Molecular Evolution and Phylogenetics

Author: Masatoshi Nei,Sudhir Kumar

Publisher: Oxford University Press, USA

ISBN: 9780195135855

Category: Medical

Page: 333

View: 2897

During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.

An Introduction to Molecular Evolution and Phylogenetics

Author: Lindell Bromham

Publisher: Oxford University Press

ISBN: 0198736363


Page: 480

View: 8987

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.

Molecular Evolution

A Phylogenetic Approach

Author: Roderick D.M. Page,Edward C. Holmes

Publisher: John Wiley & Sons

ISBN: 1444313363

Category: Science

Page: 352

View: 2835

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.

Analysis of Phylogenetics and Evolution with R

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 1461417430

Category: Science

Page: 386

View: 8739

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.

Bioinformatics and Molecular Evolution

Author: Paul G. Higgs,Teresa K. Attwood

Publisher: John Wiley & Sons

ISBN: 1118697065

Category: Science

Page: 384

View: 5655

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 - - 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.

Computational Molecular Evolution

Author: Ziheng Yang

Publisher: Oxford University Press

ISBN: 0198566999

Category: Medical

Page: 357

View: 4977

This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.

Molecular Evolution

A Statistical Approach

Author: Ziheng Yang

Publisher: Oxford University Press

ISBN: 0199602603

Category: Science

Page: 492

View: 6665

"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. 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."--back cover.

Avian Molecular Evolution and Systematics

Author: David P. Mindell

Publisher: Academic Press

ISBN: 9780080527758

Category: Nature

Page: 382

View: 9310

The use of DNA and other biological macromolecules has revolutionized systematic studies of evolutionary history. Methods that use sequences of nucleotides and amino acids are now routinely used as data for addressing evolutionary questions that, although not new questions, have defied description and analysis. The world-renowned contributors use these new methods to unravel particular aspects of the evolutionary history of birds. Avian Molecular Evolution and Systematics presents an overview of the theory and application of molecular systematics, focusing on the phylogeny and evolutionary biology of birds. New, developing areas in the phylogeny of birds at multiple taxonomic areas are covered, as well as methods of analysis for molecular data, evolutionary genetics within and between bird populations, and the application of molecular-based phylogenies to broader questions of evolution. Contains authoritative contributions from leading researchers Discusses the utility of different molecular markers for questions of avian evolution, involving populations and higher-level taxa Applies molecular-based phylogenies of birds and molecular population genetics data to broad questions of organismal and molecular evolution. Compares and contrasts molecular and morphological data sets


Theory and Practice of Phylogenetic Systematics

Author: E. O. Wiley,Bruce S. Lieberman

Publisher: John Wiley & Sons

ISBN: 1118017870

Category: Science

Page: 424

View: 8337

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.

Reading the Story in DNA

A Beginner's Guide to Molecular Evolution

Author: Lindell Bromham

Publisher: Oxford University Press on Demand


Category: Science

Page: 368

View: 8671

The world is full of DNA. The salad in your sandwich, the pollen in the air, even the dirt on your shoes contains DNA from which a vast amount of information can be gained, including the identification of individuals and species, the structure and distribution of populations, the origins oflineages and the pace and mechanisms of evolutionary change. Reading the story in DNA is a beginner's guide to molecular evolution, and is the perfect companion on the journey to a proper understanding of molecular data. The central theme of the book is that in order to get ecological or evolutionary information out of molecular data, you must understand the way that the molecular data evolves and the influence that the assumptions you make have on the answers you get. The book blends beautifully clear explanations with cutting-edge examples from the research literature, drawing on the fields of biodiversity, conservation biology, epidemiology, phylogeography, evolutionary development and ancient DNA to explore topics such as molecular evolutionary theory,phylogenetics, molecular clocks, detecting selection and recombination, and identifying individuals from molecular data.Technical detail is set apart from the main text, allowing the student to approach the material in different ways: read only the text and skip the finer details, use the text to understand the technical details or vice versa, or identify key case studies and read the concepts and methods particularto that case. The use of "bioinformatic" analyses has revolutionized biology, and there are now few areas of evolution and ecology that remain untouched by molecular data. Today's biology students and researchers need to be familiar with the application of molecular data to answering evolutionary questions. Butthe most pressing question is usually: "Where do I start?!" This book is the answer.Online Resource Centre:The Online Resource Centre features:- Figures from the book in electronic format, ready to download- Discussion questions and tutorial exercisesFor students:- Annotated weblinks- Topical updates: links to relevant journal articles and websites that describe advancements in the field since the book's publication

