Pagel and Lutzoni 2002; Pagel and Meade 2004).”
Evolutionary Transitions in Floral Color (2008, background): “The ideal approach would take into account uncertainty due to both phylogeny and ancestral character state by averaging estimated transition rates over a large number of plausible phylogenies (Pagel and Lutzoni 2002).”
Bayesian estimation of ancestral character states on phylogenies. (2004, methodology): “A Markov chain is constructed, the states of which are different phylogenetic trees (Rannala and Yang, 1996; Wilson and Balding, 1998; Larget and Simon, 1999; Mau et al., 1999; Lutzoni et al., 2001; Huelsenbeck et al., 2001; Pagel and Lutzoni, 2002; Pagel and Meade, 2004).”
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation (2019, background): “only trees rather than the consensus tree alone [33,34].”
Innovative Approaches to the Relationship Between Diet and Mandibular Morphology in Primates (2012, methodology): “2001), results should not be conditioned on a single phylogenetic hypothesis (Huelsenbeck et al. 2000; Pagel and Lutzoni 2002).”
Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. (2003, background): “These measures allow workers to identify trees or parts of a tree that are well supported by the data and thus adequate to serve as the basis for evolutionary inference of biological systems (Huelsenbeck, Rannala, and Masly 2000; Lutzoni et al. 2001; Pagel and Lutzoni 2002).”
Mainland colonization by island lizards (2005, methodology): “This analysis was conducted using a Bayesian tree-sampling methodology (Lutzoni et al., 2001; Pagel & Lutzoni, 2002) to determine whether the most recent common ancestor to Norops was West Indian or mainland using the programme Mesquite (Maddison & Maddison, 2004).”