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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.
Genes, genetic codes, and mutation. Dynamics of genes in populations. Evolutionary change in nucleotide sequences. Rates and patterns of nucleotide substitution. Molecular phylogenetics. Gene duplication, exon shuffling, and concerted evolution. Evolution by transposition. Genome evolution. Spatial and temporal frameworks of the evolutionary process. Basics of probability.
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.
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.
Informed by many years of genetics experience, Mark Sanders and John Bowman use an approach that helps contextualize three core challenges of learning genetics: solving problems, understanding evolution, and understanding the connection between traditional genetics models and more modern approaches.
This multidisciplinary book is at the crossroads between two major scientific fields of the 21st century: evolutionary biology and infectious diseases. The genomic revolution has upset modern biology and has revolutionized our approach to ancient disciplines such as evolutionary studies. In particular, this revolution is profoundly changing our view on genetically driven human phenotypic diversity, and this is especially true in disease genetic susceptibility. Infectious diseases are indisputably the major challenge of medicine. When looking globally, they are the number one killer of humans and therefore the main selective pressure exerted on our species. Even in industrial countries, infectious diseases are now far less under control than 20 years ago. The first part of this book covers the main features and applications of modern technologies in the study of infectious diseases. The second part provides detailed information on a number of the key infectious diseases such as malaria, SARS, avian flu, HIV, tuberculosis, nosocomial infections and a few other pathogens that will be taken as examples to illustrate the power of modern technologies and the value of evolutionary approaches. Takes an integrated approach to infectious diseases Includes contributions from leading authorities Provides the latest developments in the field
Flowers are the beautiful and complex reproductive structures of the angiosperms, one of the most diverse and successful groups of living organisms. The underlying thesis of this book is that to fully understand plant development (and why flowers differ in shape, structure and colour), it is necessary to understand why it is advantageous for them to look like they do. Conversely, in order to fully understand plant ecology, it is necessary to appreciate how floral structures have developed and evolved. Uniquely, this book addresses flowers and flowering from both a molecular genetic perspective (considering flower induction, development and self-incompatibility) and an ecological perspective (looking at the selective pressures placed on plants by pollinators, and the consequences for animal-plant co-evolution). Understanding Flowers and Flowering, the first edition of which won BES Marsh Book of the Year in 2009, begins by considering the evolution of flowers and the history of research into their development. This is followed by a detailed description of the processes which lead to flower production in model plants. The book then examines how flowers differ in shape, structure and colour, and how these differences are generated. Finally it assesses the role of these various aspects of floral biology in attracting pollinators and ensuring successful reproduction. This new edition has been completely revised and updated to reflect the latest advances in the field, especially an increased understanding of the evolution of floral traits. New chapters consider the genetic basis of the floral transition in diverse species, as well as the evolutionary lability of floral form. There is a new focus throughout on both phylogenetic position and morphological diversity across the angiosperm phylogeny. Understanding Flowers and Flowering continues to provide the first truly integrated study of the topic - one that discusses both the how and why of flowering plant reproductive biology.

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