An Introduction to Molecular Evolution and Phylogenetics

Author: Lindell Bromham

Publisher: Oxford University Press

ISBN: 0198736363

Category:

Page: 480

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An Introduction to Molecular Evolution and Phylogenetics presents the fundamental concepts and intellectual tools you need to understand how the genome records information about evolutionary past and processes, how that information can be "read", and what kinds of questions we can use that information to answer. Starting with evolutionary principles, and illustrated throughout with biological examples, it is the perfect starting point on the journey to anunderstanding of the way molecular data is used in modern biology.
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Bioinformatics and Molecular Evolution

Author: Paul G. Higgs,Teresa K. Attwood

Publisher: John Wiley & Sons

ISBN: 1118697065

Category: Science

Page: 384

View: 2265

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In the current era of complete genome sequencing, Bioinformatics and Molecular Evolution provides an up-to-date and comprehensive introduction to bioinformatics in the context of evolutionary biology. This accessible text: provides a thorough examination of sequence analysis, biological databases, pattern recognition, and applications to genomics, microarrays, and proteomics emphasizes the theoretical and statistical methods used in bioinformatics programs in a way that is accessible to biological science students places bioinformatics in the context of evolutionary biology, including population genetics, molecular evolution, molecular phylogenetics, and their applications features end-of-chapter problems and self-tests to help students synthesize the materials and apply their understanding is accompanied by a dedicated website - www.blackwellpublishing.com/higgs - containing downloadable sequences, links to web resources, answers to self-test questions, and all artwork in downloadable format (artwork also available to instructors on CD-ROM). This important textbook will equip readers with a thorough understanding of the quantitative methods used in the analysis of molecular evolution, and will be essential reading for advanced undergraduates, graduates, and researchers in molecular biology, genetics, genomics, computational biology, and bioinformatics courses.
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Molecular Evolution and Phylogenetics

Author: Masatoshi,Masatoshi Nei,Sudhir Kumar,Evan Pugh Professor of Biology Masatoshi Nei

Publisher: Oxford University Press, USA

ISBN: 9780195135855

Category: Medical

Page: 333

View: 7361

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Numerical Examples. 1. Molecular Basis of Evolution. 2. Evolutionary Change of Amino Acid Sequences. 3. Evolutionary Change in DNA Sequences. 4. Synonymous and Nonsynonymous Nucleotide Substitutions. 5. Phylogenetic Trees. 6. Phylogenetic Inference: Distance Methods. 7. Phylogenetic Inference: Maximum Parsimony Methods. 8. Phylogenetic Inference: Maximum Likelihood Methods. 9. Accuracies and Statistical Tests of Phylogenetic Trees. 10. Molecular Clocks and Linearized Trees. 11. Ancestral Nucleotide and Amino Acid Sequences. 12. Genetic Polymorphism and Evolution. 13. Population Trees from Genetic Markers. 14. Perspectives. Appendices. References. Index.
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Analysis of Phylogenetics and Evolution with R

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 1461417430

Category: Science

Page: 386

View: 4407

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The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. 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: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. 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.
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An Introduction to Molecular Ecology

Author: Graham Rowe,Michael Sweet,Trevor Beebee

Publisher: Oxford University Press

ISBN: 0198716990

Category:

Page: 400

View: 1342

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An Introduction to Molecular Ecology combines theoretical concepts with practice-driven examples to showcase the latest molecular and genomic techniques and their impact on the study of ecology. The opening chapters introduce the essential molecular and genetic concepts that underpin the subject and describe key molecular tools and methods available to the ecologist. Capturing the broad scope of the field, the book goes on to explore the use of molecular tools in the context of behaviouralecology, population genetics, phylogeography, conservation, and microbial ecology. The third edition includes coverage of exciting new technological and analytical developments, such as next generation sequencing, which have revolutionized the field over the last decade. Molecular ecology is now in a position to tackle some truly ecological questions for the first time since itsinception. Blending conceptual detail with the most instructive examples, An Introduction to Molecular Ecology is an ideal resource for those new to the subject needing to develop a strong working understanding of the field. Online Resource Centre: The Online Resource Centre to accompany An Introduction to Molecular Ecology features: For students: * Suggested review articles to take your learning further * Links to useful websites and software * A range of questions to consolidate your learning and understanding For registered adopters of the book: * Journal Club; suggested research papers and discussion questions linked to topics featured in the book * Figures from the textbook to view and download
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Statistical Methods in Molecular Evolution

