BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

This paper describes the BEAST 2.5 release of a computational software platform for Bayesian evolutionary analysis, spanning phylogenetics, population genetics, and phylodynamics. It responds to the growing appreciation that some evolutionary questions can only be answered by combining evidence from multiple independent data sources, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information. BEAST 2 addresses the conceptual and computational difficulty of joint modeling by letting researchers robustly develop compatible sub-models that can be composed into a full model hierarchy.

The authors detail the major new developments in the BEAST 2 core platform and model hierarchy since its first release over four years earlier, culminating in the 2.5 release. These additions expand joint evolutionary inference in many new directions, especially joint inference over multiple data types, non-tree models, and complex phylodynamics. The work mattered because building such scientific software is itself a major research activity, and BEAST 2.5 provides a validated, extensible foundation for advanced evolutionary analysis across biology.