Phyloseminar
http://phyloseminar.org/
phyloseminar -- a free online seminar about phylogeneticsphyloseminarhttps://feedburner.google.com
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
Paul Lewis: Primer part 2: tree likelihood and rate heterogeneity, 2018-05-16 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 2 explains how the likelihood is calculated for trees, how parameters of models are estimated, and how missing data and unknown ancestral states are accommodated. This part ends with an introduction to three major ways of modeling among site rate heterogeneity (site-specific rates and the +I and +G models).</p>2018-04-18T14:00:00-07:0077lewis