Reconstructing Evolution

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Reconstructing Evolution

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Author : Olivier Gascuel
language : en
Publisher: OUP Oxford
Release Date : 2007-06-28

Reconstructing Evolution written by Olivier Gascuel and has been published by OUP Oxford this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-06-28 with Mathematics categories.

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

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Author : Elliott Sober
language : en
Publisher: MIT Press
Release Date : 1991-02-05

Reconstructing The Past written by Elliott Sober and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1991-02-05 with Psychology categories.

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.

Phylogenetic Inference Selection Theory And History Of Science

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Author : Anthony William Fairbank Edwards
language : en
Publisher: Cambridge University Press
Release Date : 2018-07-19

Phylogenetic Inference Selection Theory And History Of Science written by Anthony William Fairbank Edwards and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-07-19 with Mathematics categories.

Seminal papers by A. W. F. Edwards, published together for the first time with commentaries from leading experts to contextualise his contribution.

Molecular Systematics Of Plants Ii

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Author : Pamela Soltis
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06

Molecular Systematics Of Plants Ii written by Pamela Soltis and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-06 with Science categories.

In the five years since the publication of Molecular Systematics of Plants, the field of molecular systematics has advanced at an astonishing pace. This period has been marked by a volume of new empirical data and advances in theoretical and analytical issues related to DNA. Comparative DNA sequencing, facilitated by the amplification of DNA via the polymerase chain reaction (PCR), has become the tool of choice for molecular systematics. As a result, large portions of the Molecular Systematics of Plants have become outdated. Molecular Systematics of Plants II summarizes these recent achievements in plant molecular systematics. Like its predecessor, this completely revised work illustrates the potential of DNA markers for addressing a wide variety of phylogenetic and evolutionary questions. The volume provides guidance in choosing appropriate techniques, as well as appropriate genes for sequencing, for given levels of systematic inquiry. More than a review of techniques and previous work, Molecular Systematics of Plants II provides a stimulus for developing future research in this rapidly evolving field. Molecular Systematics of Plants II is not only written for systematists (faculty, graduate students, and researchers), but also for evolutionary biologists, botanists, and paleobotanists interested in reviewing current theory and practice in plant molecular systematics.

Gene Genealogies Variation And Evolution A Primer In Coalescent Theory

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Author : Jotun Hein
language : en
Publisher: Oxford University Press, USA
Release Date : 2004-12-09

Gene Genealogies Variation And Evolution A Primer In Coalescent Theory written by Jotun Hein and has been published by Oxford University Press, USA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004-12-09 with Population genetics categories.

Authored by leading experts, this seminal text presents a straightforward and elementary account of coalescent theory, which is a central concept in the study of genetic sequence variation observed in a population. Rich in examples and illustrations it is ideal for a graduate course in statistics, population, molecular and medical genetics, bioscience and medicine, and for students studying the evolution of human population and disease. It is also an invaluable reference for bioscientists and statisticians in the pharmaceutical industry and academia - ;Coalescent theory is a central concept in the study of genetic sequence variation that probabilistically describes the genealogy relating the sampled sequences. In this text, besides fulfilling the glaring need for such a book, the authors present this theory in a straightforward and elementary manner and describe the statistical and computational methods used in modelling and analyzing genetic sequence variation. Rich in examples and illustrations the book covers basic concepts, complications arising from geographical structure and recombination before considering aspects of statistical inference based on these models. The book ends with chapters on Gene Mapping, which combines sequence variation data with phenotypic data (such as disease) to define areas of the genome where genes are responsible for the trait, and Human Evolution, a research area that is experiencing a renaissance due to the enormous amounts of data produced in molecular studies. Authored by leading experts, this seminal text presents a straightforward and elementary account of coalescent theory, which is a central concept in the study of genetic sequence variation observed in a population. It is highly suitable for a graduate course in statistics, population, molecular and medical genetics, bioscience and medicine and students studying the evolution of human population and disease, and will be an invaluable reference for bioscientists and statisticians in the pharmaceutical industry and academia - ;an excellent and timely book that should appeal to a variety of people in genetics and applied mathematics. - Professor Montgomery Slatkin (Berkeley);the authors are outstanding experts in the field, and the book is topical and timely. - Professor David Balding (Imperial College);Hein, Schierup and Wiuf have written the first general book on the coalescent. It is an engaging combination of clear mathematical derivation and real data examples. - Professor Joe Felsenstein (University of Washington)

Research In Computational Molecular Biology

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Author : Satoru Miyano
language : en
Publisher: Springer
Release Date : 2005-05-04

Research In Computational Molecular Biology written by Satoru Miyano and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-05-04 with Computers categories.

