Download or read book Problems of Phylogenetic Reconstruction written by Systematics Association and published by Academic Press. This book was released on 1982 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Ancestral Sequence Reconstruction written by David A Liberles and published by Oxford University Press. This book was released on 2007-05-31 with total page 267 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in a range of fields.Ancestral Sequence Reconstruction starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including wholeproteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a description of the scientific questions where experimental ancestral sequence reconstruction has been utilized toprovide insights and inform future research.This research level text provides a first synthesis of the theories, methodologies and applications associated with ancestral sequence recognition, while simultaneously addressing many of the hot topics in the field. It will be of interest and use to both graduate students and researchers in the fields of molecular biology, molecular evolution, and evolutionary bioinformatics.
Download or read book Molecular Evolution written by Ziheng Yang and published by Oxford University Press. This book was released on 2014 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: Studies of evolution at the molecular level have experienced phenomenal growth in the last few decades, due to rapid accumulation of genetic sequence data, improved computer hardware and software, and the development of sophisticated analytical methods. The flood of genomic data has generated an acute need for powerful statistical methods and efficient computational algorithms to enable their effective analysis and interpretation. Molecular Evolution: a statistical approach presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. Written by an expert in the field, the book emphasizes conceptual understanding rather than mathematical proofs. The text is enlivened with numerous examples of real data analysis and numerical calculations to illustrate the theory, in addition to the working problems at the end of each chapter. The coverage of maximum likelihood and Bayesian methods are in particular up-to-date, comprehensive, and authoritative. This advanced textbook is aimed at graduate level students and professional researchers (both empiricists and theoreticians) in the fields of bioinformatics and computational biology, statistical genomics, evolutionary biology, molecular systematics, and population genetics. It will also be of relevance and use to a wider audience of applied statisticians, mathematicians, and computer scientists working in computational biology.
Download or read book Inferring Phylogenies written by Joseph Felsenstein and published by Sinauer Associates Incorporated. This book was released on 2004-01 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Combinatorics of Genome Rearrangements written by Guillaume Fertin and published by MIT Press. This book was released on 2009 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive survey of a rapidly expanding field of combinatorial optimization, mathematically oriented but offering biological explanations when required. From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs dramatically, and the mutations that affect this organization are known as genome rearrangements. Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems. This book offers the first comprehensive survey of this rapidly expanding application of combinatorial optimization. It can be used as a reference for experienced researchers or as an introductory text for a broader audience. Genome rearrangement problems have proved so interesting from a combinatorial point of view that the field now belongs as much to mathematics as to biology. This book takes a mathematically oriented approach, but provides biological background when necessary. It presents a series of models, beginning with the simplest (which is progressively extended by dropping restrictions), each constructing a genome rearrangement problem. The book also discusses an important generalization of the basic problem known as the median problem, surveys attempts to reconstruct the relationships between genomes with phylogenetic trees, and offers a collection of summaries and appendixes with useful additional information.
Download or read book Reconstructing the Past written by Elliott Sober and published by MIT Press. This book was released on 1991-02-05 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reconstructing the Past seeks to clarify and help resolve the vexing methodological issues that arise when biologists try to answer such questions as whether human beings are more closely related to chimps than they are to gorillas. It explores the case for considering the philosophical idea of simplicity/parsimony as a useful principle for evaluating taxonomic theories of evolutionary relationships. For the past two decades, evolutionists have been vigorously debating the appropriate methods that should be used in systematics, the field that aims at reconstructing phylogenetic relationships among species. This debate over phylogenetic inference, Elliott Sober observes, raises broader questions of hypothesis testing and theory evaluation that run head on into long standing issues concerning simplicity/parsimony in the philosophy of science. Sober treats the problem of phylogenetic inference as a detailed case study in which the philosophical idea of simplicity/parsimony can be tested as a principle of theory evaluation. Bringing together philosophy and biology, as well as statistics, Sober builds a general framework for understanding the circumstances in which parsimony makes sense as a tool of phylogenetic inference. Along the way he provides a detailed critique of parsimony in the biological literature, exploring the strengths and limitations of both statistical and nonstatistical cladistic arguments.
Download or read book Insect Morphology and Phylogeny written by Rolf G. Beutel and published by Walter de Gruyter. This book was released on 2013-12-12 with total page 532 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last decades a remarkable renaissance has materialized in insect morphology, mainly triggered by the development of new cutting-edge technologies. This is an exciting time for biological synthesis where the mysteries and data derived from genomes can be combined with centuries of data from morphology and development. And, now, more than ever, detailed knowledge of morphology is essential to understanding the evolution of all groups of organisms. In this “age of phylogenomics” researchers rely on morphological data to support molecular findings, test complex evolutionary scenarios, and for placing fossil taxa. This textbook provides an in-depth treatment of the structures and the phylogeny of the megadiverse Hexapoda. The first part presents an up-to-date overview of general insect morphology with detailed drawings, scanning electron micrographs, and 3-D reconstructions. Also included is a chapter covering innovative morphological techniques (e.g., μ-computer tomography, 3-D modeling), brief treatments of insect development and phylogenetic methods, and a comprehensive morphological glossary. The second part is of a modern synthesis of insect systematics that includes taxon-specific morphological information for all Orders. The work is an invaluable reference for students and researchers working in all facets of biology and is a must for evolutionary biologists. A detailed understanding of morphology is essential in unraveling phylogenetic relationships and developing complex evolutionary scenarios. Increasingly researchers in phylogenomics are re/turning to morphological data to support their findings, while the development of new cutting-edge technologies has further increased interest in this growing field. This definitive handbook provides an in-depth treatment of insect morphology. The first part presents an up-to-date overview of insect morphology with detailed drawings, brilliant scanning electron micrographs and 3-D reconstructions as interactive PDFs. This is complemented by a chapter on innovative morphological techniques (e.g., μ-computer tomography, 3-D modeling) and a comprehensive morphological glossary. The second part treats the state of the art in insect systematics and includes taxon-specific morphological information for all orders. Systematics are treated formally, with for example the arguments for relationships (“apomorphies”) always listed explicitly. The work is a useful reference for students and researchers working in different fields of biology and a must for those dealing with insects from an evolutionary perspective.
