Approaches to direct comparison include visualizing the differences between two trees with tanglegrams and exploring the differences in collections of trees using consensus networks ( Holland et al. Phylogenetic incongruence describes the (often related) issue of conflicting trees from different loci, for example, individual gene trees carrying different evolutionary signals.ĭirect qualitative comparison of trees is illustrative but becomes unwieldy and uninformative when the trees are large or differ considerably. These tools produce large posterior collections of trees which can include considerable variety and are therefore hard to summarize. Phylogenetic uncertainty is often apparent following Bayesian Markov Chain Monte Carlo (MCMC) inference of trees from data (e.g., BEAST and MrBayes ). Reasons for this include lack of informative data, differences between tree inference methods, conflicting signals from descent and selection (convergent evolution), and the fact that evolution is not always tree-like: Gene trees differ from species trees, and many organisms exchange genes horizontally. A fundamental challenge in the study of evolution is that for a given set of organisms, markedly different phylogenetic trees can be inferred from each combination of input data, software, and settings ( Sullivan et al.
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