Download or read book Bayesian Evolutionary Analysis with BEAST written by Alexei J. Drummond and published by Cambridge University Press. This book was released on 2015-08-06 with total page 263 pages. Available in PDF, EPUB and Kindle. Book excerpt: What are the models used in phylogenetic analysis and what exactly is involved in Bayesian evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you choose and apply these models, which parameterisations and priors make sense, and how can you diagnose Bayesian MCMC when things go wrong? These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. This practical guide: • Addresses the theoretical aspects of the field • Advises on how to prepare and perform phylogenetic analysis • Helps with interpreting analyses and visualisation of phylogenies • Describes the software architecture • Helps developing BEAST 2.2 extensions to allow these models to be extended further. With an accompanying website providing example files and tutorials (http://beast2.org/), this one-stop reference to applying the latest phylogenetic models in BEAST 2 will provide essential guidance for all users – from those using phylogenetic tools, to computational biologists and Bayesian statisticians.
Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2006-11-25 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. 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. 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.
Download or read book Handbook of Meta analysis in Ecology and Evolution written by Julia Koricheva and published by Princeton University Press. This book was released on 2013-04-21 with total page 515 pages. Available in PDF, EPUB and Kindle. Book excerpt: Meta-analysis is a powerful statistical methodology for synthesizing research evidence across independent studies. This is the first comprehensive handbook of meta-analysis written specifically for ecologists and evolutionary biologists, and it provides an invaluable introduction for beginners as well as an up-to-date guide for experienced meta-analysts. The chapters, written by renowned experts, walk readers through every step of meta-analysis, from problem formulation to the presentation of the results. The handbook identifies both the advantages of using meta-analysis for research synthesis and the potential pitfalls and limitations of meta-analysis (including when it should not be used). Different approaches to carrying out a meta-analysis are described, and include moment and least-square, maximum likelihood, and Bayesian approaches, all illustrated using worked examples based on real biological datasets. This one-of-a-kind resource is uniquely tailored to the biological sciences, and will provide an invaluable text for practitioners from graduate students and senior scientists to policymakers in conservation and environmental management. Walks you through every step of carrying out a meta-analysis in ecology and evolutionary biology, from problem formulation to result presentation Brings together experts from a broad range of fields Shows how to avoid, minimize, or resolve pitfalls such as missing data, publication bias, varying data quality, nonindependence of observations, and phylogenetic dependencies among species Helps you choose the right software Draws on numerous examples based on real biological datasets
Download or read book Evolutionary Genetics written by Glenn-Peter Sætre and published by . This book was released on 2019 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: With recent technological advances, vast quantities of genetic and genomic data are being generated at an ever-increasing pace. The explosion in access to data has transformed the field of evolutionary genetics. A thorough understanding of evolutionary principles is essential for making sense of this, but new skill sets are also needed to handle and analyze big data. This contemporary textbook covers all the major components of modern evolutionary genetics, carefully explaining fundamental processes such as mutation, natural selection, genetic drift, and speciation. It also draws on a rich literature of exciting and inspiring examples to demonstrate the diversity of evolutionary research, including an emphasis on how evolution and selection has shaped our own species. Practical experience is essential for developing an understanding of how to use genetic and genomic data to analyze and interpret results in meaningful ways. In addition to the main text, a series of online tutorials using the R language serves as an introduction to programming, statistics, and analysis. Indeed the R environment stands out as an ideal all-purpose source platform to handle and analyze such data. The book and its online materials take full advantage of the authors' own experience in working in a post-genomic revolution world, and introduces readers to the plethora of molecular and analytical methods that have only recently become available. Evolutionary Genetics is an advanced but accessible textbook aimed principally at students of various levels (from undergraduate to postgraduate) but also for researchers looking for an updated introduction to modern evolutionary biology and genetics.
