Browse

This book aims to present different voices and perspectives on the adaptive landscape, its past, present, and future position in evolutionary biology. Chapters have been written by scientists in different fields, including ecology, evolution, developmental biology, genetics, history of science and philosophy. The idea for this book came a few years ago, as the 80-year anniversary of Sewall Wright's classic paper was approaching rapidly (2012). This seemed to be an excellent opportunity to summarize the state of the art of the adaptive landscape. The hope is that this volume won't mark the end of the scientific discussions about the adaptive landscape, but rather a new beginning. And finally, it is hoped that if the adaptive landscape will not survive another 80 years, it will hopefully be replaced by an even better concept or metaphor that will push evolutionary biology forward and increase knowledge about adaptation, speciation, and the origins and preservation of biodiversity on this fragile planet.

Aging has long since been ascribed to the gradual accumulation of DNA mutations in the genome of somatic cells. However, it is only recently that the necessary sophisticated technology has been developed to begin testing this theory and its consequences. This book critically reviews the concept of genomic instability as a possible universal cause of aging in the context of a new, holistic understanding of genome functioning in complex organisms resulting from recent advances in functional genomics and systems biology. It provides a synthesis of current research, as well as a look ahead to the design of strategies to retard or reverse the deleterious effects of aging. This is particularly important in a time when we are urgently trying to unravel the genetic component of aging-related diseases. Moreover, there is a growing public recognition of the imperative of understanding more about the underlying biology of aging, driven by continuing demographic change.

Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in almost all fields of applied molecular biology. This book starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including whole proteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a description of the scientific questions where experimental ancestral sequence reconstruction has been utilized to provide insights and inform future research.

Animal life, now and over the past half billion years, is incredibly diverse. Describing and understanding the evolution of this diversity of body plans — from vertebrates such as humans and fish to the numerous invertebrate groups including sponges, insects, molluscs, and the many groups of worms — is a major goal of evolutionary biology. This book adopts a modern, integrated approach to describe how current molecular genetic techniques and disciplines as diverse as palaeontology, embryology, and genomics have been combined, resulting in a dramatic renaissance in the study of animal evolution. The last decade has seen growing interest in evolutionary biology fuelled by a wealth of data from molecular biology. Modern phylogenies integrating evidence from molecules, embryological data, and morphology of living and fossil taxa provide a wide consensus of the major branching patterns of the tree of life; moreover, the links between phenotype and genotype are increasingly well understood. This has resulted in a reliable tree of relationships that has been widely accepted and has spawned numerous new and exciting questions that require a reassessment of the origins and radiation of animal life. The focus of this volume is at the level of major animal groups, the morphological innovations that define them, and the mechanisms of change to their embryology that have resulted in their evolution. Current research themes and future prospects are highlighted including phylogeny reconstruction, comparative developmental biology, the value of different sources of data and the importance of fossils, homology assessment, character evolution, phylogeny of major groups of animals, and genome evolution. These topics are integrated in the light of a 'new animal phylogeny', to provide fresh insights into the patterns and processes of animal evolution.

This book provides a comprehensive analysis of evolution in the animal kingdom. It reviews the classical, morphological information from structure and embryology, as well as the new data gained from studies using immune stainings of nerves and muscles and blastomere markings, which makes it possible to follow the fate of single blastomeres all the way to early organogenesis. Until recently, the information from analyses of gene sequences has tended to produce myriads of quite diverging trees. However, the latest generation of molecular methods, using many genes, expressed sequence tags, and even whole genomes, has brought a new stability to the field. The book brings together the information from these varied fields, and demonstrates that it is indeed now possible to build a phylogenetic tree from a combination of both morphology and gene sequences. This thoroughly revised third edition brings the subject fully up to date, especially in light of the latest advances in molecular techniques. The book is illustrated throughout with finely detailed line drawings and clear diagrams, many of them new.

The role of genes in governing behavior remains one of the most controversial topics in human biology. Early in this century, over-eager promotion of a genetic basis for behavior led to the excesses, and ultimately the horrors, of eugenics. Subsequent reactions to these excesses, both within the scientific community and society as a whole, led to a nearly complete dismissal of a role for genes in human behavior. Slowly we come back to a more balanced view. Detailed studies of the biological basis of behavior in animals, from the simplest single-celled creatures through the most complex mammals, show that genes play an important role in guiding behavior. Studies in humans, especially those involving twins reared together or apart, indicate clearly that humans are no exception. The variability we see around us in the way humans respond in a given situation is strongly influenced by the variability in their genetic makeup. So are we powerless creations of our genes? Not at all. Guided by differing genetic makeups, we respond to our environment in different ways. But these responses, and the actions of our genes, are in turn modified by the environment itself. Behavior is the result of a balancing act between genes and the environment; between what we inherit and what we learn. To understand ourselves fully, we must understand both.

