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- Höhna, Sebastian, et al.
(författare)
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Probabilistic Graphical Model Representation in Phylogenetics
- 2014
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 63:5, s. 753-771
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Tidskriftsartikel (refereegranskat)abstract
- Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution.
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| 2. |
- Ronquist, Fredrik, 1962-
(författare)
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Systematics : Charting the tree of life
- 2014
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Ingår i: The Tree of Life. - Sunderland, MA : Sinauer Associates, Inc.. - 9781605352299 ; , s. 1-11
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Bokkapitel (refereegranskat)abstract
- Biological systematics has undergone dramatic changes in the last 60 years. Darwin had already used the tree of life metaphor to describe evolution in On the Origin of Species, but it was not until the first rigorous tree reconstruction techniques were introduced in the 1950s and 1960s that biologists accepted the idea of basing classification strictly on “phylogenetic relationship,” the branching of evolutionary lineages. This was followed by a series of groundbreaking advances in DNA sequencing and computational methods for phylogeny reconstruction in the 1980s and 1990s, spurring a flood of empirical studies of the tree of life. At the same time, the power of phylogenies in addressing questions in comparative biology was discovered in a wide range of disciplines, making phylogenetic inference an essential tool across the life sciences. A lot of empirical work still remains in most organism groups before the major branches in the tree of life are accurately characterized, but in the more well-studied groups, biologists are now shifting their focus from phylogenetic relationships to the dating of the splits in the tree. Computational approaches are also developing rapidly, allowing the mining of huge genomic data sets in the quest for more accurate evolutionary reconstructions. In parallel with these developments, some systematists are preparing for yet another transformational change, shifting their attention from the major branches in the tree of life (the major lineages) to the charting of the finest twigs and leaves (the species). Advances in both information technology and DNA sequencing are explored in attempts to accelerate the inventory of life on the planet, with the hope of completing our chart of the tree of life in time to save biological diversity for the future. Increasingly, people are becoming aware that this is not merely a question of ethics but that, ultimately, the survival of mankind may be on the line.
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