Comparative Methods as a Statistical Fix: The Dangers of Ignoring an Evolutionary Model

Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.
The American Naturalist (Impact Factor: 3.83). 07/2011; 178(1):E10-7. DOI: 10.1086/660272
Source: PubMed


Abstract Comparative methods are widely used in ecology and evolution. The most frequently used comparative methods are based on an explicit evolutionary model. However, recent approaches have been popularized that are without an evolutionary basis or an underlying null model. Here we highlight the limitations of such techniques in comparative analyses by using simulations to compare two commonly used comparative methods with and without evolutionary basis, respectively: generalized least squares (GLS) and phylogenetic eigenvector regression (PVR). We find that GLS methods are more efficient at estimating model parameters and produce lower variance in parameter estimates, lower phylogenetic signal in residuals, and lower Type I error rates than PVR methods. These results can very likely be generalized to eigenvector methods that control for space and both space and phylogeny. We highlight that GLS methods can be adapted in numerous ways and that the variance structure used in these models can be flexibly optimized to each data set.

6 Reads
    • "For instance, if a small number of eigenvectors are selected, one can underestimate the phylogenetic signal. This is so because different eigenvectors represent different parts of the phylogenetic relationships among the species, making the comparison with other model-based results difficult and introducing some subjectivity in the modelling process (which is usually criticized – see Freckleton et al., 2011). However, when thinking in nonstationarity, this seems to be an advantage. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Despite the longstanding interest in non-stationarity of both phenotypic evolution and diversification rates, only recently have methods been developed to study this property. Here, we propose a methodological expansion of the Phylogenetic Signal Representation (PSR) curve based on phylogenetic eigenvectors to test for non-stationarity. The PSR is built by plotting the coefficients of determination R(2) from Phylogenetic Eigenvector Regression (PVR) models increasing the number of phylogenetic eigenvectors against the accumulated eigenvalues. The PSR curve is linear under a stationary model of trait evolution (i.e., the Brownian motion model). Here we describe the distribution of shifts in the models R(2) and used a randomization procedure to compare observed and simulated shifts along the PSR curve, which allowed detecting non-stationarity in trait evolution. As an applied example, we show that the main evolutionary pattern of variation in the theropod dinosaur skull was non-stationary, with a significant shift in evolutionary rates in derived oviraptorosaurs, an aberrant group of mostly toothless, crested, bird-like theropods. This result is also supported by a recently proposed Bayesian-based method (AUTEUR). A significant deviation between Ceratosaurus and Limusaurus terminal branches was also detected. We purport that our new approach is a valuable tool for evolutionary biologists, owing to its simplicity, flexibility and comprehensiveness. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Journal of Evolutionary Biology 05/2015; 28(7). DOI:10.1111/jeb.12660 · 3.23 Impact Factor
  • Source
    • "A method for incorporating phylogeny into assemblage-level grid-cell analyses, phylogenetic eigenvector regression, exists (Diniz-Filho et al., 1998). However , this method has severe statistical limitations and probably does not adequately account for the effects of phylogeny (Adams & Church, 2011; Freckleton et al., 2011). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Aim: Climate is thought to exert a strong influence on animal body sizes. We examined the relationship between amphibian body size and several climatic variables to discern which climatic variables, if any, affect amphibian size evolution. Location: Europe and North America. Methods: We assembled a dataset of mean sizes of 356 (out of 360) amphibian species in Europe, the USA and Canada, and tested how they are related to temperature, precipitation, primary productivity and seasonality. First, we examined the body size distributions of all the species inhabiting equal-area grid cells (of 96.3 km 9 96.3 km) using randomizations to account for the effects of species richness. Second, we examined the relationship between mean species body size and the environmental predictors across their ranges accounting for phylogenetic effects. Results: The observed amphibian body size distributions were mostly statistically indistinguishable from distributions generated by random assignment of species to cells. Median sizes in grid cells were negatively correlated with temperature in anurans and positively in urodeles. The phylogenetic analysis revealed opposite trends in relation to temperature. In both clades most climatic variables were not associated with size and the few significant relationships were very weak. Main conclusions: Spatial patterns in amphibian body size probably reflect diversity gradients, and relationships with climate could result from spurious effects of richness patterns. The large explanatory power of richness in the grid-cell analysis, and the small explanatory power of climate in the interspe-cific analysis, signify that climate per se has little effect on amphibian body sizes.
    Journal of Biogeography 04/2015; 42(7):1246-1254. DOI:10.1111/jbi.12516 · 4.59 Impact Factor
  • Source
    • "All retained PCs represented deep divergences in the phylogeny , and thus trait values that show correlations with such PCs could have evolved along the tree and reflect niche conservatism . Criticisms of this approach come from PC axes that contrast paraphyletic groups, and for which it is therefore harder to interpret how a trait might evolve in such a manner (Freckleton et al. 2011). In our case, we only used PC axes that contrasted whole clades. "
    [Show abstract] [Hide abstract]
    ABSTRACT: We examined whether plant-soil feedback and plant-field abundance were phylogenetically conserved. For 57 co-occurring native and exotic plant species from an old field in Canada, we collected a data set on the effects of three soil biota treatments on plant growth: net whole-soil feedback (combined effects of mutualists and antagonists), feedback with arbuscular mycorrhizal fungi (AMF) collected from soils of conspecific plants, and feedback with Glomus etunicatum, a dominant mycorrhizal fungus. We found phylogenetic signal in both net whole-soil feedback and feedback with AMF of conspecifics; conservatism was especially strong among native plants but absent among exotics. The abundance of plants in the field was also conserved, a pattern underlain by shared plant responses to soil biota. We conclude that soil biota influence the abundance of close plant relatives in nature.
    Ecology Letters 10/2014; 17(12). DOI:10.1111/ele.12378 · 10.69 Impact Factor
Show more