Phylogenetic Networks
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Phylogenetic Networks
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Author : Daniel H. Huson
language : en
Publisher: Cambridge University Press
Release Date : 2010-12-02
Phylogenetic Networks written by Daniel H. Huson and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-12-02 with Science categories.
The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.
Spaces Of Phylogenetic Networks
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Author : Jonathan Klawitter
language : en
Publisher:
Release Date : 2020
Spaces Of Phylogenetic Networks written by Jonathan Klawitter and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020 with Biology categories.
Rooted phylogenetic trees and networks are rooted, acyclic, leaf-labelled graphs that are used to model the inferred evolutionary history of taxa; for example species. While a phylogenetic tree models only bifurcating events, a phylogenetic network can also model reticulation events like hybridisation, recombination, and horizontal gene transfer. A rearrangement operation transforms one phylogenetic tree into another via a local graph-based change. For example, the subtree prune and regraft (SPR) operation prunes(cuts) a subtree of a phylogenetic tree and then regrafts (attaches) it to an edge of the remaining tree, resulting in another phylogenetic tree. Another operation is nearest neighbour interchange (NNI), which is a special case of SPR where the pruned edge has to be regrafted closely to where it was pruned. The set of all phylogenetic trees for a fixed set of taxa together with a rearrangement operations forms a graph where the vertices are the trees and two trees are adjacent when one can be transformed into the other by applying the rearrangement operation exactly once. In such a space, the distance of two trees is given by the minimum number of operations needed to transform one into the other. The SPR-distance of two trees can be characterised with a maximum agreement forest; a forest with a minimum number of components that covers both trees. In this thesis we study spaces of phylogenetic networks under generalisations of NNI and SPR, in particular, the subnet prune and regraft (SNPR) operation and the here introduced prune and regraft (PR) operation. First, we consider connectedness and diameters of spaces of different classes of phylogenetic networks. We then look at the size of the neighbourhood of a phylogenetic network. Furthermore, we investigate properties of shortest paths under SNPR and PR. This includes several bounds on the distances of two networks. Finally, we introduce maximum agreement graphs as a generalisation of maximum agreement forests for phylogenetic networks. We show that maximum agreement graphs induce a metric - the agreement distance - and study its relation to the SNPR-and PR-distance.
Phylogenetic Networks
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Author : Daniel H. Huson
language : en
Publisher:
Release Date : 2010
Phylogenetic Networks written by Daniel H. Huson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with Cladistic analysis categories.
"In the first part of this book we give an introduction to basic concepts from graph theory and systematics (Chapter 1). We briefly discuss the problem of aligning molecular sequences (Chapter 2) and give a more detailed introduction to the computation of phylogenetic trees from aligned sequences and distances (Chapter 3). Finally, we give a brief introduction to the computation of phyloge-netic networks, which also serves as an overview for the material presented in the second and third parts of the book (Chapter 4). Chapters 2 and 3 are provided for the sake of completeness and reference. They can be skipped by readers who have a basic knowledge of phylogenetic "--
Recombinatorics
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Author : Dan Gusfield
language : en
Publisher: MIT Press
Release Date : 2014-07-03
Recombinatorics written by Dan Gusfield and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-07-03 with Mathematics categories.
When a Philadelphia girl intercepts a message about an impending British attack against her father's regiment, commanded by General Washington, in White Marsh, she travels alone by horseback to warn the Patriot army.
Estimating Phylogenetic Networks From Concatenated Sequence Alignments
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Author : Cora Allen-Savietta
language : en
Publisher:
Release Date : 2020
Estimating Phylogenetic Networks From Concatenated Sequence Alignments written by Cora Allen-Savietta and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020 with categories.
