Analysis of Phylogenetics and Evolution with R

Analysis of Phylogenetics and Evolution with R

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 ...

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 9781461417439

Category: Science

Page: 386

View: 524

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.
Categories: Science

Analysis of Phylogenetics and Evolution with R

Analysis of Phylogenetics and Evolution with R

This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language.

Author: Emmanuel Paradis

Publisher: Springer

ISBN: 0387329145

Category: Science

Page: 211

View: 323

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.
Categories: Science

Bayesian Evolutionary Analysis with BEAST

Bayesian Evolutionary Analysis with BEAST

Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.

Author: Alexei J. Drummond

Publisher: Cambridge University Press

ISBN: 9781107019652

Category: Science

Page: 260

View: 507

Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.
Categories: Science

Parasite Diversity and Diversification

Parasite Diversity and Diversification

Concluding remarks Comparative analysis has been one of the favourite
techniques of evolutionary biologists over the last ... R Core Team, 2013)
Package name Package short description Trait evolution Diversification analysis
Phylogenetic ...

Author: Serge Morand

Publisher: Cambridge University Press

ISBN: 9781107037656

Category: Science

Page: 488

View: 710

By joining phylogenetics and evolutionary ecology, this book explores the patterns of parasite diversity while revealing diversification processes.
Categories: Science

Ecological Statistics

Ecological Statistics

Evolutionary Inferences from Phylogenies: A Review of Methods. Annual ... Effect
size in ecological experiments: The application of biological models in meta-
analysis. American ... Analysis of Phylogenetics and Evolution with R, 2nd ed.

Author: Gordon A. Fox

Publisher: OUP Oxford

ISBN: 9780191652882

Category: Science

Page: 400

View: 882

The application and interpretation of statistics are central to ecological study and practice. Ecologists are now asking more sophisticated questions than in the past. These new questions, together with the continued growth of computing power and the availability of new software, have created a new generation of statistical techniques. These have resulted in major recent developments in both our understanding and practice of ecological statistics. This novel book synthesizes a number of these changes, addressing key approaches and issues that tend to be overlooked in other books such as missing/censored data, correlation structure of data, heterogeneous data, and complex causal relationships. These issues characterize a large proportion of ecological data, but most ecologists' training in traditional statistics simply does not provide them with adequate preparation to handle the associated challenges. Uniquely, Ecological Statistics highlights the underlying links among many statistical approaches that attempt to tackle these issues. In particular, it gives readers an introduction to approaches to inference, likelihoods, generalized linear (mixed) models, spatially or phylogenetically-structured data, and data synthesis, with a strong emphasis on conceptual understanding and subsequent application to data analysis. Written by a team of practicing ecologists, mathematical explanations have been kept to the minimum necessary. This user-friendly textbook will be suitable for graduate students, researchers, and practitioners in the fields of ecology, evolution, environmental studies, and computational biology who are interested in updating their statistical tool kits. A companion web site provides example data sets and commented code in the R language.
Categories: Science

Methods in Comparative Plant Population Ecology

Methods in Comparative Plant Population Ecology

... qtl sem taxize VEGAN Comparative phylogenetics, PICS Listing and
description of R packages for comparative phylogenetic methods Comparative
analyses of phylogenetics and evolution in R Methods for comparative
phylogenetic biology ...

Author: David Gibson

Publisher: Oxford University Press, USA

ISBN: 9780199671472

Category: Science

Page: 320

View: 112

This second edition provides authoritative guidance on research methodology for plant population ecology. Practical advice is provided to assist senior undergraduates and post-graduate students, and all researchers, design their own field and greenhouse experiments and establish a research programme in plant population ecology.
Categories: Science

Scales and Hierarchies

Scales and Hierarchies

APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:
289−290. R Development Core Team. 2007. R: A Language and Environment
for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.

Author: Ina Bornkessel-Schlesewsky

Publisher: Walter de Gruyter GmbH & Co KG

ISBN: 9783110395006

Category: Language Arts & Disciplines

Page: 361

View: 531

The volume advances our understanding of the role of scales and hierarchies across the linguistic sciences. Although scales and hierarchies are widely assumed to play a role in the modelling of linguistic phenomena, their status remains controversial, and it is these controversies that the present volume tackles head-on.
Categories: Language Arts & Disciplines

Metabolic Ecology

Metabolic Ecology

Nunn, G. B. and Stanley, S. E. (1998) Body size effects and rates of cytochrome b
evolution in tube-nosed seabirds. ... S. A., and Isaac, N. J. B. (2011 ) CAPER:
Comparative Analyses of Phylogenetics and Evolution in R. R package version
0.4.

