Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution

By Marguerite Butler, Aaron M. King. 2004

1,399 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

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Citations in the corpus

Batch Stationary Distribution Estimation (2020, methodology): “We next apply VPM to solve a class of SDEs known as the Ornstein-Uhlenbeck process (OUP), which finds many applications in biology (Butler and King, 2004), financial mathematics and physical sciences (Oksendal, 2013).”
A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. (2014, methodology): “The more general model of adaptive evolution considered by Butler and King (2004) includes variable optima, to allow for different constraints on different lineages.”
Phylogenetic signal, evolutionary process, and rate. (2008, background): “…a better approach might be to consider fitting alternative models for the evolutionary process to the data and tree (e.g., Hansen, 1997; Mooers et al., 1999; Harvey and Rambaut, 2000; Blomberg et al., 2003; Butler and King, 2004; Oakley et al., 2005; Lee et al., 2006; Estes and Arnold, 2007).”
TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD (2006, methodology): “Brownian motion does not necessarily imply a process of neutral evolution, such as genetic drift (contra Butler and King 2004).”
Climate variability predicts thermal limits of aquatic insects across elevation and latitude (2017, methodology): “critical thermal limits To test the effects of latitude and elevation on CTMAX, CTMIN, and thermal breadth we used phylogenetic generalized least squares regression (PGLS; Grafen, 1989) fit with an Ornstein–Uhlenbeck model of trait evolution (OU; Butler & King, 2004; Hansen, 1997).”
A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data (2014, methodology): “…to calculate the weighted average of adaptive optima, discounted by an exponentially decreasing function that depends on the rate parameter α and the elapsed time since the species evolved under a given adaptive optimum (For a full explanation and derivation, see Hansen 1997; Butler and King 2004).”
Phylogenetic approaches in comparative physiology (2005, methodology): “…making it possible to incorporate phylogenetic uncertainty directly into comparative analyses that include simultaneous estimation of the phylogeny from DNA sequence data (Huelsenbeck and Rannala, 2003; see also p. 693 in Butler and King, 2004), as was originally suggested by Felsenstein (1985).”
The functional role of soil seed banks in natural communities. (2014, background): “More precise comparative methods (Butler and King, 2004), and comparative investigations on closely related species (Evans et al.”
Using Phylogenetic, Functional and Trait Diversity to Understand Patterns of Plant Community Productivity (2009, neutral): “. Further, alternative models have been proposed that incorporate explicit models of stabilizing or strong directional selection”
Functional distinctiveness of major plant lineages (2014, background): “More complex models of trait evolution have been developed, which allow for heterogeneity in both rates and models (i.e. not just Brownian motion) across the tree (Butler & King 2004; O’Meara et al. 2006).”
Multispecies comparison reveals that invasive and native plants differ in their traits but not in their plasticity (2011, methodology): “Furthermore, we dealt with polytomies in the input tree (Butler & King 2004) by randomly generating 100 fully resolved trees using MESQUITE (Maddison & Maddison 2009).”
Phylogenetic scale in ecology and evolution (2016, neutral): “…2014), surface (Ingram & Mahler, 2013), nodiv (Borregaard et al., 2014), MOTMOT (Thomas & Freckleton, 2012), ape and geiger2 (Blomberg et al., 2003; Butler & King, 2004; Edwards & Cavalli-Sforza, 1964; Felsen-stein, 1985; Hansen, 1997; Paradis et al., 2004; Pennell et al., 2014), consenTRAIT…”
Two new graphical methods for mapping trait evolution on phylogenies (2013, methodology): “For simplicity, I assume Brownian motion as a model for trait evolution (Cavalli-Sforza & Edwards 1967; Felsenstein 1973, 1985); however, the method could be adapted to other evolutionary models such as the Ornstein–Uhlenbeck model (Hansen 1997; Butler & King 2004).”
Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters (2008, methodology): “Nonetheless, Brownian motion has been criticized as representing an overly simplistic, frequently inappropriate model for the evolutionary process (Butler et al., 2000; Butler and King, 2004; Estes and Arnold, 2007).”
Measurement errors should always be incorporated in phylogenetic comparative analysis (2015, background): “On the other hand, when natural selection towards both an optimum and random drift act on a phenotypic trait (Lande 1976; Hansen 1997; Butler & King 2004) or when neutral evolution occurs in a constrained part of morphospace (Wiens et al. 2010; Crisp & Cook 2012), then an OU model might provide a…”