Folding into shape.
Peer reviewed: True / A new computational tool provides insights into the structure of the cerebellum in mammals.
phylosem: A fast and simple R package for phylogenetic inference and trait imputation using phylogenetic structural equa...
Published in Journal of evolutionary biology
Phylogenetic comparative methods (PCMs) can be used to study evolutionary relationships and trade-offs among species traits. Analysts using PCM may want to (1) include latent variables, (2) estimate complex trait interdependencies, (3) predict missing trait values, (4) condition predicted traits upon phylogenetic correlations and (5) estimate relat...
Climatic adaptation explains responses to Pleistocene oscillations and diversification in European vipers
AimAllopatric speciation is the primary mode of diversification in the Mediterranean Basin. However, the contribution of climatic adaptation during this process is contradictory. In this work, we investigate the eco-evolutionary processes that drove diversification in this region, using European vipers as a case study. We describe the climatic requ...
Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance.
Published in Proceedings of the National Academy of Sciences of the United States of America
Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating phylogenetic tree describing the shared history among species. However, modern phylogenomic analyses have shown...
Data Integration in Bayesian Phylogenetics
Published in Annual Review of Statistics and Its Application
Researchers studying the evolution of viral pathogens and other organisms increasingly encounter and use large and complex data sets from multiple different sources. Statistical research in Bayesian phylogenetics has risen to this challenge. Researchers use phylogenetics not only to reconstruct the evolutionary history of a group of organisms, but ...
Data Integration in Bayesian Phylogenetics
status: published
Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equ...
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Traits underlie organismal responses to their environment and are essential to predict community responses to environmental conditions under global change. Species differ in life-history traits, morphometrics, diet type, reproductive characteristics and habitat utilization. Trait associations are widely analysed using phylogenetic comparative metho...
A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data
Abstract Interspecies RNA-Seq datasets are increasingly common, and have the potential to answer new questions about the evolution of gene expression. Single-species differential expression analysis is now a well-studied problem that benefits from sound statistical methods. Extensive reviews on biological or synthetic datasets have provided the com...
A quantitative global test of the complexity trade-off hypothesis: the case of nominal and verbal grammatical marking
Published in Linguistics Vanguard
Nouns and verbs are known to differ in the types of grammatical information they encode. What is less well known is the relationship between verbal and nominal coding within and across languages. The equi-complexity hypothesis holds that all languages are equally complex overall, which entails trade-offs between coding in different domains. From a ...
One size does not fit all: Variation in anatomical traits associated with emersion behavior in mudskippers (Gobiidae: Ox...
Published in Frontiers in Ecology and Evolution
Life histories involving transitions between differing habitats (i.e., aquatic to terrestrial or marine to freshwater) require numerous anatomical, physiological, and behavioral changes. Often, the traits associated with these changes are thought to come in suites, but all traits thought to be associated with particular life histories may not be re...
