Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and computational science, they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution.
This book describes the important role that the transfer of genes between organisms has played during the origin and evolution of humans, and the evolution of organisms on which the human species depends for shelter, sustenance and companionship.
The advances in genomic technologies, such as microarrays and high throughput sequencing, have expanded the realm of possibilities for capturing data and analyzing it using automated computer driven bioinformatics tools. With the completion of the sequencing of genomes of human and several model organisms, a quest for scientific discoveries being fueled by integrative and multidimensional techniques in mathematics and computational sciences. In this volume, leading researchers and experts have provided an overview of significant concepts from biological, mathematical, and computational perspectives. It provides a high level view of fungal genomic data integration and annotation, classification of proteins and identification of vaccine targets, identification of secretome or secreted proteins in fungal genomes, as well as tools for analyzing microarray expression profiles. Provides a survey of theoretical underpinnings on the technological tools and applications Discusses the tools utilized for the annotation of fungal genomes and addresses issues related to automated annotation generation in a high throughput biotechnology environment Describes the applications of the concepts and methodologies presented throughout the book
As concerns about the change in global climate and the loss of biodiversity have mounted, attention has focused on the depletion of the ozone layer and the destruction of tropical rainforests. But recently scientists have identified another seriously endangered ecosystem: coral reefs. In Corals in Space and Time, J.E.N. Veron provides a richly detailed study of corals that will inform investigations of these fragile ecosystems. Drawing on twenty-five years of research, Veron brings together extensive field observations about the taxonomy, biogeography, paleontology, and biology of corals. After introducing coral taxonomy and biogeography, as well as relevant aspects of coral biology for the non-specialist, he provides an interpretation of the fossil record and paleoclimates, an analysis of modern coral distribution, and a discussion of the evolutionary nature and origins of coral species. Revealing a sharp conflict between empirical observations about the geographical variation within species, Veron introduces a non-Darwinian theory of coral evolution. He proposes that the evolution of coral species is driven not primarily by natural selection, but by constantly shifting patterns of ocean circulation, which produce changing variations of genetic connectivity. This mechanism of speciation and hybridization has far-reaching consequences for the study of all types of corals and potentially many other groups of organisms as well.
Molecular Systematics and Plant Evolution discusses the diversity and evolution of plants with a molecular approach. It looks at population genetics, phylogeny (history of evolution) and developmental genetics, to provide a framework from which to understand evolutionary patterns and relationships amongst plants. The international panel of contributors are all respected systematists and evolutionary biologists, who have brought together a wide range of topics from the forefront of research while keeping the text accessible to students. It has been written for senior undergraduates, postgraduates and researchers in the fields of botany, systematics, population / conservation genetics, phylogenetics and evolutionary biology.
This book covers in one volume materials scattered in hundreds of research articles, in most cases focusing on specialized aspects of coral biology. In addition to the latest developments in coral evolution and physiology, it presents chapters devoted to novel frontiers in coral reef research. These include the molecular biology of corals and their symbiotic algae, remote sensing of reef systems, ecology of coral disease spread, effects of various scenarios of global climate change, ocean acidification effects of increasing CO2 levels on coral calcification, and damaged coral reef remediation. Beyond extensive coverage of the above aspects, key issues regarding the coral organism and the reef ecosystem such as calcification, reproduction, modeling, algae, reef invertebrates, competition and fish are re-evaluated in the light of new research and emerging insights. In all chapters novel theories as well as challenges to established paradigms are introduced, evaluated and discussed. This volume is indispensible for all those involved in coral reef management and conservation.
