B. O'Meara

dentist: Computing uncertainty by sampling points around maximum likelihood estimates

The paper introduces the dentist R package for estimating confidence intervals around parameter estimates using a Metropolis-Hastings sampling approach, without relying on analytic solutions or local curvature approximations.

A spatially-explicit model of stabilizing selection for improving phylogenetic inference

This paper introduces SelON, a spatially-explicit model of stabilizing selection for phylogenetic inference, showing improved model fit and supporting turtles as sister to lepidosaurs.

The Implications of Over-Estimating Gene Tree Discordance on a Rapid-Radiation Species Tree (Blattodea: Blaberidae)

The paper evaluates gene tree discordance in Blaberidae cockroaches, finding that certain codon models reduce discordance, leading to more robust species trees.

Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach

The paper introduces SelAC, a phylogenetic model that improves tree inference by incorporating stabilizing selection and protein synthesis rates, showing better fit than existing models on yeast data.

Hidden state models improve the adequacy of state-dependent diversification approaches using empirical trees, including biogeographical models

This paper introduces GeoHiSSE, an extension of hidden Markov models to geographic state-dependent speciation and extinction models, showing improved detection of diversification shifts.