Download or read book The Future of Phylogenetic Systematics written by David Williams and published by Cambridge University Press. This book was released on 2016-07-21 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: Willi Hennig (1913–76), founder of phylogenetic systematics, revolutionised our understanding of the relationships among species and their natural classification. An expert on Diptera and fossil insects, Hennig's ideas were applicable to all organisms. He wrote about the science of taxonomy or systematics, refining and promoting discussion of the precise meaning of the term 'relationship', the nature of systematic evidence, and how those matters impinge on a precise understanding of monophyly, paraphyly, and polyphyly. Hennig's contributions are relevant today and are a platform for the future. This book focuses on the intellectual aspects of Hennig's work and gives dimension to the future of the subject in relation to Hennig's foundational contributions to the field of phylogenetic systematics. Suitable for graduate students and academic researchers, this book will also appeal to philosophers and historians interested in the legacy of Willi Hennig.
Download or read book Phylogeny written by Mike Steel and published by SIAM. This book was released on 2016-09-29 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenetics is a topical and growing area of research. Phylogenies (phylogenetic trees and networks) allow biologists to study and graph evolutionary relationships between different species. These are also used to investigate other evolutionary processes?for example, how languages developed or how different strains of a virus (such as HIV or influenza) are related to each other. This self-contained book addresses the underlying mathematical theory behind the reconstruction and analysis of phylogenies. The theory is grounded in classical concepts from discrete mathematics and probability theory as well as techniques from other branches of mathematics (algebra, topology, differential equations). The biological relevance of the results is highlighted throughout. The author supplies proofs of key classical theorems and includes results not covered in existing books, emphasizes relevant mathematical results derived over the past 20 years, and provides numerous exercises, examples, and figures.
Download or read book The Phylogenetic Handbook written by Marco Salemi and published by Cambridge University Press. This book was released on 2009-03-26 with total page 750 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.
Download or read book Bioinformatics and Phylogenetics written by Tandy Warnow and published by Springer. This book was released on 2019-04-08 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Batch Effects and Noise in Microarray Experiments written by Andreas Scherer and published by John Wiley & Sons. This book was released on 2009-11-03 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Batch Effects and Noise in Microarray Experiments: Sources and Solutions looks at the issue of technical noise and batch effects in microarray studies and illustrates how to alleviate such factors whilst interpreting the relevant biological information. Each chapter focuses on sources of noise and batch effects before starting an experiment, with examples of statistical methods for detecting, measuring, and managing batch effects within and across datasets provided online. Throughout the book the importance of standardization and the value of standard operating procedures in the development of genomics biomarkers is emphasized. Key Features: A thorough introduction to Batch Effects and Noise in Microrarray Experiments. A unique compilation of review and research articles on handling of batch effects and technical and biological noise in microarray data. An extensive overview of current standardization initiatives. All datasets and methods used in the chapters, as well as colour images, are available on www.the-batch-effect-book.org, so that the data can be reproduced. An exciting compilation of state-of-the-art review chapters and latest research results, which will benefit all those involved in the planning, execution, and analysis of gene expression studies.
Download or read book Atlas of Protein Sequence and Structure written by and published by . This book was released on 1973 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Homology and Systematics written by Robert Scotland and published by CRC Press. This book was released on 2014-04-21 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: When looking at groups of organisms, shared characteristics (homologues) provide the raw data from which hypotheses of common ancestry may be suggested. In order to explore the relationship between homologues and particular hypotheses of common ancestry, complex matrices are devised, where homologues are coded, allowing theories of homology to be developed and tested. Practically nothing has been written about this matrix-building process, which is fundamental to our understanding of diversity and evolutionary history. This book fills the gap by discussing the ways observations are coded and the consequences for resulting hypotheses using case studies and theoretical examples.
Download or read book Dynamic Homology and Phylogenetic Systematics written by Ward Wheeler and published by . This book was released on 2006 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Phylogenetic Inference Selection Theory and History of Science written by Anthony William Fairbank Edwards and published by Cambridge University Press. This book was released on 2018-07-19 with total page 553 pages. Available in PDF, EPUB and Kindle. Book excerpt: Seminal papers by A. W. F. Edwards, published together for the first time with commentaries from leading experts to contextualise his contribution.
Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2006-11-25 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.