Avoiding Attack discusses the diversity of mechanisms by which prey avoid predator attacks and explores how such defensive mechanisms have evolved through natural selection. It considers how potential prey avoid detection, how they make themselves unprofitable to attack, how they communicate this status, and how other species have exploited these signals. Using carefully selected examples of camouflage, mimicry, and warning signals drawn from a wide range of species and ecosystems, the authors summarize the latest research into these fascinating adaptations, developing mathematical models where appropriate and making recommendations for future study.This second edition has been extensively rewritten, particularly in the application of modern genetic research techniques which have transformed our recent understanding of adaptations in evolutionary genomics and phylogenetics. The book also employs a more integrated and systematic approach, ensuring that each chapter has a broader focus on the evolutionary and ecological consequences of anti-predator adaptation. The field has grown and developed considerably over the last decade with an explosion of new research literature, making this new edition timely.

Much is conserved in vertebrate evolution, but significant changes in the nervous system occurred at the origin of vertebrates and in most of the major vertebrate lineages. This book examines these innovations and relates them to evolutionary changes in other organ systems, animal behavior, and ecological conditions at the time. The resulting perspective clarifies what makes the major vertebrate lineages unique and helps explain their varying degrees of ecological success. One of the book’s major conclusions is that vertebrate nervous systems are more diverse than commonly assumed, at least among neurobiologists. Examples of important innovations include not only the emergence of novel brain regions, such as the cerebellum and neocortex, but also major changes in neuronal circuitry and functional organization. A second major conclusion is that many of the apparent similarities in vertebrate nervous systems resulted from convergent evolution, rather than inheritance from a common ancestor. For example, brain size and complexity increased numerous times, in many vertebrate lineages. In conjunction with these changes, olfactory inputs to the telencephalic pallium were reduced in several different lineages, and this reduction was associated with the emergence of pallial regions that process non-olfactory sensory inputs. These conclusions cast doubt on the widely held assumption that all vertebrate nervous systems are built according to a single, common plan. Instead, the book encourages readers to view both species similarities and differences as fundamental to a comprehensive understanding of nervous systems.

About 99.9% of vertebrate species reproduce sexually. This makes the exceptional 0.1%—the asexual or clonal reproducers—fascinating in their own right, and also uniquely instructive about the biological significance of alternative reproductive modes. This book describes the genetics, ecology, natural history, and evolution of all of the world's approximately 100 “species” of vertebrate animal that routinely display one form or another of clonal or quasi-clonal reproduction. The book investigates the astounding realm of sexual abstinence, from the levels of DNA molecules and somatic cells to whole animals and natural populations. Also described is how scientists have learned to mimic and extend nature's own clonal processes by engineering perfect copies of genes, genomes, and whole animals in the laboratory. By considering the many facets of sexual abstinence and clonal reproduction in vertebrate animals, new light is also shed on the biological meaning and ramifications of standard sexuality.

Codon-based models of evolution are a relatively new addition to the toolkit of computational biologists, and in recent years remarkable progress has been made in this area. The study of evolution at the codon level captures information contained in both amino acid and synonymous DNA substitutions. By combining these two types of information, codon analyses are more powerful than those of either amino acid or DNA evolution alone. This is a clear benefit for most evolutionary analyses, including phylogenetic reconstruction, detection of selection, ancestral sequence reconstruction, and alignment of coding DNA. Despite the theoretical advantages of codon-based models, their relative complexity delayed their widespread use. Only in recent years, when large-scale sequencing projects produced sufficient genomic data and computational power increased, did their usage become more common. This book provides the latest insights from codon-based analyses of genetic sequences. The first part of the book provides comprehensive coverage of the developments of various types of codon-substitution models such as parametric and empirical models used in maximum likelihood as well as Bayesian frameworks. Subsequent chapters examine the use of codon models to infer selection and other applications of codon models to biological systems. The second part of the book focuses on codon usage bias. Both the underlying mechanisms as well as current methods to analyse codon usage bias are presented.

The field of molecular evolution has experienced explosive growth in recent years due to the rapid accumulation of genetic sequence data, continuous improvements to computer hardware and software, and the development of sophisticated analytical methods. The increasing availability of large genomic data sets requires powerful statistical methods to analyse and interpret them, generating both computational and conceptual challenges for the field. This book provides a comprehensive coverage of modern statistical and computational methods used in molecular evolutionary analysis, such as maximum likelihood and Bayesian statistics. It describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes. The book emphasizes essential concepts rather than mathematical proofs. It includes detailed derivations and implementation details, as well as numerous illustrations, worked examples, and exercises.

