• Publications
  • Influence
MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN–UHLENBECK MODEL OF ADAPTIVE EVOLUTION
TLDR
The OU model of adaptive evolution is expanded to include models that variously relax the assumption of a constant rate and strength of selection, and can assign each selective regime a separate trait optimum, a rate of stochastic motion parameter, and a parameter for the strength ofselection.
Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction.
TLDR
An extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait is described, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods.
TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD
TLDR
General predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes, showing that these tests are more powerful than existing tests using standardized contrasts.
Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms.
TLDR
A new method for identifying different rates of evolution in a binary character along different branches of a phylogeny is developed and implemented and demonstrates a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade.
Prospects for Building the Tree of Life from Large Sequence Databases
TLDR
An analysis of two “supermatrices” suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.
treePL: divergence time estimation using penalized likelihood for large phylogenies
TLDR
A method is implemented that combines the standard derivative-based optimization with a stochastic simulated annealing approach to overcome optimization challenges and is compared with existing software including r8s, PATHd8 and BEAST.
Three keys to the radiation of angiosperms into freezing environments
TLDR
It is shown that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits and/or shutting down hydraulic function by dropping leaves during freezing.
New Heuristic Methods for Joint Species Delimitation and Species Tree Inference
  • B. O’Meara
  • Environmental Science
    Systematic biology
  • 10 November 2009
TLDR
This paper quantifies the difficulty of jointly finding the division of samples to species and estimating a species tree without constraining the possible assignments a priori and introduces a parametric and a nonparametric method to do this delimitation and tree inference using individual gene trees as input.
The iPlant Collaborative: Cyberinfrastructure for Plant Biology
TLDR
These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.
THE EVOLUTION OF AGRICULTURE IN BEETLES (CURCULIONIDAE: SCOLYTINAE AND PLATYPODINAE)
TLDR
The unusual habit of adult burrowing likely facilitated the diversification of these beetle‐fungus associations, enabling them to use the biomass‐rich resource that trees represent and set the stage for at least one origin of eusociality.
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