Download or read book The New Evolutionary Sociology written by Jonathan Turner and published by Routledge. This book was released on 2018-03-09 with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt: For decades, evolutionary analysis was overlooked or altogether ignored by sociologists. Fears and biases persisted nearly a century after Auguste Comte gave the discipline its name, as did concerns that its effect would only reduce sociology to another discipline – whether biology, psychology, or economics. Worse, apprehension that the application of evolutionary theory would encourage heightened perceptions of racism, sexism, ethnocentrism and reductionism pervaded. Turner and Machalek argue instead for a new embrace of biology and evolutionary analysis. Sociology, from its very beginnings in the early 19th century, has always been concerned with the study of evolution, particularly the transformation of societies from simple to ever-more complex forms. By comprehensively reviewing the original ways that sociologists applied evolutionary theory and examining the recent renewal and expansion of these early approaches, the authors confront the challenges posed by biology, neuroscience, and psychology to distinct evolutionary approaches within sociology. They emerge with key theoretical and methodological discoveries that demonstrate the critical – and compelling – case for a dramatically enriched sociology that incorporates all forms of comparative evolutionary analysis to its canon and study of sociocultural phenomena.
Download or read book Statistical and Evolutionary Analysis of Biological Networks written by Michael P. H. Stumpf and published by World Scientific. This book was released on 2010 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt: Networks provide a very useful way to describe a wide range of different data types in biology, physics and elsewhere. Apart from providing a convenient tool to visualize highly dependent data, networks allow stringent mathematical and statistical analysis. In recent years, much progress has been achieved to interpret various types of biological network data such as transcriptomic, metabolomic and protein interaction data as well as epidemiological data. Of particular interest is to understand the organization, complexity and dynamics of biological networks and how these are influenced by network evolution and functionality. This book reviews and explores statistical, mathematical and evolutionary theory and tools in the understanding of biological networks. The book is divided into comprehensive and self-contained chapters, each of which focuses on an important biological network type, explains concepts and theory and illustrates how these can be used to obtain insight into biologically relevant processes and questions. There are chapters covering metabolic, transcriptomic, protein interaction and epidemiological networks as well as chapters that deal with theoretical and conceptual material. The authors, who contribute to the book, are active, highly regarded and well-known in the network community. Sample Chapter(s). Chapter 1: A Network Analysis Primer (350 KB). Contents: A Network Analysis Primer (M P H Stumpf & C Wiuf); Evolutionary Analysis of Protein Interaction Networks (C Wiuf & O Ratmann); Motifs in Biological Networks (F Schreiber & H SchwAbbermeyer); Bayesian Analysis of Biological Networks: Clusters, Motifs, Cross-Species Correlations (J Berg & M Lnssig); Network Concepts and Epidemiological Models (R R Kao & I Z Kiss); Evolutionary Origin and Consequences of Design Properties of Metabolic Networks (T Pfeiffer & S Bonhoeffer); Protein Interactions from an Evolutionary Perspective (F Pazos & A Valencia); Statistical Null Models for Biological Network Analysis (W P Kelly et al.). Readership: Academics, researchers, postgraduates and advanced undergraduates in bioinformatics. Biologists, mathematicians/statisticians, physicists and computer scientists.
Download or read book A Biologist s Guide to Mathematical Modeling in Ecology and Evolution written by Sarah P. Otto and published by Princeton University Press. This book was released on 2011-09-19 with total page 745 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thirty years ago, biologists could get by with a rudimentary grasp of mathematics and modeling. Not so today. In seeking to answer fundamental questions about how biological systems function and change over time, the modern biologist is as likely to rely on sophisticated mathematical and computer-based models as traditional fieldwork. In this book, Sarah Otto and Troy Day provide biology students with the tools necessary to both interpret models and to build their own. The book starts at an elementary level of mathematical modeling, assuming that the reader has had high school mathematics and first-year calculus. Otto and Day then gradually build in depth and complexity, from classic models in ecology and evolution to more intricate class-structured and probabilistic models. The authors provide primers with instructive exercises to introduce readers to the more advanced subjects of linear algebra and probability theory. Through examples, they describe how models have been used to understand such topics as the spread of HIV, chaos, the age structure of a country, speciation, and extinction. Ecologists and evolutionary biologists today need enough mathematical training to be able to assess the power and limits of biological models and to develop theories and models themselves. This innovative book will be an indispensable guide to the world of mathematical models for the next generation of biologists. A how-to guide for developing new mathematical models in biology Provides step-by-step recipes for constructing and analyzing models Interesting biological applications Explores classical models in ecology and evolution Questions at the end of every chapter Primers cover important mathematical topics Exercises with answers Appendixes summarize useful rules Labs and advanced material available