This volume contains the papers presented at the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), which was held in Cambridge, Massachusetts, on May 14–18, 2005. The RECOMB conference series was started in 1997 by Sorin Istrail, Pavel Pevzner and Michael Waterman. The list of previous meetings is shown below in the s- tion “Previous RECOMB Meetings. ” RECOMB 2005 was hosted by the Broad Institute of MIT and Harvard, and Boston University’s Center for Advanced - nomic Technology, and was excellently organized by the Organizing Committee Co-chairs Jill Mesirov and Simon Kasif. This year, 217 papers were submitted, of which the Program Committee - lected 39 for presentation at the meeting and inclusion in this proceedings. Each submission was refereed by at least three members of the Program Committee. After the completion of the referees’ reports, an extensive Web-based discussion took place for making decisions. From RECOMB 2005, the Steering Committee decided to publish the proceedings as a volume of Lecture Notes in Bioinf- matics (LNBI) for which the founders of RECOMB are also the editors. The prominent volume number LNBI 3500 was assigned to this proceedings. The RECOMB conference series is closely associated with the Journal of Compu- tional Biology which traditionally publishes special issues devoted to presenting full versions of selected conference papers. The RECOMB Program Committee consistedof42members,aslistedonaseparatepage. Iwouldliketothank the RECOMB 2005 Program Committee members for their dedication and hard work.

Biomacromolecules

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Author : C. Stan Tsai
language : en
Publisher: John Wiley & Sons
Release Date : 2007-01-16

Biomacromolecules written by C. Stan Tsai and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-01-16 with Science categories.

This book provides an integrated treatment of the structure and function of nucleic acids, proteins, and glycans, including thorough coverage of relevant computational biochemistry. The text begins with an introduction to the biomacromolecules, followed by discussion of methods of isolation and purification, physiochemical and biochemical properties, and structural characteristics. The next section of the book deals with sequence analysis, analysis of conformation using spectroscopy, chemical synthesis, and computational approaches. The following chapters discuss biomolecular interactions, enzyme action, gene transmission, signal transduction, and biomacromolecular informatics. The author concludes with presenting the latest findings in genomics, proteomics, glycomics, and biomacromolecular evolution. This text is an invaluable resource for research professionals wishing to move into genomics, proteomics, and glycomics research. It is also useful for students in biochemistry, molecular biology, bioengineering, biotechnology, and bioinformatics.

Encyclopedia Of Time

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Author : H. James Birx
language : en
Publisher: SAGE Publications
Release Date : 2009-01-07

Encyclopedia Of Time written by H. James Birx and has been published by SAGE Publications this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-01-07 with Science categories.

"With a strong interdisciplinary approach to a subject that does not lend itself easily to the reference format, this work may not seem to support directly academic programs beyond general research, but it is a more thorough and up-to-date treatment than Taylor and Francis′s 1994 Encyclopedia of Time. Highly recommended." —Library Journal STARRED Review Surveying the major facts, concepts, theories, and speculations that infuse our present comprehension of time, the Encyclopedia of Time: Science, Philosophy, Theology, & Culture explores the contributions of scientists, philosophers, theologians, and creative artists from ancient times to the present. By drawing together into one collection ideas from scholars around the globe and in a wide range of disciplines, this Encyclopedia will provide readers with a greater understanding of and appreciation for the elusive phenomenon experienced as time. Features Surveys historical thought about time, including those ideas that emerged in ancient Greece, early Christianity, the Italian Renaissance, the Age of Enlightenment, and other periods Covers the original and lasting insights of evolutionary biologist Charles Darwin, physicist Albert Einstein, philosopher Alfred North Whitehead, and theologian Pierre Teilhard de Chardin Discusses the significance of time in the writings of Isaac Asimov, Samuel Taylor Coleridge, Fyodor M. Dostoevsky, Francesco Petrarch, H. G. Wells, and numerous other authors Contains the contributions of naturalists and religionists, including astronomers, cosmologists, physicists, chemists, geologists, paleontologists, anthropologists, psychologists, philosophers, and theologians Includes artists′ portrayals of the fluidity of time, including painter Salvador Dali′s The Persistence of Memory and The Discovery of America by Christopher Columbus, and writers Gustave Flaubert′s The Temptation of Saint Anthony and Henryk Sienkiewicz′s Quo Vadis Provides a truly interdisciplinary approach, with discussions of Aztec, Buddhist, Christian, Egyptian, Ethiopian, Hindu, Islamic, Navajo, and many other cultures′ conceptions of time Key Themes Biography Biology/Evolution Culture/History Geology/Paleontology Philosophy Physics/Chemistry Psychology/Literature Religion/Theology Theories/Concepts

Philosophy Of Biology

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Author :
language : en
Publisher: Elsevier
Release Date : 2007-02-05

Philosophy Of Biology written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-02-05 with Science categories.

Philosophy of Biology is a rapidly expanding field. It is concerned with explanatory concepts in evolution, genetics, and ecology. This collection of 25 essays by leading researchers provides an overview of the state of the field. These essays are wholly new; none of them could have been written even ten years ago. They demonstrate how philosophical analysis has been able to contribute to sometimes contested areas of scientific theory making.-Written by internationally acknowledged leaders in the field- Entries make original contributions as well as summarizing state of the art discoveries in the field- Easy to read and understand

Phylogenetic Networks

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Author : Daniel H. Huson
language : en
Publisher: Cambridge University Press
Release Date : 2010-12-02

Phylogenetic Networks written by Daniel H. Huson and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-12-02 with Science categories.

The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.