At a glance, most species seem adapted to the environment in which they live. Yet species relentlessly evolve, and populations within species evolve in different ways. Evolution, as it turns out, is much more dynamic than biologists realized just a few decades ago. In Relentless Evolution, John N. Thompson explores why adaptive evolution never ceases and why natural selection acts on species in so many different ways. Thompson presents a view of life in which ongoing evolution is essential and inevitable. Each chapter focuses on one of the major problems in adaptive evolution: How fast is evolution? How strong is natural selection? How do species co-opt the genomes of other species as they adapt? Why does adaptive evolution sometimes lead to more, rather than less, genetic variation within populations? How does the process of adaptation drive the evolution of new species? How does coevolution among species continually reshape the web of life? And, more generally, how are our views of adaptive evolution changing? Relentless Evolution draws on studies of all the major forms of life—from microbes that evolve in microcosms within a few weeks to plants and animals that sometimes evolve in detectable ways within a few decades. It shows evolution not as a slow and stately process, but rather as a continual and sometimes frenetic process that favors yet more evolutionary change.
Based on observational and experimental data, in natural populations of plants and animals studied in the field and in the laboratory, this perspective unravels the hidden and often poorly founded assumptions underlying some of the more troublesome controversies in evolutionary biology today
During the last few years, software evolution research has explored new domains such as the study of socio-technical aspects and collaboration between different individuals contributing to a software system, the use of search-based techniques and meta-heuristics, the mining of unstructured software repositories, the evolution of software requirements, and the dynamic adaptation of software systems at runtime. Also more and more attention is being paid to the evolution of collections of inter-related and inter-dependent software projects, be it in the form of web systems, software product families, software ecosystems or systems of systems. With this book, the editors present insightful contributions on these and other domains currently being intensively explored, written by renowned researchers in the respective fields of software evolution. Each chapter presents the state of the art in a particular topic, as well as the current research, available tool support and remaining challenges. The book is complemented by a glossary of important terms used in the community, a reference list of nearly 1,000 papers and books and tips on additional resources that may be useful to the reader (reference books, journals, standards and major scientific events in the domain of software evolution and datasets). This book is intended for all those interested in software engineering, and more particularly, software maintenance and evolution. Researchers and software practitioners alike will find in the contributed chapters an overview of the most recent findings, covering a broad spectrum of software evolution topics. In addition, it can also serve as the basis of graduate or postgraduate courses on e.g., software evolution, requirements engineering, model-driven software development or social informatics.
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.
"This book arises from the Mathematics of Evolution & Phylogenetics meeting at the Mathematical Institute Henri Poincare, Paris, in June 2005 and is based on ... reports presented by keynote speakers"--Back cover.
Although plants comprise more than 90% of all visible life, and land plants and algae collectively make up the most morphologically, physiologically, and ecologically diverse group of organisms on earth, books on evolution instead tend to focus on animals. This organismal bias has led to an incomplete and often erroneous understanding of evolutionary theory. Because plants grow and reproduce differently than animals, they have evolved differently, and generally accepted evolutionary views—as, for example, the standard models of speciation—often fail to hold when applied to them. Tapping such wide-ranging topics as genetics, gene regulatory networks, phenotype mapping, and multicellularity, as well as paleobotany, Karl J. Niklas’s Plant Evolution offers fresh insight into these differences. Following up on his landmark book The Evolutionary Biology of Plants—in which he drew on cutting-edge computer simulations that used plants as models to illuminate key evolutionary theories—Niklas incorporates data from more than a decade of new research in the flourishing field of molecular biology, conveying not only why the study of evolution is so important, but also why the study of plants is essential to our understanding of evolutionary processes. Niklas shows us that investigating the intricacies of plant development, the diversification of early vascular land plants, and larger patterns in plant evolution is not just a botanical pursuit: it is vital to our comprehension of the history of all life on this green planet.
The theory of evolution has changed so much- claiming that humans are closely related genetically to chimps, mice, donkeys, and even fish - that the theory is now a blurred mess masquerading as a scientific fact. It's a theory built on countless speculations, scientific fraud, and multiple conflicting theories. Garnering the evidence from biology, chemistry, genetics, geology, history, paleontology, and physics, evolution is exposed as a racist philosophy and a false science that provided the "scientific" justification for the Holocaust and other genocides, including the plot to silently exterminate American minorities through abortion and birth control. The evidence for evolution is examined in the light of genuine science. You may not like what you read, but you can't argue with the facts.