Download or read book Evolutionary Relationships among Rodents written by W. Patrick Luckett and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 720 pages. Available in PDF, EPUB and Kindle. Book excerpt: The order Rodentia is the most abundant and successful group of mammals, and it has been a focal point of attention for compar ative and evolutionary biologists for many years. In addition, rodents are the most commonly used experimental mammals for bio medical research, and they have played a central role in investi gations of the genetic and molecular mechanisms of speciation in mammals. During recent decades, a tremendous amount of new data from various aspects of the biology of living and fossil rodents has been accumulated by specialists from different disciplines, ranging from molecular biology to paleontology. Paradoxically, our understanding of the possible evolutionary relationships among different rodent families, as well as the possible affinities of rodents with other eutherian mammals, has not kept pace with this information "explosion. " This abundance of new biological data has not been incorporated into a broad synthesis of rodent phylo geny, in part because of the difficulty for any single student of rodent evolution to evaluate the phylogenetic significance of new findings from such diverse disciplines as paleontology, embryology, comparative anatomy, molecular biology, and cytogenetics. The origin and subsequent radiation of the order Rodentia were based primarily on the acquisition of a key character complex: specializations of the incisors, cheek teeth, and associated mus culoskeletal features of the jaws and skull for gnawing and chewing.
Download or read book Analysis of Evolutionary Processes written by Fabio Dercole and published by Princeton University Press. This book was released on 2008-02-11 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantitative approaches to evolutionary biology traditionally consider evolutionary change in isolation from an important pressure in natural selection: the demography of coevolving populations. In Analysis of Evolutionary Processes, Fabio Dercole and Sergio Rinaldi have written the first comprehensive book on Adaptive Dynamics (AD), a quantitative modeling approach that explicitly links evolutionary changes to demographic ones. The book shows how the so-called AD canonical equation can answer questions of paramount interest in biology, engineering, and the social sciences, especially economics. After introducing the basics of evolutionary processes and classifying available modeling approaches, Dercole and Rinaldi give a detailed presentation of the derivation of the AD canonical equation, an ordinary differential equation that focuses on evolutionary processes driven by rare and small innovations. The authors then look at important features of evolutionary dynamics as viewed through the lens of AD. They present their discovery of the first chaotic evolutionary attractor, which calls into question the common view that coevolution produces exquisitely harmonious adaptations between species. And, opening up potential new lines of research by providing the first application of AD to economics, they show how AD can explain the emergence of technological variety. Analysis of Evolutionary Processes will interest anyone looking for a self-contained treatment of AD for self-study or teaching, including graduate students and researchers in mathematical and theoretical biology, applied mathematics, and theoretical economics.
Download or read book Race Differences in Intelligence written by Richard Lynn and published by . This book was released on 2014-08-01 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt: Through more than 50 years of academic research, Richard Lynn has distinguished himself as one of the world's preeminent authorities on intelligence, personality, and human biodiversity. *Race Differences in Intelligence* is his essential work on this most controversial and consequential topic. Covering more than 500 published studies that span 10 population groups, Lynn demonstrates both the validity of innate intelligence as well as its heritability across racial groups. The Second Edition (2014) has been revised and updated to reflect the latest research.
Download or read book Sequence Evolution Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.
Download or read book Topological Data Analysis for Genomics and Evolution written by Raúl Rabadán and published by Cambridge University Press. This book was released on 2019-10-31 with total page 521 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology has entered the age of Big Data. The technical revolution has transformed the field, and extracting meaningful information from large biological data sets is now a central methodological challenge. Algebraic topology is a well-established branch of pure mathematics that studies qualitative descriptors of the shape of geometric objects. It aims to reduce questions to a comparison of algebraic invariants, such as numbers, which are typically easier to solve. Topological data analysis is a rapidly-developing subfield that leverages the tools of algebraic topology to provide robust multiscale analysis of data sets. This book introduces the central ideas and techniques of topological data analysis and its specific applications to biology, including the evolution of viruses, bacteria and humans, genomics of cancer and single cell characterization of developmental processes. Bridging two disciplines, the book is for researchers and graduate students in genomics and evolutionary biology alongside mathematicians interested in applied topology.