In this dissertation, I present five chapters. The first chapter stems from a rotation project. In it, we explore a clustered ranking method for small area health outcomes in several applied data sets. By applying clustering to these rankings, we hope to improve rankings' effectiveness as a public health communication tool. In the remaining four chapters, I present an estimation method for phylogenetic networks. Evolution is often depicted as a tree, with an ancestral species at the root and modern species branching out to portray a leaf-filled canopy of biological diversity. While this model of evolution fits some species, evidence now indicates that many lineages cannot be well represented by a tree. Reticulate events such as hybridization and horizontal gene flow create connections between branches of this ancestral tree, turning it from a tree into a network. Even when scientists are mainly interested in the tree-like components of inheritance, ignoring these reticulate events has been shown to lead to inaccurate estimation. Without a network-based model of evolution, we miss these important events in evolutionary history and may even incorrectly estimate a species' primary ancestry. In this work, we develop a new method to extend phylogenetic analysis from trees to networks, allowing analysts to infer both the tree-like and reticulate events in evolutionary history with concatenated sequence data. In chapter two, we introduce the graphical model for estimating parameterized semi-directed phylogenetic networks. Then, in chapter three, we present identifiability results, as well as practical consequences for network estimation. Finally, we combine our identifiability results to define a canonical phylogenetic network from concatenated sequence data. In chapters four and five, we introduce our phylogenetic network estimation method, which we call PhyLiNC. PhyLiNC estimates a fully parameterized network topology with edge lengths, hybrid edge inheritance percentages, and rates of DNA evolution from concatenated DNA sequences. We describe our method's topology estimation algorithm and introduce our extension to nearest neighbor interchange moves for parameterized semi-directed networks. We conclude, in chapter five, with a user-friendly manual, which includes examples and step-by-step instructions for estimating networks with our software.
Basic Phylogenetic Combinatorics
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Author : Andreas Dress
language : en
Publisher: Cambridge University Press
Release Date : 2012
Basic Phylogenetic Combinatorics written by Andreas Dress and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with Mathematics categories.
The first book to systematically introduce the emerging area of phylogenetic combinatorics.
Analysis Of Biological Networks
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Author : Björn H. Junker
language : en
Publisher: John Wiley & Sons
Release Date : 2011-09-20
Analysis Of Biological Networks written by Björn H. Junker and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-09-20 with Computers categories.
An introduction to biological networks and methods for their analysis Analysis of Biological Networks is the first book of its kind to provide readers with a comprehensive introduction to the structural analysis of biological networks at the interface of biology and computer science. The book begins with a brief overview of biological networks and graph theory/graph algorithms and goes on to explore: global network properties, network centralities, network motifs, network clustering, Petri nets, signal transduction and gene regulation networks, protein interaction networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks. Analysis of Biological Networks is a self-contained introduction to this important research topic, assumes no expert knowledge in computer science or biology, and is accessible to professionals and students alike. Each chapter concludes with a summary of main points and with exercises for readers to test their understanding of the material presented. Additionally, an FTP site with links to author-provided data for the book is available for deeper study. This book is suitable as a resource for researchers in computer science, biology, bioinformatics, advanced biochemistry, and the life sciences, and also serves as an ideal reference text for graduate-level courses in bioinformatics and biological research.
Efficient Reconstruction Of Phylogenetic Networks Of Snps With Constrained Recombination
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Author : Satish Eddhu
language : en
Publisher:
Release Date : 2003
Efficient Reconstruction Of Phylogenetic Networks Of Snps With Constrained Recombination written by Satish Eddhu and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003 with categories.
Phylogenetic Networks
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Author : Daniel H. Huson
language : en
Publisher: Cambridge University Press
Release Date : 2010-12-02
Phylogenetic Networks written by Daniel H. Huson and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-12-02 with Science categories.
The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.
Statistical Approaches To Phylogenetic Networks Recombination And Testing Of Incongruence
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Author : Alethea Rea
language : en
Publisher:
Release Date : 2011
Statistical Approaches To Phylogenetic Networks Recombination And Testing Of Incongruence written by Alethea Rea and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with DNA categories.
Phylogenetics is the study of relationships between species using Deoxyribose Nucleic Acid (DNA). This thesis takes a statistical approach to two phenomenon which violate the assumption that evolution is treelike, and examines ways of visualising non-treelike signal. We use networks to display phylogenetic signal as they are robust and capable of displaying uncertainty. Phylogenetic network inference involves estimating discrete (topology) and continuous (branch length) parameters. One particular class of phylogenetic networks, split networks, can be viewed as points in Euclidean space of high dimension. In theory, then, phylogenetic analysis become a problem of inferring simple real valued parameters. In this thesis we report on our experiences turning this theory into practice. We use the Least Absolute Shrinkage and Selection Operator (LASSO) approach to regression in the first instance and then extend the LASSO to a partial LASSO. Within genes, phenomena like recombination (combining genetic material from more than one source) leads to non-treelike evolutionary histories. We introduce two methods for estimating the location of a recombination event. The first method is based on detecting a regime shift in the presence of recombination and the second method models the signal in each pair of DNA sites. Even if each gene has a treelike evolutionary history, the histories may not be shared. Therefore, we developed an approach to constructing a confidence set of topologies for a set of genes. If this set is empty then the genes do not share an evolutionary history. We conclude that the new statistical approaches to these phenomena, developed here, can give further insight into an evolutionary history.