Darwin’s nineteenth-century writings laid the foundations for modern studies of evolution, and theoretical developments in the mid-twentieth century fostered the Modern Synthesis. Since that time, a great deal of new biological knowledge has been generated, including details of the genetic code, lateral gene transfer, and developmental constraints. Our improved understanding of these and many other phenomena have been working their way into evolutionary theory, changing it and improving its correspondence with evolution in nature. And while the study of evolution is thriving both as a basic science to understand the world and in its applications in agriculture, medicine, and public health, the broad scope of evolution—operating across genes, whole organisms, clades, and ecosystems—presents a significant challenge for researchers seeking to integrate abundant new data and content into a general theory of evolution. This book gives us that framework and synthesis for the twenty-first century. The Theory of Evolution presents a series of chapters by experts seeking this integration by addressing the current state of affairs across numerous fields within evolutionary biology, ranging from biogeography to multilevel selection, speciation, and macroevolutionary theory. By presenting current syntheses of evolution’s theoretical foundations and their growth in light of new datasets and analyses, this collection will enhance future research and understanding.
In recent years, the relation between contemporary academic philosophy and evolutionary theory has become ever more active, multifaceted, and productive. The connection is a bustling two-way street. In one direction, philosophers of biology make significant contributions to theoretical discussions about the nature of evolution (such as "What is a species?"; "What is reproductive fitness?"; "Does selection operate primarily on genes?"; and "What is an evolutionary function?"). In the other direction, a broader group of philosophers appeal to Darwinian selection in an attempt to illuminate traditional philosophical puzzles (such as "How could a brain-state have representational content?"; "Are moral judgments justified?"; "Why do we enjoy fiction?"; and "Are humans invariably selfish?"). In grappling with these questions, this interdisciplinary collection includes cutting-edge examples from both directions of traffic. The thirty contributions, written exclusively for this volume, are divided into six sections: The Nature of Selection; Evolution and Information; Human Nature; Evolution and Mind; Evolution and Ethics; and Evolution, Aesthetics, and Art. Many of the contributing philosophers and psychologists are international leaders in their fields.
A modern approach to understanding the evolution and diversification of land plants, one of the most exciting areas of plant systematics. It consists of three sections - origin and diversification of primitive land plants; origin and diversification of angiosperms; speciation and mechanisms of diversification - each section corresponding to a major area in plant evolution. In each case, data from molecular, morphological, and paleontological approaches are presented, backed by recent progress and new findings, together with proposals for future research. A guide to the latest in plant systematics, heightening awareness of prospective future problems.
Bioinformatics is growing by leaps and bounds; theories/algorithms/statistical techniques are constantly evolving. Nevertheless, a core body of algorithmic ideas have emerged and researchers are beginning to adopt a "problem solving" approach to bioinformatics, wherein they use solutions to well-abstracted problems as building blocks to solve larger scope problems. Problem Solving Handbook for Computational Biology and Bioinformatics is an edited volume contributed by world renowned leaders in this field. This comprehensive handbook with problem solving emphasis, covers all relevant areas of computational biology and bioinformatics. Web resources and related themes are highlighted at every opportunity in this central easy-to-read reference. Designed for advanced-level students, researchers and professors in computer science and bioengineering as a reference or secondary text, this handbook is also suitable for professionals working in this industry.
This book presents 19 selected contributions to the 16th Evolutionary Biology Meeting, which took place in September 2012 in Marseilles. The aims of these annual meetings, which gather together leading evolutionary biologists and other scientists, are to promote the exchange of ideas and to encourage interdisciplinary collaborations. The first chapter deals with the history of a great discovery: The first experiments on ascidian and sea urchin egg fertilization. The remaining contributions are grouped under the following categories: · Evolutionary biology concepts · Exobiology and the origin of life · Evolutionary mechanisms Offering an up-to-date overview of recent findings in the field of evolutionary biology, this book is an invaluable source of information for scientists, teachers and advanced students.