Reconstructing Evolution

"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.

Evolution is a complex process, acting at multiple scales, from DNA sequences and proteins to populations of species. Understanding and reconstructing evolution is of major importance in numerous subfields of biology. For example, phylogenetics and sequence evolution is central to comparative genomics, attempts to decipher genomes, and molecular epidemiology. Phylogenetics is also the focal point of large-scale international biodiversity assessment initiatives such as the 'Tree of Life' project, which aims to build the evolutionary tree for all extant species. Since the pioneering work in phylogenetics in the 1960s, models have become increasingly sophisticated to account for the inherent complexity of evolution. They rely heavily on mathematics and aim at modelling and analyzing biological phenomena such as horizontal gene transfer, heterogeneity of mutation, and speciation and extinction processes. This book presents these recent models, their biological relevance, their mathematical basis, their properties, and the algorithms to infer them from data. A number of subfields from mathematics and computer science are involved: combinatorics, graph theory, stringology, probabilistic and Markov models, information theory, statistical inference, Monte Carlo methods, continuous and discrete algorithmics. This book arises from the Mathematics of Evolution & Phylogenetics meeting at the Mathematical Institute Henri Poincaré, Paris, in June 2005 and is based on the outstanding state-of-the-art reports presented by the conference speakers. Ten chapters - based around five themes - provide a detailed overview of key topics, from the underlying concepts to the latest results, some of which are at the forefront of current research.

Reconstructing the Past seeks to clarify and help resolve the vexing methodological issues that arise when biologists try to answer such questions as whether human beings are more closely related to chimps than they are to gorillas. It explores the case for considering the philosophical idea of simplicity/parsimony as a useful principle for evaluating taxonomic theories of evolutionary relationships. For the past two decades, evolutionists have been vigorously debating the appropriate methods that should be used in systematics, the field that aims at reconstructing phylogenetic relationships among species. This debate over phylogenetic inference, Elliott Sober observes, raises broader questions of hypothesis testing and theory evaluation that run head on into long standing issues concerning simplicity/parsimony in the philosophy of science. Sober treats the problem of phylogenetic inference as a detailed case study in which the philosophical idea of simplicity/parsimony can be tested as a principle of theory evaluation. Bringing together philosophy and biology, as well as statistics, Sober builds a general framework for understanding the circumstances in which parsimony makes sense as a tool of phylogenetic inference. Along the way he provides a detailed critique of parsimony in the biological literature, exploring the strengths and limitations of both statistical and nonstatistical cladistic arguments.

The Earth's biological, chemical, and physical systems are increasingly shaped by the activities of one species-ours. In our decisions about everything from manufacturing technologies to restaurant menus, the health of the planet has become a product of human choice. Environmentalism, however, has largely failed to adapt to this new reality. Reconstructing Earth offers seven essays that explore ways of developing a new, more sophisticated approach to the environment that replaces the fantasy of recovering pristine landscapes with a more grounded viewpoint that can foster a better relationship between humans and the planet. Braden Allenby, a lawyer with degrees in both engineering and environmental studies, explains the importance of technological choice, and how that factor is far more significant in shaping our environment (in ways both desirable and not) than environmental controls. Drawing on his varied background and experience in both academia and the corporate world, he describes the emerging field of "earth systems engineering and management," which offers an integrated approach to understanding and managing complex human/natural systems that can serve as a basis for crafting better, more lasting solutions to widespread environmental problems. Reconstructing Earth not only critiques dysfunctional elements of current environmentalism but establishes a foundation for future environmental management and progress, one built on an understanding of technological evolution and the cultural systems that support modern technologies. Taken together, the essays offer an important means of developing an environmentalism that is robust and realistic enough to address the urgent realities of our planet. Reconstructing Earth is a thought-provoking new work for anyone concerned with the past or future of environmental thought, including students and teachers of environmental studies, environmental policy, technology policy, technological evolution, or sustainability.

To document the world’s diversity of species and reconstruct the tree of life we need to undertake some simple but mountainous tasks. Most importantly, we need to tackle species rich groups. We need to collect, name, and classify them, and then position them on the tree of life. We need to do this systematically across all groups of organisms and because of the biodiversity crisis we need to do it quickly. With contributions from key systematic and taxonomic researchers, Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa outlines the core of the problem and explores strategies that bring us closer to its solution. The editors split the book into three parts: introduction and general concepts, reconstructing and using the tree of life, and taxonomy and systematics of species rich groups (case studies). They introduce, with examples, the concept of species rich groups and discuss their importance in reconstructing the tree of life as well as their conservation and sustainable utilization in general. The book highlights how phylogenetic trees are becoming “supersized” to handle species rich groups and the methods that are being developed to deal with the computational complexity of such trees. It discusses factors that have lead some groups to speciate to a staggering degree and also provides case studies that highlight the problems and prospects of dealing with species rich groups in taxonomy. To understand species rich taxa, evolution has set scientists a difficult, but not unattainable, challenge that requires the meshing together of phylogenetics and taxonomy, considerable advances in informatics, improved and increased collecting, training of taxonomists, and significant financial support. This book provides the tools and methods needed to meet that challenge.

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.

This volume brings together a series of papers that address the topic of reconstructing behavior in the primate fossil record. The literature devoted to reconstructing behavior in extinct species is ovelWhelming and very diverse. Sometimes, it seems as though behavioral reconstruction is done as an afterthought in the discussion section of papers, relegated to the status of informed speculation. But recent years have seen an explosion in studies of adaptation, functional anatomy, comparative sociobiology, and development. Powerful new comparative methods are now available on the internet. At the same time, we face a rapidly growing fossil record that offers more and more information on the morphology and paleoenvironments of extinct species. Consequently, inferences of behavior in extinct species have become better grounded in comparative studies of living species and are becoming increas ingly rigorous. We offer here a series of papers that review broad issues related to reconstructing various aspects of behavior from very different types of evi dence. We hope that in so doing, the reader will gain a perspective on the various types of evidence that can be brought to bear on reconstructing behavior, the strengths and weaknesses of different approaches, and, perhaps, new approaches to the topic. We define behavior as broadly as we can including life-history traits, locomotion, diet, and social behavior, giving the authors considerable freedom in choosing what, exactly, they wish to explore.

As Bowler tracks major scientific debates over the emergence of the vertebrates, the origins of the main types of living animals, and the rise and extinction of groups such as the dinosaurs, his richly detailed accounts bring to light complex interactions among specialists in various fields of biology.