Fábio K. Mendes

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: This work uses simulations to demonstrate that SPILS has a larger effect with increasing levels of ILS, and on trees with larger numbers of taxa, and uses data from multiple Drosophila species to show that SPils can be detected in nature.

TL;DR: This work presents CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions, including improved support for multithreading, the explicit modelling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts.

TL;DR: Through extensive simulations of hard- and soft-sweep models, it is shown that indeed the two might not be separable through the use of simple summary statistics, and recombination in regions linked to, but distant from, sites of hard sweeps can create patterns of polymorphism that closely mirror what is expected to be found near soft sweeps.