316 research outputs found
πBUSS:a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios
Background: Simulated nucleotide or amino acid sequences are frequently used
to assess the performance of phylogenetic reconstruction methods. BEAST, a
Bayesian statistical framework that focuses on reconstructing time-calibrated
molecular evolutionary processes, supports a wide array of evolutionary models,
but lacked matching machinery for simulation of character evolution along
phylogenies.
Results: We present a flexible Monte Carlo simulation tool, called piBUSS,
that employs the BEAGLE high performance library for phylogenetic computations
within BEAST to rapidly generate large sequence alignments under complex
evolutionary models. piBUSS sports a user-friendly graphical user interface
(GUI) that allows combining a rich array of models across an arbitrary number
of partitions. A command-line interface mirrors the options available through
the GUI and facilitates scripting in large-scale simulation studies. Analogous
to BEAST model and analysis setup, more advanced simulation options are
supported through an extensible markup language (XML) specification, which in
addition to generating sequence output, also allows users to combine simulation
and analysis in a single BEAST run.
Conclusions: piBUSS offers a unique combination of flexibility and
ease-of-use for sequence simulation under realistic evolutionary scenarios.
Through different interfaces, piBUSS supports simulation studies ranging from
modest endeavors for illustrative purposes to complex and large-scale
assessments of evolutionary inference procedures. The software aims at
implementing new models and data types that are continuously being developed as
part of BEAST/BEAGLE.Comment: 13 pages, 2 figures, 1 tabl
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics
Summary: SPREAD is a user-friendly, cross-platform application to analyze and visualize Bayesian phylogeographic reconstructions incorporating spatial–temporal diffusion. The software maps phylogenies annotated with both discrete and continuous spatial information and can export high-dimensional posterior summaries to keyhole markup language (KML) for animation of the spatial diffusion through time in virtual globe software. In addition, SPREAD implements Bayes factor calculation to evaluate the support for hypotheses of historical diffusion among pairs of discrete locations based on Bayesian stochastic search variable selection estimates. SPREAD takes advantage of multicore architectures to process large joint posterior distributions of phylogenies and their spatial diffusion and produces visualizations as compelling and interpretable statistical summaries for the different spatial projections
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST
Advances in sequencing technology continue to deliver increasingly large molecular sequence datasets that are often heavily partitioned in order to accurately model the underlying evolutionary processes. In phylogenetic analyses, partitioning strategies involve estimating conditionally independent models of molecular evolution for different genes and different positions within those genes, requiring a large number of evolutionary parameters that have to be estimated, leading to an increased computational burden for such analyses. The past two decades have also seen the rise of multi-core processors, both in the central processing unit (CPU) and Graphics processing unit processor markets, enabling massively parallel computations that are not yet fully exploited by many software packages for multipartite analyses.status: publishe
Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction
Reconstructing pathogen dynamics from genetic data as they become available
during an outbreak or epidemic represents an important statistical scenario in
which observations arrive sequentially in time and one is interested in
performing inference in an 'online' fashion. Widely-used Bayesian phylogenetic
inference packages are not set up for this purpose, generally requiring one to
recompute trees and evolutionary model parameters de novo when new data arrive.
To accommodate increasing data flow in a Bayesian phylogenetic framework, we
introduce a methodology to efficiently update the posterior distribution with
newly available genetic data. Our procedure is implemented in the BEAST 1.10
software package, and relies on a distance-based measure to insert new taxa
into the current estimate of the phylogeny and imputes plausible values for new
model parameters to accommodate growing dimensionality. This augmentation
creates informed starting values and re-uses optimally tuned transition kernels
for posterior exploration of growing data sets, reducing the time necessary to
converge to target posterior distributions. We apply our framework to data from
the recent West African Ebola virus epidemic and demonstrate a considerable
reduction in time required to obtain posterior estimates at different time
points of the outbreak. Beyond epidemic monitoring, this framework easily finds
other applications within the phylogenetics community, where changes in the
data -- in terms of alignment changes, sequence addition or removal -- present
common scenarios that can benefit from online inference.Comment: 20 pages, 3 figure
Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication
Host species switches by bacterial pathogens leading to new endemic infections are important evolutionary events that are difficult to reconstruct over the long term. We investigated the host switching of Staphylococcus aureus over a long evolutionary timeframe by developing Bayesian phylogenetic methods to account for uncertainty about past host associations and using estimates of evolutionary rates from serially sampled whole-genome data. Results suggest multiple jumps back and forth between human and bovids with the first switch from humans to bovids taking place around 5500 BP, coinciding with the expansion of cattle domestication throughout the Old World. The first switch to poultry is estimated at around 275 BP, long after domestication but still preceding large-scale commercial farming. These results are consistent with a central role for anthropogenic change in the emergence of new endemic diseases.status: publishe
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