This book explains the history and strategy of the intelligent design creationist movement, which is headquartered at the Discovery Institute’s Center for Science and Culture in Seattle, WA. The movement’s twenty-year “Wedge Strategy,” implementation of which began in 1998, is aimed at bringing intelligent design into American public schools, public policymaking, and the cultural mainstream. Beginning with a brief history of the movement and the authentication of the “Wedge Document,” in which the Wedge Strategy is outlined, the book critiques the incompetent science and rhetorical tactics of the movement’s leaders: Douglas Axe, Paul Chien, Jonathan Wells, Michael Behe, and William Dembski. The movement’s own documents reveal its religious funding sources and its execution of all phases of the strategy except the production of genuine scientific data, including its development of a legal defense against challenges to the teaching of intelligent design. The book recounts the movement’s political maneuvering in its effort to influence science curricula in individual states, most notably Kansas and Ohio, and to develop political support among members of Congress. Importantly, the book documents the centrality of religion to intelligent design, its leaders’ associations with Christian extremists, its continuity with earlier forms of creationism, and its ambitions for academic legitimacy. This 2007 edition provides updates on the movement’s efforts in Kansas and Ohio and offers a firsthand account by Barbara Forrest, who was an expert witness for the plaintiffs, of the landmark legal case involving intelligent design, Kitzmiller et al. v. Dover Area School District (2005).

Some six million years ago, two branches of the evolutionary tree diverged: one that led to chimpanzees and bonobos, and one that led to us. Extraordinary advances in our ability to obtain and process DNA sequence information permits scientists to address fundamental questions about the evolutionary histories of varied species, including our own. Ascertaining the sequence of the genome — the complete complement of DNA information — from both humans and chimpanzees allows scientists to address such questions as: which genes were subjected to natural selection along our evolutionary branch? Are these the genetic changes that made us human? The book addresses these and other questions about human evolutionary history, including our domestication of other animals and of plants. It also explores how researchers use the tools of molecular genetics and population genetics theory to unravel the secrets of the natural histories of genes and genomes. Much like detectives looking to ascertain the circumstances behind a crime, these scientists can develop and test inferences about the nature of the natural selection and other evolutionary pressures that have shaped the organisms that harbor these genes.

Now that so many ecosystems face rapid and major environmental change, the ability of species to respond to these changes by dispersing or moving between different patches of habitat can be crucial to ensuring their survival. Understanding dispersal has become key to understanding how populations may persist. This book provides an overview of the fast expanding field of dispersal ecology, incorporating the very latest research. The causes, mechanisms, and consequences of dispersal at the individual, population, species, and community levels are considered. Perspectives and insights are offered from the fields of evolution, behavioural ecology, conservation biology, and genetics. Throughout the book theoretical approaches are combined with empirical data, and care has been taken to include examples from as wide a range of species as possible — both plant and animal.

This book is an investigation into processes associated with evolutionary divergence and diversification. The focus, as the title indicates, is on the role played by the exchange of genes between divergent lineages. This process has been given various names, with one of the most recent being “divergence-with-gene-flow.” Examples of genetic exchange-mediated evolution include organisms from all domains of life. Though the mechanisms by which such divergent forms of life exchange genomic material differ widely, the outcomes of interest—i.e. adaptive evolution and the formation of new “hybrid” lineages—do not. The various chapter and section divisions thus reflect the history, methodologies for detecting, outcomes, implications for conservation programs, and the effects on the human lineage associated with the process of genetic transfer between divergent lineages.

This book addresses the most paradoxical finding of recent aging research: the cessation of demographic aging. The authors show that aging stops at the level of the individual organism, and explain why evolution allows this. The implications of this counter-intuitive conclusion are profound. Aging research now needs to accept three uncomfortable truths. First, aging is not a cumulative physiological process. Second, the fundamental theory that is required to explain, manipulate, and probe the phenomena of aging comes from evolutionary biology. Third, strong-inference experimental strategies for aging must be founded in evolutionary research, not cell or molecular biology. But there are also significant consequences of this work for human aging. First, biomedical strategies that are founded on the traditional cell-molecular theories of aging are bound to fail, because their fundamental premises are incorrect. Second, the ultimate technological problem of controlling human aging is redefined by the authors as having two parts:(a) ameliorating an aging phase that can now be seen as merely transitory; and (b) achieving an earlier and healthier post-aging phase. Third, the authors propose one possibility by which both of these goals might be achieved. The outcome of fifteen years of research by the authors, this book brings together new applications of evolutionary theory, new models for demography, and massive experimentation. As hard as it is to deal scientifically with the paradoxes and complexities of aging that stops, this key finding unlocks the box containing one of the most profound mysteries of biology.

