The Causes of Molecular Evolution

Author: John H. Gillespie

Publisher: Oxford University Press

ISBN: 9780195357745

Category: Science

Page: 351

View: 4111

This work provides a unified theory that addresses the important problem of the origin and maintenance of genetic variation in natural populations. With modern molecular techniques, variation is found in all species, sometimes at astonishingly high levels. Yet, despite these observations, the forces that maintain variation within and between species have been difficult subjects of study. Because they act very weakly and operate over vast time scales, scientists must rely on indirect inferences and speculative mathematical models. However, despite these obstacles, many advances have been made. The author's research in molecular genetics, evolution, and bio-mathematics has enabled him to draw on this work, and present a coherent and valuable view of the field. The book is divided into three parts. The first consists of three chapters on protein evolution, DNA evolution, and molecular mechanisms. This section reviews the experimental observations on genetic variation. The second part gives a unified treatment of the mathematical theory of selection in a fluctuating environment. The final two chapters combine the earlier assessments in a treatment of the scientific status of two competing theories for the maintenance of genetic variation. Steeped in the enormous advances population genetics has made over the past 25 years, this book has proven highly popular among human geneticists, biologists, evolutionary theorists, and bio-mathematicians.

Elements of Evolutionary Genetics

Author: Brian Charlesworth

Publisher: Roberts Publishers

ISBN: N.A

Category: Science

Page: 734

View: 7150

Evolutionary genetics considers the causes of evolutionary change and the nature of variability in evolution. The methods of evolutionary genetics are critically important for the analysis and interpretation of the massive datasets on DNA sequence variation and evolution that are becoming available, as well for our understanding of evolution in general. This book shows readers how models of the genetic processes involved in evolution are made (including natural selection, migration, mutation, and genetic drift in finite populations), and how the models are used to interpret classical and molecular genetic data. The material is intended for advanced level undergraduate courses in genetics and evolutionary biology, graduate students in evolutionary biology and human genetics, and researchers in related fields who wish to learn evolutionary genetics. The topics covered include genetic variation, DNA sequence variability and its measurement, the different types of natural selection and their effects (e.g. the maintenance of variation, directional selection, and adaptation), the interactions between selection and mutation or migration, the description and analysis of variation at multiple sites in the genome, genetic drift, and the effects of spatial structure. The final two chapters demonstrate how the theory illuminates our understanding of the evolution of breeding systems, sex ratios and life histories, and some aspects of genome evolution.

The Neutral Theory of Molecular Evolution

Author: Motoo Kimura

Publisher: Cambridge University Press

ISBN: 1139935674

Category: Science

Page: N.A

View: 3024

Motoo Kimura, as founder of the neutral theory, is uniquely placed to write this book. He first proposed the theory in 1968 to explain the unexpectedly high rate of evolutionary change and very large amount of intraspecific variability at the molecular level that had been uncovered by new techniques in molecular biology. The theory - which asserts that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants - has caused controversy ever since. This book is the first comprehensive treatment of this subject and the author synthesises a wealth of material - ranging from a historical perspective, through recent molecular discoveries, to sophisticated mathematical arguments - all presented in a most lucid manner.

Molecular Evolutionary Genetics

Author: Masatoshi Nei

Publisher: Columbia University Press

ISBN: 9780231063210

Category: Science

Page: 512

View: 8216

-- "The Scientist"

