Bayesian inference of phylogeny and its impact on evolutionary biology pdf
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- A biologist’s guide to Bayesian phylogenetic analysis
- Inference of Phylogenetic Trees
- Accelerating Bayesian inference for evolutionary biology models
A biologist’s guide to Bayesian phylogenetic analysis
Phylogenetic reconstruction is a fast-growing field that is enriched by different statistical approaches and by findings and applications in a broad range of biological areas. Fundamental to these are the mathematical models used to describe the patterns of DNA base substitution and amino acid replacement. These may become some of the basic models for comparative genome research. We discuss these models, including the analysis of observed DNA base and amino acid mutation patterns, the concept of site heterogeneity, and the incorporation of structural biology data, all of which have become particularly important in recent years. We also describe the use of such models in phylogenetic reconstruction and statistical methods for the comparison of different models.
Inference of Phylogenetic Trees
Metrics details. Bayesian phylogenetic inference holds promise as an alternative to maximum likelihood, particularly for large molecular-sequence data sets. We have investigated the performance of Bayesian inference with empirical and simulated protein-sequence data under conditions of relative branch-length differences and model violation. With simulated 7-taxon protein-sequence datasets, Bayesian posterior probabilities are somewhat more generous than bootstrap proportions, but do not saturate. Compared with likelihood, Bayesian phylogenetic inference can be as or more robust to relative branch-length differences for datasets of this size, particularly when among-sites rate variation is modeled using a gamma distribution. At ratios more extreme than fold, topological accuracy of reconstruction degraded only slowly when only one branch was of relatively greater length, but more rapidly when there were two such branches.
Johan A. Nylander, Fredrik Ronquist, John P. The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo MCMC techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic and complex and have been extended to new types of data, such as morphology. Based on this foundation, we developed a Bayesian MCMC approach to the analysis of combined data sets and explored its utility in inferring relationships among gall wasps based on data from morphology and four genes nuclear and mitochondrial, ribosomal and protein coding. Examined models range in complexity from those recognizing only a morphological and a molecular partition to those having complex substitution models with independent parameters for each gene.
Accelerating Bayesian inference for evolutionary biology models
Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use. Bayesian phylogenetic methods were introduced in the s 1 , 2 and have since revolutionised the way we analyse genomic sequence data 3.
Bock, W. Brower, A. Cleland, C. Geology Dayrat, Benoit Ancestor-descendant relationships and the reconstruction of the Tree of Lif Paleobiology
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