An Introduction to Molecular Evolution and Phylogenetics

An Introduction to Molecular Evolution and Phylogenetics

Starting with evolutionary principles, and illustrated throughout with biological examples, it is the perfect starting point on the journey to an understanding of the way molecular data is used in modern biology.Online Resource CentreThe ...

Author: Lindell Bromham

Publisher: Oxford University Press

ISBN: 9780198736363

Category: DNA.

Page: 536

View: 316

DNA can be extracted and sequenced from a diverse range of biological samples, providing a vast amount of information about evolution and ecology. The analysis of DNA sequences contributes to evolutionary biology at all levels, from dating the origin of the biological kingdoms to untanglingfamily relationships.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 thatinformation to answer. Starting with evolutionary principles, and illustrated throughout with biological examples, it is the perfect starting point on the journey to an understanding of the way molecular data is used in modern biology.Online Resource CentreThe Online Resource Centre features:For registered adopters of the book:- Class plans for one-hour hands-on sessions associated with each chapter- Figures from the textbook to view and download
Categories: DNA.

Bioinformatics and Molecular Evolution

Bioinformatics and Molecular Evolution

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 ...

Author: Paul G. Higgs

Publisher: John Wiley & Sons

ISBN: 9781118697061

Category: Science

Page: 384

View: 779

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.
Categories: Science

Molecular Evolution and Phylogenetics

Molecular Evolution and Phylogenetics

Crow,]. F. andM. Kimura. (1970) An introduction to population genetics theory.
Harper & Row, New York. Cummings, M. P., S. P. Otto and ). Wakeley. (1995)
Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol.
Evol.

Author: Masatoshi

Publisher: Oxford University Press, USA

ISBN: 0195135857

Category: Medical

Page: 333

View: 282

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.
Categories: Medical

Statistical Methods in Molecular Evolution

Statistical Methods in Molecular Evolution

(Rubin [38]) 16.1 Introduction Bayesian statistical approaches are becoming
increasingly common in the field of molecular evolution and phylogenetics. Rubin
[38] makes an eloquent ar- gument for the value of Bayesian approaches through
 ...

Author: Rasmus Nielsen

Publisher: Springer Science & Business Media

ISBN: 9780387277332

Category: Science

Page: 505

View: 851

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
Categories: Science

Analysis of Phylogenetics and Evolution with R

Analysis of Phylogenetics and Evolution with R

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 ...

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 9781461417439

Category: Science

Page: 386

View: 744

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.
Categories: Science

Molecular Evolution and Adaptive Radiation

Molecular Evolution and Adaptive Radiation

This volume surveys advances in the study of adaptive radiation showing how molecular characters can be used to analyze the origin and pattern of diversification within a lineage in a non-circular fashion.

Author: Thomas J. Givnish

Publisher: Cambridge University Press

ISBN: 0521779294

Category: Science

Page: 621

View: 172

This volume surveys advances in the study of adaptive radiation showing how molecular characters can be used to analyze the origin and pattern of diversification within a lineage in a non-circular fashion.
Categories: Science

An Introduction to Molecular Ecology

An Introduction to Molecular Ecology

Revised edition of: Introduction to molecular ecology / Trevor J. C. Beebee, Graham Rowe. 2008. 2nd ed.

Author: Graham Rowe

Publisher: Oxford University Press

ISBN: 9780198716990

Category: Biologie moléculaire

Page: 535

View: 185

Revised edition of: Introduction to molecular ecology / Trevor J. C. Beebee, Graham Rowe. 2008. 2nd ed.
Categories: Biologie moléculaire

Plant Molecular Evolution

Plant Molecular Evolution

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 ...

Author: J.J. Doyle

Publisher: Springer Science & Business Media

ISBN: 9789401142212

Category: Science

Page: 272

View: 576

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.
Categories: Science

Molecular Evolution

Molecular Evolution

A Phylogenetic Approach Roderick D.M. Page, Edward C. Holmes. Chapter 6
Inferring Molecular Phylogeny 6.1 Introduction 6.5.1 Models, data and
hypotheses 6.1.1 Kinds of data: distances versus 6.5.2 Likelihood ratio tests
discrete ...