Fundamentals of Molecular Evolution

Author: Wen-Hsiung Li,Dan Graur

Publisher: Sinauer Associates Incorporated

ISBN: 9780878934522

Category: Science

Page: 284

View: 1218

Gene structure and mutation. Protein-coding genes. RNA-specifying genes. Regulatory genes. Nucleotide substitutions. Deletions and insertions. Spatial distribution of mutations. Dynamics of genes in populations. Changes in allele frequencies. Natural selection. Codominance. Overdominance. Random genetic drift. Effective population size. Gene substitution. Fixation probability. Fixation time. Rate of gene substitution. Genetic polymorphism. The neo-darwinian theory and the neutral mutation hypothesis. Evolutionary change in nucleotide sequences. Jukes and cantor's one-parameter model. Kimura's two-parameter model. Number of substitutions between two noncoding sequences. Protein-coding. Alignment of nucleotide and amino acid sequences. The dot-matrix method. The sequence-distance method. Indirect estimation of the number of nucleotide substitutions. Restriction endonuclease fragment patterns and site maps DNA-DNA hybridization. Rates and patterns of nucleotide substitution. Variation among different gene regions. A case of positive selection: lysozyme in cows and langurs. Relative-rate tests. Nearly equal rates in mice and rats. Lower rates in humans than in monkeys. Higher rates in rodents than in primates. Causes of variation in substitution rates among evolutionary lineages. Organelle. Pseudogenes. Nonrandom usage of synonymous codons. Phylogeny. Impact of molecular data on phylogenetic studies. Rooted and unrooted trees. True and inferred trees. Gene trees and species trees. Unweighted pair group method with arithmetic mean (UPGMA). Transformed distance method. Neighbors relation methods. Maximum parsimony methods. Phenetics versus cladistics. Estimation of branch lengths. Rooting unrooted trees. Estimation of species-divergence times clades. Phylogeny of humans and apes. Endosymbiotic origin of mitochondria and chloroplasts. Molecular paleontology. The dusky seaside sparrow: a lesson in conservation biology. Evolution by gene duplication and exon shuffling. Domain duplication and gene elongation. The ovomucoid gene. Formation of gene families and the acquisition of new functions. RNA-specifying genes. Isozymes. Color-sensitive pigment proteins. The globin superfamily of genes. Exon shuffling. Mosaic proteins. Phase limitations on exon shuffling. Alternative pathways for producing new functions. Overlapping genes. Alternative splicing. Gene sharing. Concerted evolution of multigene families. Mechanisms of concerted evolution. Evolution by transposition. Transposable elements. Transposons. Retroelements. Retrosequences. Retrogenes. Processed pseudogenes. Effects of transposition on the host genome. Hybrid dysgenesis. Horizontal transfer of virogenes from baboons to cats. Drosophila. Genome organization and evolution. Genome size of eukaryotes and the C-value paradox. Mechanisms for increasing genome size. Chromosomal duplication. Maintenance of nongenic DNA. Bacteria. Compositional organization of the vertebrate genome. Origins of isochores.

In Search of the Causes of Evolution

From Field Observations to Mechanisms

Author: Peter R. Grant,B. Rosemary Grant

Publisher: Princeton University Press

ISBN: 0691146950

Category: Science

Page: 380

View: 2441

Evolutionary biology has witnessed breathtaking advances in recent years. Some of its most exciting insights have come from the crossover of disciplines as varied as paleontology, molecular biology, ecology, and genetics. This book brings together many of today's pioneers in evolutionary biology to describe the latest advances and explain why a cross-disciplinary and integrated approach to research questions is so essential. Contributors discuss the origins of biological diversity, mechanisms of evolutionary change at the molecular and developmental levels, morphology and behavior, and the ecology of adaptive radiations and speciation. They highlight the mutual dependence of organisms and their environments, and reveal the different strategies today's researchers are using in the field and laboratory to explore this interdependence. Peter and Rosemary Grant--renowned for their influential work on Darwin's finches in the Galápagos--provide concise introductions to each section and identify the key questions future research needs to address. In addition to the editors, the contributors are Myra Awodey, Christopher N. Balakrishnan, Rowan D. H. Barrett, May R. Berenbaum, Paul M. Brakefield, Philip J. Currie, Scott V. Edwards, Douglas J. Emlen, Joshua B. Gross, Hopi E. Hoekstra, Richard Hudson, David Jablonski, David T. Johnston, Mathieu Joron, David Kingsley, Andrew H. Knoll, Mimi A. R. Koehl, June Y. Lee, Jonathan B. Losos, Isabel Santos Magalhaes, Albert B. Phillimore, Trevor Price, Dolph Schluter, Ole Seehausen, Clifford J. Tabin, John N. Thompson, and David B. Wake.

Statistical Methods in Molecular Evolution

Author: Rasmus Nielsen

Publisher: Springer Science & Business Media

ISBN: 0387277331

Category: Science

Page: 505

View: 4821

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

Mutation-Driven Evolution

Author: Masatoshi Nei

Publisher: OUP Oxford

ISBN: 0191637823

Category: Science

Page: 256

View: 6005

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.

Molecular Evolution

A Phylogenetic Approach

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

Publisher: John Wiley & Sons

ISBN: 1444313363

Category: Science

Page: 352

View: 4878

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.