Author: Rasmus Nielsen

Publisher: Springer Science & Business Media

ISBN: 0387277331

Category: Science

Page: 505

View: 492

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In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently living species. With the availability of genomic data from multiple related species, molecular evolution has become one of the most active and fastest growing fields of study in genomics and bioinformatics. Most studies in molecular evolution rely heavily on statistical procedures based on stochastic process modelling and advanced computational methods including high-dimensional numerical optimization and Markov Chain Monte Carlo. This book provides an overview of the statistical theory and methods used in studies of molecular evolution. It includes an introductory section suitable for readers that are new to the field, a section discussing practical methods for data analysis, and more specialized sections discussing specific models and addressing statistical issues relating to estimation and model choice. The chapters are written by the leaders of field and they will take the reader from basic introductory material to the state-of-the-art statistical methods. This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular evolutionary biologists with an interest in learning more about the theory behind the statistical methods applied in the field. The chapters of the book assume no advanced mathematical skills beyond basic calculus, although familiarity with basic probability theory will help the reader. Most relevant statistical concepts are introduced in the book in the context of their application in molecular evolution, and the book should be accessible for most biology graduate students with an interest in quantitative methods and theory. Rasmus Nielsen received his Ph.D. form the University of California at Berkeley in 1998 and after a postdoc at Harvard University, he assumed a faculty position in Statistical Genomics at Cornell University. He is currently an Ole Rømer Fellow at the University of Copenhagen and holds a Sloan Research Fellowship. His is an associate editor of the Journal of Molecular Evolution and has published more than fifty original papers in peer-reviewed journals on the topic of this book. From the reviews: "...Overall this is a very useful book in an area of increasing importance." Journal of the Royal Statistical Society "I find Statistical Methods in Molecular Evolution very interesting and useful. It delves into problems that were considered very difficult just several years ago...the book is likely to stimulate the interest of statisticians that are unaware of this exciting field of applications. It is my hope that it will also help the 'wet lab' molecular evolutionist to better understand mathematical and statistical methods." Marek Kimmel for the Journal of the American Statistical Association, September 2006 "Who should read this book? We suggest that anyone who deals with molecular data (who does not?) and anyone who asks evolutionary questions (who should not?) ought to consult the relevant chapters in this book." Dan Graur and Dror Berel for Biometrics, September 2006 "Coalescence theory facilitates the merger of population genetics theory with phylogenetic approaches, but still, there are mostly two camps: phylogeneticists and population geneticists. Only a few people are moving freely between them. Rasmus Nielsen is certainly one of these researchers, and his work so far has merged many population genetic and phylogenetic aspects of biological research under the umbrella of molecular evolution. Although Nielsen did not contribute a chapter to his book, his work permeates all its chapters. This book gives an overview of his interests and current achievements in molecular evolution. In short, this book should be on your bookshelf." Peter Beerli for Evolution, 60(2), 2006
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Plant Molecular Evolution

Author: J.J. Doyle,Brandon S. Gaut

Publisher: Springer Science & Business Media

ISBN: 9780792360964

Category: Medical

Page: 272

View: 9310

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Plant molecular biology has produced an ever-increasing flood of data about genes and genomes. Evolutionary biology and systematics provides the context for synthesizing this information. This book brings together contributions from evolutionary biologists, systematists, developmental geneticists, biochemists, and others working on diverse aspects of plant biology whose work touches to varying degrees on plant molecular evolution. The book is organized in three parts, the first of which introduces broad topics in evolutionary biology and summarizes advances in plant molecular phylogenetics, with emphasis on model plant systems. The second segment presents a series of case studies of gene family evolution, while the third gives overviews of the evolution of important plant processes such as disease resistance, nodulation, hybridization, transposable elements and genome evolution, and polyploidy.
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New Approaches to Prokaryotic Systematics

Author: Michael Goodfellow,Iain Sutcliffe,Jongsik Chun

Publisher: Academic Press

ISBN: 0128004436

Category: Science

Page: 348

View: 5452

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Volume 41 of Methods in Microbiology is a methods book designed to highlight procedures that will revitalize the purposes and practices of prokaryotic systematics. This volume will notably show that genomics and computational biology are pivotal to the new direction of travel and will emphasise that new developments need to be built upon historical good practices, notably the continued use of the nomenclatural type concept and the requirement to deposit type strains in at least two service culture collections in different countries. Detailed protocols on cutting edge methods Prepared by leading international experts in the relevant fields
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Bringing Fossils to Life

An Introduction to Paleobiology

Author: Donald R. Prothero

Publisher: Columbia University Press

ISBN: 0231536909

Category: Science

Page: 672

View: 860

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One of the leading textbooks in its field, Bringing Fossils to Life applies paleobiological principles to the fossil record while detailing the evolutionary history of major plant and animal phyla. It incorporates current research from biology, ecology, and population genetics, bridging the gap between purely theoretical paleobiological textbooks and those that describe only invertebrate paleobiology and that emphasize cataloguing live organisms instead of dead objects. For this third edition Donald R. Prothero has revised the art and research throughout, expanding the coverage of invertebrates and adding a discussion of new methodologies and a chapter on the origin and early evolution of life.
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An Introduction to Human Evolutionary Anatomy

Author: Leslie Aiello,Christopher Dean

Publisher: Academic Press

ISBN: 008057100X

Category: Social Science

Page: 608

View: 1153

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An anthropologist and an anatomist have combined their skills in this book to provide students and research workers with the essentials of anatomy and the means to apply these to investigations into hominid form and function. Using basic principles and relevant bones, conclusions can be reached regarding the probable musculature, stance, brain size, age, weight, and sex of a particular fossil specimen. The sort of deductions which are possible are illustrated by reference back to contemporary apes and humans, and a coherent picture of the history of hominid evolution appears. Written in a clear and concise style and beautifully illustrated, An Introduction to Human Evolutionary Anatomy is a basic reference for all concerned with human evolution as well as a valuable companion to both laboratory practical sessions and new research using fossil skeletons.
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