Josef C. Uyeda

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Our understanding of macroevolutionary patterns of adaptive evolution has greatly increased with the advent of large-scale phylogenetic comparative methods. Widely used Ornstein-Uhlenbeck (OU) models can describe an adaptive process of divergence and selection. However, inference of the dynamics of adaptive landscapes from comparative data is complicated by(More)
We lack a comprehensive understanding of evolutionary pattern and process because short-term and long-term data have rarely been combined into a single analytical framework. Here we test alternative models of phenotypic evolution using a dataset of unprecedented size and temporal span (over 8,000 data points). The data are body-size measurements taken from(More)
SUMMARY Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger(More)
Theoretical and empirical results demonstrate that the G-matrix, which summarizes additive genetic variances and covariances of quantitative traits, changes over time. Such evolution and fluctuation of the G-matrix could potentially have wide-ranging effects on phenotypic evolution. Nevertheless, no studies have yet addressed G-matrix stability and(More)
Most existing methods for modeling trait evolution are univariate, although researchers are often interested in investigating evolutionary patterns and processes across multiple traits. Principal components analysis (PCA) is commonly used to reduce the dimensionality of multivariate data so that univariate trait models can be fit to individual principal(More)
Metabolism is the link between ecology and physiology-it dictates the flow of energy through individuals and across trophic levels. Much of the predictive power of metabolic theories of ecology derives from the scaling relationship between organismal size and metabolic rate. There is growing evidence that this scaling relationship is not universal, but we(More)
Quantitative genetic models of sexual selection have generally failed to provide a direct connection to speciation and to explore the consequences of finite population size. The connection to speciation has been indirect because the models have treated only the evolution of male and female traits and have stopped short of modeling the evolution of sexual(More)
The long-controversial theory of punctuated equilibrium (PE) asserts that speciation causes rapid evolution against a backdrop of stasis. PE is currently undergoing a resurgence driven by new developments in statistical methods. However, we argue that PE is actually a tangle of four unnecessarily conflated questions: (i) is evolution gradualistic or pulsed?(More)
Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record-phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods.(More)
estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny. Evolution 62, 2718–2726 4 Webster, A.J. et al. (2003) Molecular phylogenies link rates of evolution and speciation. Science 301, 478 5 Pagel, M. et al. (2006) Large punctuational contribution of speciation(More)