Genetics and the Origin of Species

Author: Theodosius Dobzhansky,Theodosius Grigorievich Dobzhansky

Publisher: Columbia University Press

ISBN: 9780231054751

Category: Science

Page: 364

View: 8833

Featuring an introduction by Stephen Jay Gould, "Genetics and the Origin of Species" presents the first edition of Dobzhansky's groundbreaking and now classic inquiry into what has emerged as the most important single area of scientific inquiry in the twentieth century: biological theory of evolution. Genetics and the Origin of Species went through three editions (1937, 1941, and 1951) in which the importance accorded natural selection changed radically.

The Environmental and Genetic Causes of Autism

Author: James Lyons-Weiler

Publisher: Skyhorse Publishing, Inc.

ISBN: 1510710876

Category: Medical

Page: 320

View: 1472

The Environmental and Genetic Causes of Autism delves deep into the full body of past and current research to reveal how genetic predispositions and environmental factors can combine to produce the conditions autism and autism spectrum disorders (ASD). To make this groundbreaking volume, Dr. James Lyons-Weiler combed through the past fifty years of published research on autism, exploring subjects such as genetic variation, mechanisms of neurotoxicity of metals and pesticides, and the central and combined roles of each in causing autism. Lyons-Weiler provides a major overview of all aspects of the condition of autism, reviews changes in diagnoses and treatments, and explains how genetic information can be used to tailor effective treatments, and sometimes reversals, of the symptoms. He also presents practical forward-looking suggestions on how to design future studies to facilitate the discovery of biomarkers for autism risk and how to classify the full range of autism spectrum disorders. Autism is considered one of the most mystifying conditions of our day, and alarmed scientists, doctors, politicians, and parents are desperately trying to understand why the condition is escalating. According to the CDC, rates in the United States have risen from an estimated one in two thousand children in 1980, to one in sixty-eight in 2012, and a new National Health Interview Survey shows a rate of one in forty-five. By the time you read this book, that number may have changed yet again. While most autism researchers focus on either environmental or genetic causes of autism, Lyons-Weiler’s opus demonstrates that to fully understand the condition and to finally put its rate on the decrease, it is essential to pay attention to the science showing how the two classes of factors interact.

A Primer of Population Genetics

Author: Daniel L. Hartl

Publisher: Sinauer Associates Incorporated

ISBN: 9780878933044

Category: Science

Page: 221

View: 2797

In response to many requests, the Third Edition of A Primer of Population Genetics has been dramatically shortened and streamlined for greater accessibility. Designed primarily for undergraduates, it will also serve for graduate students and professionals in biology and other sciences who desire a concise but comprehensive overview of the field with a primary focus on the integration of experimental results with theory. The abundance of experimental data generated by the use of molecular methods to study genetic polymorphisms sparked a transformation in the field of population genetics. Present in virtually all organisms, molecular polymorphisms allow populations to be studied without regard to species or habitat, and without the need for controlled crosses, mutant genes, or for any prior genetic studies. Thus a familiarity with population genetics has become essential for any biologist whose work is at the population level. These fields include evolution, ecology, systematics, plant breeding, animal breeding, conservation and wildlife management, human genetics, and anthropology. Population genetics seeks to understand the causes of genetic differences within and among species, and molecular biology provides a rich repertoire of techniques for identifying these differences.

Molecular Evolution

A Phylogenetic Approach

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

Publisher: John Wiley & Sons

ISBN: 1444313363

Category: Science

Page: 352

View: 8688

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.

Computational and Evolutionary Analysis of HIV Molecular Sequences

Author: Allen G. Rodrigo,Gerald H. Learn Jr.

Publisher: Springer Science & Business Media

ISBN: 0306469006

Category: Medical

Page: 300

View: 1653

Computational and Evolutionary Analysis of HIV Molecular Sequences is for all researchers interested in HIV research, even those who only have a nodding acquaintance with computational biology (or those who are familiar with some, but not all, aspects of the field). HIV research is unusual in that it brings together scientists from a wide range of disciplines: clinicians, pathologists, immunologists, epidemiologists, virologists, computational biologists, structural biologists, evolutionary biologists, statisticians and mathematicians. This book seeks to bridge the gap between these groups, in both subject matter and terminology. Focused largely on HIV genetic variation, Computational and Evolutionary Analysis of HIV Molecular Sequences covers such issues as sampling and processing sequences, population genetics, phylogenetics and drug targets.

