Comparative methods as a statistical fix: the dangers of ignoring an evolutionary model.
ABSTRACT 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.
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- "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). "
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). DOI:10.1111/jbi.12516 · 4.97 Impact Factor
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- "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. "
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; DOI:10.1111/ele.12378 · 13.04 Impact Factor
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- "We chose four different measures commonly used to estimate phylogenetic signal in evolutionary biology and ecology – see Münkemüller et al. (2012) and references therein for a comprehensive review: Pagel's λ (Pagel, 1999), Abouheif's C mean (Abouheif, 1999), Blomberg's K (Blomberg, Garland & Ives, 2003), and Diniz-Filho's phylogenetic eigenvector regressions (PVR; Diniz-Filho, de Sant'Ana & Bini, 1998). The efficiency of PVR has been criticised in recent literature (Adams & Church, 2011; Freckleton, Cooper & Jetz, 2011). However, Diniz-Filho et al. (2012) found PVR to perform well with an appropriate phylogenetic eigenvector selection procedure, and suggested directly minimizing residual Moran's I as a powerful iterative approach; for this reason, we used this method for eigenvector selection. "
ABSTRACT: The presence of a phylogenetic signal in the variation of osteohistological features has been recently debated in the literature. Previous studies have found a significant signal for some features, but these results were obtained on a small amount of characters and a reduced sample. Here we perform a comprehensive study in which we quantify the phylogenetic signal on 62 osteohistological features in an exhaustive sample of palaeognathous birds. We used four different estimators to measure phylogenetic signal – Pagel's λ, Abouheif's Cmean, Blomberg's K, and Diniz-Filho's phylogenetic eigenvector regressions PVR – and four topologies taken from the literature. Bone size and bone vascular density exhibit a strong phylogenetic signal, whereas all but four of the remaining features measured at the histological level – cellular size in caudal and medial transects of femora, and proportion of oblique vascular canals in rostral and caudal transects of tibiotarsi – exhibit a weaker signal. We also found that the impact of the topologies used in the analyses is very low compared with that of sample size. We conclude that the analysis of a comprehensive sample is crucial to obtain reliable quantifications of the phylogenetic signal. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 688–700.Biological Journal of the Linnean Society 08/2014; 112(4). DOI:10.1111/bij.12312 · 2.54 Impact Factor