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.
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.
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.