Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe 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.

The Making of Amazonian Diversity The biodiversity of the Amazon Basin is legendary, but the processes by which it has been generated have been debated. In the late 20th century the prevalent view was that the engine of diversity was repeated contraction and expansion of forest refugia during the past 3 million years or so. Hoorn et al. (p. 927 ) analyze findings from a diverse range of disciplines, including molecular phylogeny, ecology, sedimentology, structural geology, and palaeontology, to offer an overview of the entire history of this region during the Cenozoic era (66 million years ago). The uplift of the Andes was a pivotal event in the evolution of Amazonian landscapes because it continually altered river drainage patterns, which in turn put a variety of pressures on organisms to adapt to changing conditions in a multiplicity of ways. Hence, the diversity of the modern biota of the Amazon has more ancient origins than previously thought.

Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data-most commonly, fossil age estimates-are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the "fossilized birth-death" (FBD) process-a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene.A phylogenetic analysis of species has two goals: to infer the evolutionary relationships and the amount of divergence among species. Preferably, divergence is estimated in units proportional to time, thus revealing the times at which speciation events occurred. Once orthologous DNA sequences from the species have been aligned, both goals can be accomplished by assuming that nucleotide substitutions occur at the same rate in all lineages [the "molecular clock" assumption (1)] and that the time of at least one speciation event on the tree is known, i.e., one speciation event acts to "calibrate" the substitution rate.The goal of reconstructing rooted, time-calibrated phylogenies is complicated by substitution rates changing over the tree and by the difficulty of determining the date of any speciation event. Substitution rate variation among lineages is pervasive and has been accommodated in several ways. The most widely used method to account for rate heterogeneity is to assign an independent parameter to each branch of the tree. Branch lengths, then, are the product of substitution rate and time, and usually measured in units of expected number of substitutions per site. This solution allows estimation of the tree topology-which is informative about interspecies relationships-but does not attempt to estimate the rate and time separately. Thus, under this "unconstrained" parameterization, molecular sequence data allow inference of phylogenetic relationships and ge...