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.
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.
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.
Molecular evolution, phylogenetics, genomics, and other related topics are all critical to understanding evolutionary processes. All too frequently, however, they are treated separately in textbooks and courses, such that students fail to connect all of the concepts, principles, and nuances of the evolutionary processes. Integrated Molecular Evolution brings these related areas together in one volume, facilitating student comprehension of often difficult concepts. Incorporating the emerging fields of genomics and bioinformatics with traditional fields such as evolution, genetics, and molecular biology, this volume explores a myriad of topics, including Life on Earth and the possible origins of life The evolution of organisms on Earth and the history of the study of evolution Basic structures of DNA, RNA, proteins, and other biological molecules, and the synthesis of each Molecular biology and the evolution, structure, and function of ribosomes DNA replication and the various ways in which chromosomes are separated Ways in which DNA can be changed to produce mutations, infectious causes of mutation, and repair of DNA Definitions, evolution, and the importance of multigene families Phylogenetic analysis and how researchers use the raw sequence data to reconstruct portions of evolutionary processes Details of the genomes of a variety of organisms, from RNA viruses to eukaryotes, presented in order of complexity Each chapter ends with a summary of key points, forming an effective review and enabling students to isolate critical material. The series of topics and the masterful integration of these topics lead students to a full understanding of evolution and the component processes that have led to biological evolution on Earth.
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
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 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 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.
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
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.
p”Ein auch heute noch bedeutsamer Klassiker“ Daily Express Sind wir Marionetten unserer Gene? Nach Richard Dawkins ́ vor über 30 Jahren entworfener und heute noch immer provozierender These steuern und dirigieren unsere von Generation zu Generation weitergegebenen Gene uns, um sich selbst zu erhalten. Alle biologischen Organismen dienen somit vor allem dem Überleben und der Unsterblichkeit der Erbanlagen und sind letztlich nur die "Einweg-Behälter" der "egoistischen" Gene. Sind wir Menschen also unserem Gen-Schicksal hilflos ausgeliefert? Dawkins bestreitet dies und macht uns Hoffnung: Seiner Meinung nach sind wir nämlich die einzige Spezies mit der Chance, gegen ihr genetisches Schicksal anzukämpfen.
Through an integration of systematics, genetics, and related disciplines, the Modern Synthesis of Evolutionary Biology came into being over fifty years ago. Knowledge of evolution has since been transformed by several revolutions: the way we interpret the fossil record has been radically affected by theories of continental drift and asteroid impacts; the way we classify organisms has been influenced by the development of cladistics. Perhaps the most dramatic revolution has been the explosion in molecular biology of information about the genome. Aiming to capture the excitement of modern evolutionary biology, six prominent scientists here explore important issues and problems in their areas of specialization and identify the most promising directions of future research. The scope of this volume ranges from macroevolutionary patterns in the Precambrian to molecular evolution of the genome. Major themes include the origin and maintenance of variation and the causes of evolutionary change. Chapters on paleontology, ecology, behavior, development, and cell and molecular biology are contributed by Jim Valentine, Graham Bell, Mary Jane West Eberhard, Leo Buss, Marc Kirschner, and Marty Kreitman. The book contains an introductory chapter by John Bonner, whose seminal work is honored here. Originally published in 1992. The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These editions preserve the original texts of these important books while presenting them in durable paperback and hardcover editions. The goal of the Princeton Legacy Library is to vastly increase access to the rich scholarly heritage found in the thousands of books published by Princeton University Press since its founding in 1905.
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.
New species are discovered every day—and cataloguing all of them has grown into a nearly insurmountable task worldwide. Now, this definitive reference manual acts as a style guide for writing and filing species descriptions. New collecting techniques and new technology have led to a dramatic increase in the number of species that are discovered. Explorations of unstudied regions and new habitats for almost any group of organisms can result in a large number of new species discoveries—and hence the need to be described. Yet there is no one source a student or researcher can readily consult to learn the basic practical aspects of taxonomic procedures. Species description can present a variety of difficulties: Problems arise when new species are not given names because their discoverers do not know how to write a formal species description or when these species are poorly described. Biologists may also have to deal with nomenclatural problems created by previous workers or resulting from new information generated by their own research. This practical resource for scientists and students contains instructions and examples showing how to describe newly discovered species in both the animal and plant kingdoms. With special chapters on publishing taxonomic papers and on ecology in species description, as well as sections covering subspecies, genus-level, and higher taxa descriptions, Describing Species enhances any writer's taxonomic projects, reports, checklists, floras, faunal surveys, revisions, monographs, or guides. The volume is based on current versions of the International Codes of Zoological and Botanical Nomenclature and recognizes that systematics is a global and multicultural exercise. Though Describing Species has been written for an English-speaking audience, it is useful anywhere Taxonomy is spoken and will be a valuable tool for professionals and students in zoology, botany, ecology, paleontology, and other fields of biology.
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.
In 1974, Richard Lewontin published The Genetic Basis of Evolutionary Change, focusing enormous attention on protein variation as both a model of underlying genetic variation and a level of selection itself. In the twenty years since, scientific research has been shifted by the power of molecular biological techniques to explore the nature of variation directly at the DNA and gene levels. The "protein chapter" is coming to a close. In this book, Jeff Mitton explains the questions that geneticists hoped to answer by studying protein variation. He reviews the extensive literature on protein variation, describes the successes and failures of the research program, and evaluates the results of a rich and controversial body of research. The laboratory and field studies using protein polymorphisms revealed dynamic interactions among genotypes, fitness differentials, and fluctuating environmental conditions, and inadvertently wedded the fields of physiological ecology and population biology. Mitton's book is a useful analysis for all scientists interested in the genetic structure and evolution of populations.
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.