Mathematics of Evolution and Phylogeny

Author: Olivier Gascuel

Publisher: OUP Oxford

ISBN: 9780191513732

Category: Mathematics

Page: 444

View: 6258

This book considers evolution at different scales: sequences, genes, gene families, organelles, genomes and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation. Recent years have witnessed rapid progress in the mathematics of evolution and phylogeny, with models and methods becoming more realistic, powerful, and complex. Aimed at graduates and researchers in phylogenetics, mathematicians, computer scientists and biologists, and including chapters by leading scientists: A. Bergeron, D. Bertrand, D. Bryant, R. Desper, O. Elemento, N. El-Mabrouk, N. Galtier, O. Gascuel, M. Hendy, S. Holmes, K. Huber, A. Meade, J. Mixtacki, B. Moret, E. Mossel, V. Moulton, M. Pagel, M.-A. Poursat, D. Sankoff, M. Steel, J. Stoye, J. Tang, L.-S. Wang, T. Warnow, Z. Yang, this book of contributed chapters explains the basis and covers the recent results in this highly topical area.

Mutation-Driven Evolution

Author: Masatoshi Nei

Publisher: OUP Oxford

ISBN: 0191637823

Category: Science

Page: 256

View: 7234

The purpose of this book is to present a new mechanistic theory of mutation-driven evolution based on recent advances in genomics and evolutionary developmental biology. The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance. The word 'mutation' is used to describe any kind of change in DNA such as nucleotide substitution, gene duplication/deletion, chromosomal change, and genome duplication. A brief history of the principal evolutionary theories (Darwinism, mutationism, neo-Darwinism, and neo-mutationism) that preceded the theory of mutation-driven evolution is also presented in the context of the last 150 years of research. However, the core of the book is concerned with recent studies of genomics and the molecular basis of phenotypic evolution, and their relevance to mutation-driven evolution. In contrast to neo-Darwinism, mutation-driven evolution is capable of explaining real examples of evolution such as the evolution of olfactory receptors, sex-determination in animals, and the general scheme of hybrid sterility. In this sense the theory proposed is more realistic than its predecessors, and gives a more logical explanation of various evolutionary events. Mutation-Driven Evolution is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of molecular evolution and population genetics. It assumes that the readers are acquainted with basic knowledge of genetics and molecular biology.

Decapod Crustacean Phylogenetics

Author: Joel W. Martin,Keith A. Crandall,Darryl L. Felder

Publisher: CRC Press

ISBN: 9781420092592

Category: Science

Page: 632

View: 3664

Decapod crustaceans are of tremendous interest and importance evolutionarily, ecologically, and economically. There is no shortage of publications reflecting the wide variety of ideas and hypotheses concerning decapod phylogeny, but until recently, the world’s leading decapodologists had never assembled to elucidate and discuss relationships among the major decapod lineages and between decapods and other crustaceans. Based on the findings presented by an international group of scientists at a symposium supported by the Society for Integrative and Comparative Biology, The Crustacean Society, and several other societies, and with major funding from the National Science Foundation, Decapod Crustacean Phylogenetics provides a comprehensive synopsis of the current knowledge of this vast and important group of animals. This volume contains state-of-the-art reviews of literature and methodologies for elucidating decapod phylogeny. The contributions include studies on the fossil origin of decapods, morphological and molecular phylogenetic analyses, the evolution of mating and its bearing on phylogeny, decapod "evo-devo" studies, decapod spermiocladistics, and phylogenetic inference. The experts also present research on preliminary attempts to construct the first known phylogenetic tree for various groups of decapods. Several contributions offer the most comprehensive analyses to date on major clades of decapods, and others introduce data or approaches that could be used in the future to help resolve the phylogeny of the Decapoda. Currently, the Decapoda contain an estimated 15,000 species, some of which support seafood and marine industries worth billions of dollars each year to the world’s economy. This volume is a fascinating overview of where we are currently in our understanding of these important creatures and their phylogeny and also provides a window into the future of decapod research. This work will be of great interest to researchers, instructors, and students in marine biology, evolutionary biology, crustacean biology, resource management, and biodiversity database management.