Author: Roderick D.M. Page

Publisher: John Wiley & Sons

ISBN: 9781444313369

Category: Science

Page: 352

View: 551

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.
Categories: Science

Bioinformatics Sequences Structures Phylogeny

Bioinformatics  Sequences  Structures  Phylogeny

This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis.

Author: Asheesh Shanker

Publisher: Springer

ISBN: 9789811315626

Category: Science

Page: 402

View: 761

This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files.
Categories: Science

Molecular Markers Natural History and Evolution

Molecular Markers  Natural History and Evolution

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 ...

Author: J. C. Avise

Publisher: Springer Science & Business Media

ISBN: 0412037718

Category: Science

Page: 511

View: 229

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.
Categories: Science

Origins of Biodiversity

Origins of Biodiversity

This book is a unique introduction to the fields of macroevolution and macroecology, taking an enquiry-led approach to exploring the evolution and distribution of biodiversity across time, space and lineages.The only introduction to ...

Author: Lindell Bromham

Publisher:

ISBN: 9780199608713

Category: Biodiversity

Page: 456

View: 476

This book is a unique introduction to the fields of macroevolution and macroecology, taking an enquiry-led approach to exploring the evolution and distribution of biodiversity across time, space and lineages.The only introduction to macroevolution and macroecology to adopt an innovative enquiry-led, case study-based framework to encourage active learning and critical thinking, this book:Extends the study of evolutionary biology and ecology beyond the topics covered in typical undergraduate textsExplores the nature of scientific investigation by emphasising hypothesis testing and highlighting the range of analytical tools available to contemporary researchersEncourages active student-driven learning by using open questions and current debates to promote critical thinking, identify interesting and important problems, and demonstrate how to frame testable research hypothesesCombines these three skills--an understanding of macroevolutionary and macroecological principles and patterns, a grasp of hypothesis testing, and the ability to identify important questions--to allow students to look at the world with new eyes, and develop an understanding of why the biological world is as it is.
Categories: Biodiversity

Plant Breeding Past Present and Future

Plant Breeding  Past  Present and Future

Evolution. and. Polyploidy. Introduction. It is not my intention in this book to
review our current knowledge of genome ... Molecular. Evolution. and.
Phylogenetic. Trees. At the start of Part II of this book we encountered DNA as the
chemical ...

Author: John E. Bradshaw

Publisher: Springer

ISBN: 9783319232850

Category: Science

Page: 693

View: 624

This book aims to help plant breeders by reviewing past achievements, currently successful practices, and emerging methods and techniques. Theoretical considerations are also presented to strike the right balance between being as simple as possible but as complex as necessary. The United Nations predicts that the global human population will continue rising to 9.0 billion by 2050. World food production will need to increase between 70-100 per cent in just 40 years. First generation bio-fuels are also using crops and cropland to produce energy rather than food. In addition, land area used for agriculture may remain static or even decrease as a result of degradation and climate change, despite more land being theoretically available, unless crops can be bred which tolerate associated abiotic stresses. Lastly, it is unlikely that steps can be taken to mitigate all of the climate change predicted to occur by 2050, and beyond, and hence adaptation of farming systems and crop production will be required to reduce predicted negative effects on yields that will occur without crop adaptation. Substantial progress will therefore be required in bridging the yield gap between what is currently achieved per unit of land and what should be possible in future, with the best farming methods and best storage and transportation of food, given the availability of suitably adapted cultivars, including adaptation to climate change. My book is divided into four parts: Part I is an historical introduction; Part II deals with the origin of genetic variation by mutation and recombination of DNA; Part III explains how the mating system of a crop species determines the genetic structure of its landraces; Part IV considers the three complementary options for future progress: use of sexual reproduction in further conventional breeding, base broadening and introgression; mutation breeding; and genetically modified crops.
Categories: Science

Molecular Evolution Producing the Biochemical Data

Molecular Evolution  Producing the Biochemical Data

... we also present research aimed at handling the full range of whole-genome
data. Introduction: Molecular Sequence Phylogenetics A phylogeny represents
the evolutionary history of a collection of organisms, usually in the form of a tree.

