Alex Popinga

TL;DR: A series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release are described.

TL;DR: The full range of new tools and models available on the BEAST 2.5 platform are described, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.

TL;DR: The usefulness of this new MCMC sampler is demonstrated by using it to infer migration rates and effective population sizes of H3N2 influenza between New Zealand, New York and Hong Kong from publicly available hemagglutinin gene sequences under the structured coalescent.

TL;DR: Stochastic and deterministic coalescent susceptible–infected–removed (SIR) tree priors are developed in a Bayesian phylogenetic inference framework to permit joint estimation of SIR epidemic parameters and the sample genealogy and it is found that the stochastic variant generally outperforms its deterministic counterpart in terms of error, bias, and highest posterior density coverage.

TL;DR: The first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago is reported, and the ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics of centralized industrial scale farming of sacrificed birds.