Molecular Markers, Natural History and Evolution

Author: J. C. Avise

Publisher: Springer Science & Business Media

ISBN: 1461523818

Category: Science

Page: 511

View: 4606

Molecular approaches have opened new windows on a host of ecological and evolutionary disciplines, ranging from population genetics and behavioral ecology to conservation biology and systematics. Molecular Markers, Natural History and Evolution summarizes the multi-faceted discoveries about organisms in nature that have stemmed from analyses of genetic markers provided by polymorphic proteins and DNAs. The first part of the book introduces rationales for the use of molecular markers, provides a history of molecular phylogenetics, and describes a wide variety of laboratory methods and interpretative tools in the field. The second and major portion of the book provides a cornucopia of biological applications for molecular markers, organized along a scale from micro-evolutionary topics (such as forensics, parentage, kinship, population structure, and intra-specific phylogeny) to macro-evolutionary themes (including species relationships and the deeper phylogenetic structure in the tree of life). Unlike most prior books in molecular evolution, the focus is on organismal natural history and evolution, with the macromolecules being the means rather than the ends of scientific inquiry. Written as an intellectual stimulus for the advanced undergraduate, graduate student, or the practicing biologist desiring a wellspring of research ideas at the interface of molecular and organismal biology, this book presents material in a manner that is both technically straightforward, yet rich with concepts and with empirical examples from the world of nature.

Statistical Methods in Molecular Evolution

Author: Rasmus Nielsen

Publisher: Springer Science & Business Media

ISBN: 0387277331

Category: Science

Page: 505

View: 3165

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

Molecular Systematics and Plant Evolution

Author: Peter M. Hollingsworth,Richard M. Bateman,Richard J. Gornall

Publisher: CRC Press

ISBN: 9781439833278

Category: Science

Page: 504

View: 7184

Molecular Systematics and Plant Evolution discusses the diversity and evolution of plants with a molecular approach. It looks at population genetics, phylogeny (history of evolution) and developmental genetics, to provide a framework from which to understand evolutionary patterns and relationships amongst plants. The international panel of contributors are all respected systematists and evolutionary biologists, who have brought together a wide range of topics from the forefront of research while keeping the text accessible to students. It has been written for senior undergraduates, postgraduates and researchers in the fields of botany, systematics, population / conservation genetics, phylogenetics and evolutionary biology.

Molecular Phylogeny of Microorganisms

Author: Aharon Oren,R. Thane Papke

Publisher: Horizon Scientific Press

ISBN: 1904455670

Category: Science

Page: 220

View: 1649

An introduction to molecular phylogeny, this text provides an overview of the diversity, systematics and nomenclature of microbes in many branches of biological science.

The Phylogenetic Handbook

A Practical Approach to DNA and Protein Phylogeny

Author: Marco Salemi,Anne-Mieke Vandamme

Publisher: Cambridge University Press

ISBN: 9780521803908

Category: Computers

Page: 406

View: 991

Introduction to the theory and practice of phylogenetic analysis for molecular evolution students and professionals.

The Evolution and Emergence of RNA Viruses

Author: Edward C. Holmes

Publisher: Oxford University Press

ISBN: 0199211124

Category: Medical

Page: 254

View: 1331

While the study of viral evolution has developed rapidly in the last 30 years, little attention has been directed toward linking the mechanisms of viral evolution to the epidemiological outcomes of these processes. This book intends to fill this gap by considering the patterns and processes of viral evolution at all its spatial and temporal scales.