Download or read book The Phylogenetic Handbook written by Marco Salemi and published by Cambridge University Press. This book was released on 2009-03-26 with total page 750 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.
Download or read book Evolution Of Life Histories written by Derek Roff and published by Springer Science & Business Media. This book was released on 1993-04-30 with total page 554 pages. Available in PDF, EPUB and Kindle. Book excerpt: There are many different types of organisms in the world: they differ in size, physiology, appearance, and life history. The challenge for evolutionary biology is to explain how such diversity arises. The Evolution of Life Histories does this by showing that natural selection is the principal underlying force molding life history variation. The book describes in particular the ways in which variation can be analyzed and predicted. It covers both the genetic and optimization approaches to life history analysis and gives an overview of the general framework of life history theory and the mathematical tools by which predictions can be made and tested. Factors affecting the age schedule of birth and death and the costs of reproduction are discussed. The Evolution of Life Histories concentrates on those theoretical developments that have been tested experimentally. It will interest both students and professionals in evolution, evolutionary ecology, mathematical and theoretical biology, and zoology and entomology.
Download or read book An Evolutionary Theory of Economic Change written by Richard R. Nelson and published by Harvard University Press. This book was released on 1985-10-15 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contains the most sustained and serious attack on mainstream, neoclassical economics in more than forty years. Nelson and Winter focus their critique on the basic question of how firms and industries change overtime. They marshal significant objections to the fundamental neoclassical assumptions of profit maximization and market equilibrium, which they find ineffective in the analysis of technological innovation and the dynamics of competition among firms. To replace these assumptions, they borrow from biology the concept of natural selection to construct a precise and detailed evolutionary theory of business behavior. They grant that films are motivated by profit and engage in search for ways of improving profits, but they do not consider them to be profit maximizing. Likewise, they emphasize the tendency for the more profitable firms to drive the less profitable ones out of business, but they do not focus their analysis on hypothetical states of industry equilibrium. The results of their new paradigm and analytical framework are impressive. Not only have they been able to develop more coherent and powerful models of competitive firm dynamics under conditions of growth and technological change, but their approach is compatible with findings in psychology and other social sciences. Finally, their work has important implications for welfare economics and for government policy toward industry.
Download or read book Computational and Evolutionary Analysis of HIV Molecular Sequences written by Allen G. Rodrigo and published by Springer Science & Business Media. This book was released on 2001 with total page 303 pages. Available in PDF, EPUB and Kindle. Book excerpt: HIV research is unusual in that it brings together scientists from a wide range of disciplines; clinicians: pathologists, immunologists, epidemiologists, virologists, computational biologists, structural biologists, evolutionary biologists, statisticians and mathematicians. The book seeks to bridge the gap between these groups, in both subject matter and terminology."--BOOK JACKET.
Download or read book The Character Concept in Evolutionary Biology written by Günter P. Wagner and published by Elsevier. This book was released on 2000-10-31 with total page 647 pages. Available in PDF, EPUB and Kindle. Book excerpt: Almost all evolutionary biologists, indeed all biologists, use particular features to study life. These characteristics or features used by evolutionary biologists are used in a particular way to unravel a tangled evolutionary history, document the rate of evolutionary change, or as evidence of biodiversity. "Characters" are the "data" of evolutionary biology and they can be employed differently in research providing both opportunities and limitations. The Character Concept in Evolutionary Biology is about characters, their use, how different sorts of characters are limited, and what are appropriate methods for character analysis. Leading evolutionary biologists from around the world are contributors to this authoritative review of the "character concept." Because characters and the conception of characters are central to all studies of evolution, and because evolution is the central organizing principle of biology, this book will appeal to a wide cross-section of biologists. - Focuses upon "characters" -- fundamental data for evolutionary biology - Covers the myriad ways in which characters are defined, described, and distinguished - Includes historical, morphological, molecular, behavioral, and philosophical perspectives
