Estimating Species Trees From Gene Trees Despite Gene Tree Incongruence Under Realistic Model Conditions
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Author | : Tandy Warnow |
Publisher | : Springer |
Total Pages | : 426 |
Release | : 2019-04-08 |
Genre | : Computers |
ISBN | : 3030108376 |
This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.
Author | : John Wakely |
Publisher | : Roberts |
Total Pages | : 0 |
Release | : 2016-04-22 |
Genre | : Science |
ISBN | : 9780974707754 |
This textbook provides the foundation for molecular population genetics and genomics. It shows the conceptual framework for studies of DNA sequence variation within species, and is the source of essential tools for making inferences about mutation, recombination, population structure and natural selection from DNA sequence data.
Author | : Joseph Felsenstein |
Publisher | : Sinauer Associates Incorporated |
Total Pages | : 664 |
Release | : 2004-01 |
Genre | : Science |
ISBN | : 9780878931774 |
Phylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.
Author | : Charles W. Fox |
Publisher | : Oxford University Press |
Total Pages | : 618 |
Release | : 2006-04-27 |
Genre | : Science |
ISBN | : 9780199775040 |
Charles Fox and Jason Wolf have brought together leading researchers to produce a cutting-edge primer introducing readers to the major concepts in modern evolutionary genetics. This book spans the continuum of scale, from studies of DNA sequence evolution through proteins and development to multivariate phenotypic evolution, and the continuum of time, from ancient events that lead to current species diversity to the rapid evolution seen over relatively short time scales in experimental evolution studies. Chapters are accessible to an audience lacking extensive background in evolutionaryy genetics but also current and in-depth enough to be of value to established researchers in evolution biology.
Author | : Tandy Warnow |
Publisher | : Cambridge University Press |
Total Pages | : 399 |
Release | : 2018 |
Genre | : Computers |
ISBN | : 1107184711 |
This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.
Author | : Olaf R.P. Bininda-Emonds |
Publisher | : Springer Science & Business Media |
Total Pages | : 547 |
Release | : 2004-05-31 |
Genre | : Science |
ISBN | : 1402023308 |
This is the first book on "phylogenetic supertrees", a recent, but controversial development for inferring evolutionary trees. Rather than analyze the combined primary character data directly, supertree construction proceeds by combining the tree topologies derived from those data. This difference in strategy has allowed for the exciting possibility of larger, more complete phylogenies than are otherwise currently possible, with the potential to revolutionize evolutionarily-based research. This book provides a comprehensive look at supertrees, ranging from the methods used to build supertrees to the significance of supertrees to bioinformatic and biological research. Reviews of many the major supertree methods are provided and four new techniques, including a Bayesian implementation of supertrees, are described for the first time. The far-reaching impact of supertrees on biological research is highlighted both in general terms and through specific examples from diverse clades such as flowering plants, even-toed ungulates, and primates. The book also critically examines the many outstanding challenges and problem areas for this relatively new field, showing the way for supertree construction in the age of genomics. Interdisciplinary contributions from the majority of the leading authorities on supertree construction in all areas of the bioinformatic community (biology, computer sciences, and mathematics) will ensure that this book is a valuable reference with wide appeal to anyone interested in phylogenetic inference.
Author | : Roderick D.M. Page |
Publisher | : John Wiley & Sons |
Total Pages | : 352 |
Release | : 2009-07-14 |
Genre | : Science |
ISBN | : 1444313363 |
The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.
Author | : Christoph Bleidorn |
Publisher | : Springer |
Total Pages | : 227 |
Release | : 2017-06-01 |
Genre | : Science |
ISBN | : 3319540645 |
This unique textbook provides a clear and concise overview of the key principles of the complex field of phylogenomics, with a particular focus on sequencing technologies that are crucial to studying and understanding interrelations in evolutionary genomics. It includes chapters dedicated to the analysis of nucleotide sequences using assembling and alignment methods and also discusses the main strategies for phylogenetic studies, systematic errors and their correction. This highly readable textbook is intended for graduate students and young researchers with an interest in phylogenetics and evolutionary developmental biology.
Author | : Jonathan B. Losos |
Publisher | : Univ of California Press |
Total Pages | : 528 |
Release | : 2011-02-09 |
Genre | : Nature |
ISBN | : 0520269845 |
"In a book both beautifully illustrated and deeply informative, Jonathan Losos, a leader in evolutionary ecology, celebrates and analyzes the diversity of the natural world that the fascinating anoline lizards epitomize. Readers who are drawn to nature by its beauty or its intellectual challenges—or both—will find his book rewarding."—Douglas J. Futuyma, State University of New York, Stony Brook "This book is destined to become a classic. It is scholarly, informative, stimulating, and highly readable, and will inspire a generation of students."—Peter R. Grant, author of How and Why Species Multiply: The Radiation of Darwin's Finches "Anoline lizards experienced a spectacular adaptive radiation in the dynamic landscape of the Caribbean islands. The radiation has extended over a long period of time and has featured separate radiations on the larger islands. Losos, the leading active student of these lizards, presents an integrated and synthetic overview, summarizing the enormous and multidimensional research literature. This engaging book makes a wonderful example of an adaptive radiation accessible to all, and the lavish illustrations, especially the photographs, make the anoles come alive in one's mind."—David Wake, University of California, Berkeley "This magnificent book is a celebration and synthesis of one of the most eventful adaptive radiations known. With disarming prose and personal narrative Jonathan Losos shows how an obsession, beginning at age ten, became a methodology and a research plan that, together with studies by colleagues and predecessors, culminated in many of the principles we now regard as true about the origins and maintenance of biodiversity. This work combines rigorous analysis and glorious natural history in a unique volume that stands with books by the Grants on Darwin's finches among the most informed and engaging accounts ever written on the evolution of a group of organisms in nature."—Dolph Schluter, author of The Ecology of Adaptive Radiation
Author | : László Zsolt Garamszegi |
Publisher | : Springer |
Total Pages | : 553 |
Release | : 2014-07-29 |
Genre | : Science |
ISBN | : 3662435500 |
Phylogenetic comparative approaches are powerful analytical tools for making evolutionary inferences from interspecific data and phylogenies. The phylogenetic toolkit available to evolutionary biologists is currently growing at an incredible speed, but most methodological papers are published in the specialized statistical literature and many are incomprehensible for the user community. This textbook provides an overview of several newly developed phylogenetic comparative methods that allow to investigate a broad array of questions on how phenotypic characters evolve along the branches of phylogeny and how such mechanisms shape complex animal communities and interspecific interactions. The individual chapters were written by the leading experts in the field and using a language that is accessible for practicing evolutionary biologists. The authors carefully explain the philosophy behind different methodologies and provide pointers – mostly using a dynamically developing online interface – on how these methods can be implemented in practice. These “conceptual” and “practical” materials are essential for expanding the qualification of both students and scientists, but also offer a valuable resource for educators. Another value of the book are the accompanying online resources (available at: http://www.mpcm-evolution.com), where the authors post and permanently update practical materials to help embed methods into practice.