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Computational Molecular Evolution

Author: Ziheng Yang
Publisher: OUP Oxford
ISBN: 9780198567028
Size: 34.41 MB
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This book 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 Evolution And Emergence Of Rna Viruses

Author: Edward C. Holmes
Publisher: Oxford University Press
ISBN: 0199211124
Size: 33.28 MB
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While the study of viral evolution has developed rapidly in the last 30 years, little attention has been directed toward linking the mechanisms of viral evolution to the epidemiological outcomes of these processes. This book intends to fill this gap by considering the patterns and processes of viral evolution at all its spatial and temporal scales.

The Causes Of Molecular Evolution

Author: John H. Gillespie
Publisher: Oxford University Press
ISBN: 9780195357745
Size: 16.29 MB
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This work provides a unified theory that addresses the important problem of the origin and maintenance of genetic variation in natural populations. With modern molecular techniques, variation is found in all species, sometimes at astonishingly high levels. Yet, despite these observations, the forces that maintain variation within and between species have been difficult subjects of study. Because they act very weakly and operate over vast time scales, scientists must rely on indirect inferences and speculative mathematical models. However, despite these obstacles, many advances have been made. The author's research in molecular genetics, evolution, and bio-mathematics has enabled him to draw on this work, and present a coherent and valuable view of the field. The book is divided into three parts. The first consists of three chapters on protein evolution, DNA evolution, and molecular mechanisms. This section reviews the experimental observations on genetic variation. The second part gives a unified treatment of the mathematical theory of selection in a fluctuating environment. The final two chapters combine the earlier assessments in a treatment of the scientific status of two competing theories for the maintenance of genetic variation. Steeped in the enormous advances population genetics has made over the past 25 years, this book has proven highly popular among human geneticists, biologists, evolutionary theorists, and bio-mathematicians.

Analysis Of Phylogenetics And Evolution With R

Author: Emmanuel Paradis
Publisher: Springer Science & Business Media
ISBN: 1461417430
Size: 21.96 MB
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The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

Asymmetry Developmental Stability And Evolution

Author: Anders Pape MØller
Publisher: Oxford University Press, UK
ISBN: 019158939X
Size: 31.81 MB
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Why does nature love symmetry? In Asymmetry, Developmental Stability and Evolution, M--oslash--;ller and Swaddle analyse the evolutionary implications of symmetry. They advance and explain their theory that asymmetry is related to genetic stability and fitness, and that symmetric individuals appear to have quantifiable and significant advantages over their asymmetric counterparts. When assessing potential mates or competitors, animals may be able to use symmetry as an honest indication of quality. This interdisciplinary book, with its associated Web-site, will be of interest to students and researchers in the fields of ecology, evolutionary biology, genetics, and animal behaviour. - ;Why does nature love symmetry? In Asymmetry, Developmental Stability and Evolution, M--oslash--;ller and Swaddle analyse the evolutionary implications of symmetry. They advance and explain their theory that symmetry is related to genetic stability and fitness, and that symmetric individuals appear to have quantifiable and significant advantages over their asymmetric counterparts. When assessing potential mates or competitors, animals may be able to use symmetry as an honest indication of quality. This interdisciplinary book, with its associated Web-site, will be of interest to students and researchers in the fields of ecology, evolutionary biology, genetics, and animal behaviour. -

Introduction To Evolutionary Genomics

Author: Naruya Saitou
Publisher: Springer Science & Business Media
ISBN: 1447153049
Size: 43.42 MB
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This book is the first of its kind to explain the fundamentals of evolutionary genomics. The comprehensive coverage includes concise descriptions of a variety of genome organizations, a thorough discussion of the methods used, and a detailed review of genome sequence processing procedures. The opening chapters also provide the necessary basics for readers unfamiliar with evolutionary studies. Features: introduces the basics of molecular biology, DNA replication, mutation, phylogeny, neutral evolution, and natural selection; presents a brief evolutionary history of life from the primordial seas to the emergence of humans; describes the genomes of prokaryotes, eukaryotes, vertebrates, and humans; reviews methods for genome sequencing, phenotype data collection, homology searches and analysis, and phylogenetic tree and network building; discusses databases of genome sequences and related information, evolutionary distances, and population genomics; provides supplementary material at an associated website.