This book recreates the story of life before Homo sapiens walked the earth. It was once thought that “Peking Man”, the remains of a cave man discovered at the famous fossil site of Dragon Bone Hill in China, had been a great hunter. But Peking Man was actually a composite of the remains of some fifty women, children, and men unfortunate enough to have been the prey of a giant cave hyena. The book retells the story of the cave's unique species of early human, Homo erectus. New evidence shows that Homo erectus was an opportunist who rode a tide of environmental change out of Africa into Eurasia, puddle-jumping from one gene pool to the next. Armed with a shaky hold on fire and some sharp rocks, Homo erectus survived for over 1.5 million years, much longer than Homo sapiens, our own species, has been on Earth. Tell-tale marks on fossil bones show that the lives of these early humans were brutal, yet there are fleeting glimpses of human compassion as well. The small brain of Homo erectus and its strangely unchanging culture indicate that the species could not talk. Part of that primitive culture included ritualized aggression, to which the extremely thick skulls of Homo erectus bear witness.

The ever‐increasing knowledge of whole genome sequences is unveiling a variety of new structures and mechanisms that impinge on current evolutionary theory. The origin of species, the evolution of form and the evolutionary impact of transposable elements are just a few of the many processes that have been revolutionized by ongoing genome studies. These novelties are examined in this book in relation to their significance for evolution, emphasizing their human relevance. For example, the small genomic differences between humans and chimps challenges our understanding of what makes us humans in terms of genetic differences. Certainly, neither the increase in number of genes nor, probably, the changes in coding sequences are the key evolutionary differences that define our humanity. Most probably the relevant steps towards the evolution of higher forms, humans among them, have arisen in regulatory and assembling processes that decide when, where, and in which combination the already existing genetic blocks operate. These are just a few glimpses of these controversial issues that this book examines in the context of Darwinian evolution. Recently this debate has centred on arguments extracted from genomic and molecular information that have been intended to ‘deconstruct’ the Darwinian Theory. The purpose of this book is to show that whilst genome dynamism is providing new, and previously unanticipated, sources of variability, there is no reason to dismiss the role of natural selection as the leading mechanism that sorts out the adaptive potentialities. This book provides many examples to justify the argument to ‘reconstruct’, rather than to ‘deconstruct’, the Darwinian Theory.

The origin of biological diversity, via the formation of new species, can be inextricably linked to adaptation to the ecological environment. Specifically, ecological processes are central to the formation of new species when barriers to gene flow (reproductive isolation) evolve between populations as a result of ecologically based divergent natural selection. This process of ‘ecological speciation’ has seen a large body of focused research in the last ten-fifteen years, and a review and synthesis of the theoretical and empirical literature is now timely. The book begins by clarifying what ecological speciation is, its alternatives, and the predictions that can be used to test for it. It then reviews the three components of ecological speciation and discusses the geography and genomic basis of the process. A final chapter highlights future research directions, describing the approaches and experiments which might be used to conduct that future work. The ecological and genetic literature is integrated throughout the text with the goal of shedding new insight into the speciation process, particularly when the empirical data is then further integrated with theory.

Heliconius butterflies have contributed hugely to our understanding of evolution over the last 150 years. These brightly coloured tropical butterflies are famous for their great diversity of wing patterns and also repeated convergence of pattern due to mimicry. The book explores their ecological relationships with Passiflora host plants, which provide an example of coevolution between host and herbivore. They also have coevolved relationships with cucurbit vines that provide a reliable source of pollen for the butterflies in return for pollination services. This has led to a shift in life history, with Heliconius characterized by a long lifespan and extended reproductive period compared to other butterflies. They also have large brains and unusual behaviours involving detailed spatial memory of their local environment. Their extraordinary diversity of wing patterns is controlled by a remarkably simple system of alternate alleles at just four major wing patterning genes. These genes regulate the development of patterning and colouration in the wing through regulatory changes that control expression of these key genes. These genes therefore offer insight into how developmental processes can evolve in rapid radiations, to produce such bewildering variety from just a few genetic building blocks. The alleles at these major patterning loci have been exchanged between species through adaptive introgression, offering a mechanism for convergent evolution through allele sharing. The genomes of sympatric species also show rampant evidence for genetic material exchanged through hybridization, which challenges our notions of species identity. Divergence in wing pattern also contributes to speciation. In summary, these butterflies have a well understood ecology, genetics, and behaviour, which offer some remarkable insights into tropical rainforest biodiversity and adaptive radiation.