SURFACE: detecting convergent evolution from comparative data by fitting Ornstein‐Uhlenbeck models with stepwise Akaike Information Criterion

By T. Ingram, D. Mahler. 2013

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We present a method, ‘SURFACE’, that uses the Ornstein‐Uhlenbeck stabilizing selection model to identify cases of convergent evolution using only continuous phenotypic characters and a phylogenetic tree. SURFACE uses stepwise Akaike Information Criterion first to locate regime shifts on a tree, then to identify whether shifts are towards convergent regimes. Simulations can be used to test the hypothesis that a clade contains more convergence than expected by chance. We demonstrate the method with an application to Hawaiian Tetragnatha spiders, and present numerical simulations showing that the method has desirable statistical properties given data for multiple traits. The r package surface is available as open source software from the Comprehensive R Archive Network.

Subfields: Ecological Modeling, Genetics, Paleontology

View Paper: https://www.semanticscholar.org/paper/1e584c7e6646b4295c581bb10a886b410a3b5927

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Citations in the corpus

Intrinsic inference difficulties for trait evolution with Ornstein‐Uhlenbeck models (2014, methodology): “Ingram & Mahler (2013) counted both the magnitude and position (edge) of each shift as parameters, therefore using an AIC penalty of 29(3 + 2m) in SURFACE (m being the number of shifts), compared to the AIC penalty of 29(3 + m) when the shift locations are known (Butler & King 2004).”
mvmorph: an r package for fitting multivariate evolutionary models to morphometric data (2015, background): “…models to continuous data are becoming increasingly popular (e.g. Hansen 1997; Pagel 1999; Butler & King 2004; O’Meara et al. 2006; Thomas, Freckleton & Sz (cid:1) ekely 2006; Hansen, Pienaar & Orzack 2008; Beaulieu et al. 2012; Thomas & Freckleton 2012; Adams 2013; Ingram & Mahler 2013).”
BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees (2014, methodology): “A number of R-based software packages are now available to facilitate the modelling of evolutionary rates on phylogenetic trees (e.g. Paradis, Claude & Strimmer 2004; Harmon et al. 2008; FitzJohn 2012; Revell 2012; Thomas & Freckleton 2012; Ingram & Mahler 2013).”
A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data (2014, methodology): “…evolving continuous predictors (Hansen et al. 2008), multivariate evolution of correlated traits (Bartoszek et al. 2012), varying α and σ2 parameters across the tree (Beaulieu et al. 2012; Lapiedra et al. 2013) and identification of convergent regimes (Ingram and Mahler 2013; Mahler et al. 2013).”
Phylogenetic scale in ecology and evolution (2016, background): “(Rabosky, 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),…”
Cope's rule and the adaptive landscape of dinosaur body size evolution (2018, methodology): “Stepwise AICc searches from SURFACE (Ingram & Mahler 2013) for multi-regime OU models recovered different distributions of macroevolutionary regimes across alternative phylogenies used in our analyses (Benson et al. 2017, appendix S2).”
Fast and accurate detection of evolutionary shifts in Ornstein–Uhlenbeck models (2016, methodology): “Mahler et al. (2013) also used OU models with varying optima, but without a preselected set of hypotheses for the number and placement of these optima (see also Ingram & Mahler 2013; Ingram & Kai 2014).”
Measurement errors should always be incorporated in phylogenetic comparative analysis (2015, background): “Such ME, following Ives et al.’s (2007) definition, derives from the intraspecific variability of natural populations and from instrumental imprecision (Garamszegi and Møller 2010).”
The Molecular Basis of Phenotypic Convergence (2014, background): “For example, the independent evolution of similar phenotypes can be identified from ancestral state reconstruction, comparisons of phylogenetic and genetic distance, or inferred shared selective regime (e.g., Muschick et al. 2012, Ingram & Mahler 2013).”