A. F. Magee

Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models

This paper introduces a gradient-based Hamiltonian Monte Carlo sampler for efficient inference in episodic birth-death-sampling models, showing significant computational improvements over Metropolis-Hastings methods.

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

The paper identifies the recent origin and geographical distribution of bat viruses ancestral to SARS-CoV and SARS-CoV-2, showing they circulated in Asia before spilling over into humans.

Rapidly changing speciation and extinction rates can be inferred in spite of non-identifiability

This paper shows that strong directional trends in speciation and extinction rates can be reliably inferred despite non-identifiability in time-variable birth-death models.

ACDC: Analysis of Congruent Diversification Classes

ACDC explores congruence classes of diversification rates in phylogenies, identifying common patterns despite non-identifiability.

Impact of K-Pg Mass Extinction Event on Crocodylomorpha Inferred from Phylogeny of Extinct and Extant Taxa

This study uses a phylogenetic approach to show strong evidence of the K-Pg mass extinction event impacting crocodylomorphs, contrary to previous conclusions.

Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis

This study examines how Bayesian phylogenetic inference is affected by model misspecification due to pairwise epistasis and shows that tree accuracy improves with alignment size even when sites are epistatically coupled.

Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts

This paper introduces a Bayesian birth-death model with adaptive priors to detect rate shifts in diversification processes and applies it to macroevolutionary and epidemiological datasets.