Molecular Evolution and Phylogenetics

Author: Masatoshi Nei,Sudhir Kumar

Publisher: Oxford University Press

ISBN: 9780195350517

Category: Science

Page: 352

View: 8926

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.

A Companion to the Philosophy of Biology

Author: Sahotra Sarkar,Anya Plutynski

Publisher: John Wiley & Sons

ISBN: 0470695846

Category: Science

Page: 616

View: 2734

Comprised of essays by top scholars in the field, this volume offers detailed overviews of philosophical issues raised by biology. Brings together a team of eminent scholars to explore the philosophical issues raised by biology Addresses traditional and emerging topics, spanning molecular biology and genetics, evolution, developmental biology, immunology, ecology, mind and behaviour, neuroscience, and experimentation Begins with a thorough introduction to the field Goes beyond previous treatments that focused only on evolution to give equal attention to other areas, such as molecular and developmental biology Represents both an authoritative guide to philosophy of biology, and an accessible reference work for anyone seeking to learn about this rapidly-changing field

Randomness in Evolution

Author: John Tyler Bonner

Publisher: Princeton University Press

ISBN: 1400846420

Category: Science

Page: 152

View: 7545

John Tyler Bonner, one of our most distinguished and insightful biologists, here challenges a central tenet of evolutionary biology. In this concise, elegantly written book, he makes the bold and provocative claim that some biological diversity may be explained by something other than natural selection. With his customary wit and accessible style, Bonner makes an argument for the underappreciated role that randomness--or chance--plays in evolution. Due to the tremendous and enduring influence of Darwin's natural selection, the importance of randomness has been to some extent overshadowed. Bonner shows how the effects of randomness differ for organisms of different sizes, and how the smaller an organism is, the more likely it is that morphological differences will be random and selection may not be involved to any degree. He traces the increase in size and complexity of organisms over geological time, and looks at the varying significance of randomness at different size levels, from microorganisms to large mammals. Bonner also discusses how sexual cycles vary depending on size and complexity, and how the trend away from randomness in higher forms has even been reversed in some social organisms. Certain to provoke lively discussion, Randomness in Evolution is a book that may fundamentally change our understanding of evolution and the history of life.

The Basics of Selection

Author: Graham Bell

Publisher: Springer Science & Business Media

ISBN: 146155991X

Category: Science

Page: 404

View: 1496

This new textbook for students taking courses in evolution is addressed to one of the most difficult questions evolutionary biology, that of selection. Covering both artificial and natural selection, the author has written a short, readable text that will appeal to students and professionals alike. how the nature of the process determines the nature of evolutionary change.

The Genetic Basis of Evolutionary Change

Author: Richard C. Lewontin,University Richard C Lewontin

Publisher: N.A

ISBN: N.A

Category: Évolution

Page: 346

View: 1848

Integrated Molecular Evolution

Author: Scott Orland Rogers

Publisher: CRC Press

ISBN: 1482230925

Category: Science

Page: 574

View: 3407

Evolutionary biology has increasingly relied upon tools developed in molecular biology that allow for the structure and function of macromolecules to be used as data for exploring the patterns and processes of evolutionary change. Integrated Molecular Evolution, Second Edition is a textbook intended to expansively and comprehensive review evolutionary studies now routinely using molecular data. This new edition has been thoroughly updated and expanded, and provides a basic summary of evolutionary biology as well as a review of current phylogenetics and phylogenomics. Reflecting a burgeoning pedagogical landscape, this new edition includes nearly double the number of chapters, including a new section on molecular and bioinformatic methods. Dedicated chapters were added on: Evolution of the genetic code Mendelian genetics and population genetics Natural selection Horizontal gene transfers Animal development and plant development Cancer Extraction of biological molecules Analytical methods Sequencing methods and sequencing analyses Omics Phylogenetics and phylogenetic networks Protein trafficking Human genomics More than 400 illustrations appear in this edition, doubling the number included in the first edition, and over 100 of these diagrams are now in color. The second edition combines and integrates extensive summaries of genetics and evolutionary biology in a manner that is accessible for students at either the graduate or undergraduate level. It also provides both the basic foundations of molecular evolution, such as the structure and function of DNA, RNA and proteins, as well as more advanced chapters reviewing analytical techniques for obtaining sequences, and interpreting and archiving molecular and genomic data.