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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
TLDR
The software package Tracer is presented, for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference, which provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more.
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Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
TLDR
The BEAST software package unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration.
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Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty.
TLDR
It is shown that PS and SS sampling substantially outperform these estimators and adjust the conclusions made concerning previous analyses for the three real-world data sets that were reanalyzed.
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The genome of Tetranychus urticae reveals herbivorous pest adaptations
TLDR
The completely sequenced and annotated spider mite genome is presented, representing the first complete chelicerate genome, and finds strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer.
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Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts
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Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.
TLDR
A comparison with recent implementations of path sampling and stepping-stone sampling shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model.
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The early spread and epidemic ignition of HIV-1 in human populations
TLDR
Using statistical approaches applied to HIV-1 sequence data from central Africa, it is shown that from the 1920s Kinshasa was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere.
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Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary.
TLDR
It is argued that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time ofpolyploidization could mitigate the stark contrast in the proposed evolutionary fates of Polyploids.
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Considerable escape of SARS-CoV-2 Omicron to antibody neutralization
TLDR
An isolate of the Omicron variant of SARS-COV-2 was completely or partially resistant to neutralization by all nine clinically approved monoclonal antibodies tested.
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SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.
TLDR
The spatial phylogenetic reconstruction of evolutionary dynamics software is overhauled, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST.
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