Phyloseminar
http://phyloseminar.org/
phyloseminar -- a free online seminar about phylogeneticsphyloseminarhttps://feedburner.google.com
Sarah Hilton: Model adequacy of experimentally informed site-specific substitution models, 2018-12-12 10:00 PST
http://phyloseminar.org/
<p>Phylogenetic substitution models are hypotheses about evolutionary process and, like all models, they contain simplifying assumptions. One common assumption is that all sites in a gene evolve identically. However, even a cursory analysis of a multiple sequence alignment will show that this assumption is violated in natural protein evolution. Relaxing this assumption greatly increases the number of model parameters to account for the effect of every amino acid at every site in the protein. We have developed a family of models, called Experimentally Informed Codon Models (ExpCMs), which describe the site-specific constraints on a protein using empirical measurements from a high-throughput functional assay in the lab. Even though the vast majority of the parameters are determined empirically rather than fit to the data, we have found that ExpCMs are generally better descriptors of natural sequence evolution than site-uniform codon models, as evaluated by model comparison techniques such as AIC. Now, we are turning to model adequacy tests as a more quantitative and comprehensive way to evaluate ExpCMs on a site-by-site basis. We believe that sites which are inadequate descriptors of natural sequence evolution may indicate sites where the selective pressure differs between the lab and nature and point to interesting biological mechanisms. Model adequacy tests will also allow us to compare how well experiments performed under different conditions are able to capture natural constraint. Overall, the site-specific ExpCMs can be used as a tool to bridge the gap between what we know about selection in the lab and in nature.</p>2018-12-03T08:00:00-08:0082hilton
Sebastian DuchĂȘne: Model adequacy in infectious disease phylodynamics, 2018-11-29 13:00 PST
http://phyloseminar.org/
<p>Statistical models are widely used in phylogenetics to infer the evolutionary history of groups of organisms. In the context of rapidly evolving pathogens, phylogenetic analyses can be used to make inferences about epidemiological processes, a field known as infectious disease phylodynamics. A key component of phylodynamic analyses is a branching model to describe transmission. For example, coalescent and birth-death models can estimate the average number of secondary infections using phylogenetic trees. However, the resulting inferences are contingent on the extent to which models describe key aspects of the data. For example, the simplest models in phylodynamics assume that transmission rates are constant over time and lineages, which is not necessarily the case for many empirical data sets. In this talk I will discuss model adequacy methods in phylodynamics. In contrast to model selection, where models are ranked according to their statistical fit, the goal of model adequacy is to determine whether key aspects of the data at hand could have been generated by the model in question. That is, to assess the absolute, rather than relative, model fit. Model adequacy typically consists of simulating data from the model and comparing them to the empirical data. The crux of such comparisons is to develop summary statistics that represent the expectation under the model. Using examples from different virus data sets I will present several approaches to assess phylodynamic models to reveal the importance of modelling population dynamics, such as population structure and variation in transmission rates, in epidemiological estimates. Finally, I will illustrate ways in which an uptake of these approaches can improve our understanding of infectious disease evolution and motivate the development of models in phylodynamics.</p>2018-11-15T10:00:00-08:0081duchene
Jeremy Brown: The role of model fit in resolving the Tree of Life, 2018-10-24 09:00 PDT
http://phyloseminar.org/
<p>More data alone will not resolve the Tree of Life. That statement encapsulates perhaps the most striking lesson of phylogenomics. While genome sequences provide us with an invaluably rich source of information about evolutionary history, our ability to properly interpret this information is sometimes flawed, which has led to protracted debates about some of the most interesting and enigmatic relationships across the Tree. However, phylogenetic inference now has a robust grounding in statistical inference. This grounding gives us tools to at least recognize the existence, and hopefully resolve the source, of errors when they occur. These tools are important and broadly applied in other areas of statistical inference, but have been slow to be adopted in phylogenetics. In this talk, I will cover some of the strategies that have been proposed for assessing model fit, some of the reasons for the slow adoption, and the challenges that remain.</p>2018-11-15T14:00:00-08:0080brown
Paul Lewis: Primer part 3b: introduction to Bayesian phylogenetics, 2018-06-27 09:00 PDT
http://phyloseminar.org/
<p>This series of 4 talks will be an introduction to phylogenetics in 4 parts from master expositor Paul Lewis.</p>
<p>Part 3b continues part 3a with proposals (updating model parameters or trees during MCMC), prior distributions, hierarchical models, and Bayes factors.</p>2018-06-20T14:00:00-07:0079lewis
Paul Lewis: Primer part 3a: introduction to Bayesian statistics, 2018-06-20 09:00 PDT
http://phyloseminar.org/
<p>This series of 4 talks will be an introduction to phylogenetics in 4 parts from master expositor Paul Lewis.</p>
<p>Part 3 is an introduction to Bayesian statistics and how it is used in phylogenetics. This part is divided into parts 3a and 3b. Part 3a explains Bayes Rule, the difference between probabilities and probability densities, the difference between joint, conditional and marginal probabilities, and illustrates how MCMC is used to approximate posterior probability distributions.</p>2018-05-17T14:00:00-07:0078lewis