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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)
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)
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)
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)
Pigment evolution was reconstructed in the subfamily Amphistichinae, a six-species clade of the surfperches, family Embiotocidae. Assignment was confirmed for all species within the subfamily, but low levels of differentiation were found among species within the subfamily, suggesting a recent radiation. The new phylogeny differs from previous hypotheses by(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)
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