Author:

Publisher: Elsevier

ISBN: 9780080455150

Category: Science

Page: 896

View: 529

The critically acclaimed laboratory standard, Methods in Enzymology, is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. The series contains much material still relevant today - truly an essential publication for researchers in all fields of life sciences. Molecular Evolution Producing the Biochemical Data part B is a continuation of methods published in Part A (1993, volume 224). The work is a very methodological look at markers, templates, genomes, datasets and analyses used in studies of biological diversity. * One of the most highly respected publications in the field of biochemistry since 1955 * Frequently consulted, and praised by researchers and reviewers alike * Truly an essential publication for anyone in any field of the life sciences
Categories: Science

Introduction to Evolutionary Genomics

Introduction to Evolutionary Genomics

This book is the first of its kind to explain the fundamentals of evolutionary genomics.

Author: Naruya Saitou

Publisher: Springer Science & Business Media

ISBN: 9781447153047

Category: Computers

Page: 461

View: 710

This book is the first of its kind to explain the fundamentals of evolutionary genomics. The comprehensive coverage includes concise descriptions of a variety of genome organizations, a thorough discussion of the methods used, and a detailed review of genome sequence processing procedures. The opening chapters also provide the necessary basics for readers unfamiliar with evolutionary studies. Features: introduces the basics of molecular biology, DNA replication, mutation, phylogeny, neutral evolution, and natural selection; presents a brief evolutionary history of life from the primordial seas to the emergence of humans; describes the genomes of prokaryotes, eukaryotes, vertebrates, and humans; reviews methods for genome sequencing, phenotype data collection, homology searches and analysis, and phylogenetic tree and network building; discusses databases of genome sequences and related information, evolutionary distances, and population genomics; provides supplementary material at an associated website.
Categories: Computers

Mathematical Models in Biology

Mathematical Models in Biology

Linear and non-linear models of populations, molecular evolution, phylogenetic tree construction, genetics, and infectious diseases are presented with minimal prerequisites.

Author: Elizabeth S. Allman

Publisher: Cambridge University Press

ISBN: 0521525861

Category: Mathematics

Page: 370

View: 214

Linear and non-linear models of populations, molecular evolution, phylogenetic tree construction, genetics, and infectious diseases are presented with minimal prerequisites.
Categories: Mathematics

Phylogenetics

Phylogenetics

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 ...

Author: E. O. Wiley

Publisher: John Wiley & Sons

ISBN: 9781118017876

Category: Science

Page: 424

View: 699

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.
Categories: Science

Molecular Evolution and Phylogenetic Utility of the ZENK Gene in Birds

Molecular Evolution and Phylogenetic Utility of the ZENK Gene in Birds

Introduction : molecular mechanisms of memory formation -- from receptor
activation to synaptic changes . Cell Mol Life Sci 55 : 521-4 . Scharff , C. , and F.
Nottebohm . 1991. A comparative study of the behavioral deficits following
lesions of ...

Author: Alison Leigh Chubb

Publisher:

ISBN: UCAL:C3482016

Category:

Page: 214

View: 180

Categories:

An Introduction to Molecular Anthropology

An Introduction to Molecular Anthropology

An Introduction to Molecular Anthropology is an invaluable resource for students studying human evolution, biological anthropology, or molecular anthropology, as well as a reference for anthropologists and anyone else interested in the ...

Author: Mark Stoneking

Publisher: John Wiley & Sons

ISBN: 9781118061626

Category: Science

Page: 400

View: 301

Molecular anthropology uses molecular genetic methods to address questions and issues of anthropological interest. More specifically, molecular anthropology is concerned with genetic evidence concerning human origins, migrations, and population relationships, including related topics such as the role of recent natural selection in human population differentiation, or the impact of particular social systems on patterns of human genetic variation. Organized into three major sections, An Introduction to Molecular Anthropology first covers the basics of genetics – what genes are, what they do, and how they do it – as well as how genes behave in populations and how evolution influences them. The following section provides an overview of the different kinds of genetic variation in humans, and how this variation is analyzed and used to make evolutionary inferences. The third section concludes with a presentation of the current state of genetic evidence for human origins, the spread of humans around the world, the role of selection and adaptation in human evolution, and the impact of culture on human genetic variation. A final, concluding chapter discusses various aspects of molecular anthropology in the genomics era, including personal ancestry testing and personal genomics. An Introduction to Molecular Anthropology is an invaluable resource for students studying human evolution, biological anthropology, or molecular anthropology, as well as a reference for anthropologists and anyone else interested in the genetic history of humans.
Categories: Science