Inferring Phylogenies

Author: Joseph Felsenstein
Publisher: Sinauer Associates Incorporated
ISBN: 9780878931774
Size: 61.55 MB
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Phylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.

Learning And Intelligent Optimization Designing Implementing And Analyzing Effective Heuristics

Author: Thomas Stützle
Publisher: Springer Science & Business Media
ISBN: 3642111688
Size: 47.16 MB
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This book constitutes the thoroughly refereed post-conference proceedings of the Third International Conference on Learning and Intelligent Optimization, LION 2009 III, held in Trento, Italy, in January 2009. The 15 revised full papers, one extended abstract and two poster sessions were carefully reviewed and selected from 86 submissions for inclusion in the book. The papers cover current issues of stochastic local search methods and meta-heuristics, hybridizations of constraint and mathematical programming with meta-heuristics, supervised, unsupervised and reinforcement learning applied to heuristic search, reactive search (online self-tuning methods), algorithm portfolios and off-line tuning methods, algorithms for dynamic, stochastic and multi-objective problems, interface(s) between discrete and continuous optimization, experimental analysis and modeling of algorithms, theoretical foundations, parallelization of optimization algorithms, memory-based optimization, prohibition-based methods (tabu search), memetic algorithms, evolutionary algorithms, dynamic local search, iterated local search, variable neighborhood search and swarm intelligence methods (ant colony optimization, particle swarm optimization etc.).

Animal Signals

Author: John Maynard Smith
Publisher: Oxford University Press
ISBN: 9780198526858
Size: 69.41 MB
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Why are animal signals reliable? This is the central problem for evolutionary biologists interested in signals. Of course, not all signals are reliable; but most are, otherwise receivers of signals would ignore them. A number of theoretical answers have been proposed and empirical studies made, but there still remains a considerable amount of confusion. The authors, one a theoretician the other a fieldworker, introduce a sense of order to this chaos. A significant cause of confusion has been the tendency for different researchers to use either the same term with different meanings, or different terms with the same meaning. The authors attempt to clarify these differences. A second cause of confusion has arisen because many biologists continue to assume that there is only one correct explanation for signal reliability. The authors argue that the reliability of signals is maintained in several ways, relevant in different circumstances, and that biologists must learn to distinguish between them. In this book they explain the different theories, give examples of signalling systems to which one or another theory applies, and point to the many areas where further work, both theoretical and empirical, is required.

Bioinformatics Research And Development

Author: Mourad Elloumi
Publisher: Springer Science & Business Media
ISBN: 3540706003
Size: 38.62 MB
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This volume contains the papers which were selected for presentation at the second Bio- formatics Research and Development (BIRD) conference held in Vienna, Austria during July 7–9, 2008. BIRD covers a wide range of topics related to bioinformatics. This year sequence analysis and alignment, pathways, networks, systems biology, protein and RNA structure and function, gene expression/regulation and microarrays, databases and data integration, machine learning and data analysis were the subjects of main interest. The decisions of the Program Committee are based on the recommendations of at least three, up to five, reviews for each paper. As a result, 30 of the 61 submitted c- tributions could be accepted for the conference. We were happy to have three invited talks presented by experienced researchers providing visitors with a good overview but also some very important insights into the fascinating domain of bioinformatics. Abstracts and more information on these talks are provided in the conference program as well as at the conference site. In the second part of this volume the selected contributions of the two workshops which were held in parallel to the main conference are presented: Workshop on - namical Aspects of Perturbation, Intervention and Transition in Biological Systems – PETRIN 2008 and Workshop on Algorithms in Molecular Biology – ALBIO 2008 Poster presentations of the BIRD conference are in the companion proceedings published by the Trauner Verlag, Linz.