Author: Richard M. Sibly

Publisher: John Wiley & Sons

ISBN: 9781119968511

Category: Science

Page: 256

View: 836

One of the first textbooks in this emerging important field of ecology. Most of ecology is about metabolism: the ways that organisms use energy and materials. The energy requirements of individuals – their metabolic rates – vary predictably with their body size and temperature. Ecological interactions are exchanges of energy and materials between organisms and their environments. So metabolic rate affects ecological processes at all levels: individuals, populations, communities and ecosystems. Each chapter focuses on a different process, level of organization, or kind of organism. It lays a conceptual foundation and presents empirical examples. Together, the chapters provide an integrated framework that holds the promise for a unified theory of ecology. The book is intended to be accessible to upper-level undergraduate, and graduate students, but also of interest to senior scientists. Its easy-to-read chapters and clear illustrations can be used in lecture and seminar courses. Together they make for an authoritative treatment that will inspire future generations to study metabolic ecology.
Categories: Science

Molecular Evolution and Phylogenetics

Molecular Evolution and Phylogenetics

133–147, Oxford University Press, Oxford, U.K. Nei, M. (1996) Phylogenetic
analysis in molecular evolutionary genetics. Annu. Rev. Genet. 30: 371–403. Nei,
M., R. Chakraborty and P. A. Fuerst, (1976a) Infinite allele model with varying ...

Author: Masatoshi Nei

Publisher: Oxford University Press

ISBN: 0195350510

Category: Science

Page: 352

View: 992

During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.
Categories: Science

Issues in Life Sciences Molecular Biology 2011 Edition

Issues in Life Sciences  Molecular Biology  2011 Edition

Nevertheless, combined analyses of all genes provided stronger support for this
relationship than that obtained from 18S data alone. ... Yoshizawa and
colleagues published their study in Molecular Phylogenetics and Evolution (How
stable is the ... Both SAI-1 and RanaCR1 sequences support the sister group
relationship of R. perezi and R. saharica, which are placed in the phylogenetic
tree at a basal ...

Author:

Publisher: ScholarlyEditions

ISBN: 9781464963490

Category: Science

Page: 3330

View: 826

Issues in Life Sciences: Molecular Biology / 2011 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Life Sciences—Molecular Biology. The editors have built Issues in Life Sciences: Molecular Biology: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Life Sciences—Molecular Biology in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Issues in Life Sciences: Molecular Biology: 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.
Categories: Science

Molecular Phylogeny of Microorganisms

Molecular Phylogeny of Microorganisms

An introduction to molecular phylogeny, this text provides an overview of the diversity, systematics and nomenclature of microbes in many branches of biological science.

Author: Aharon Oren

Publisher: Horizon Scientific Press

ISBN: 9781904455677

Category: Science

Page: 220

View: 849

An introduction to molecular phylogeny, this text provides an overview of the diversity, systematics and nomenclature of microbes in many branches of biological science.
Categories: Science

Proceedings

Proceedings

Chicago , IL : The University of Chicago Press . Paradis , E. et al . 2006 APE :
analyses of phylogenetics and evolution . R package , version 1.8-5 . Partridge ,
L. 1988 Lifetime reproductive success in Drosophila . In Reproductive success (
ed .

Author:

Publisher:

ISBN: UCSD:31822020762605

Category: Biology

Page:

View: 419

Categories: Biology

Molecular Systematics of Plants II

Molecular Systematics of Plants II

In Molecular Ecology and Evolution: Approaches and Applications, eds. B.
Schierwater ... Use of random PCR (RAPD) technology to analyze phylogenetic
relationships in the Lolium/Festuca complex. ... Swerdlow, H., and R. Gesteland.
1990.

Author: Pamela Soltis

Publisher: Springer Science & Business Media

ISBN: 9781461554196

Category: Science

Page: 574

View: 957

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.
Categories: Science

Molecular Approaches To Ecology And Evolution

Molecular Approaches To Ecology And Evolution

R. deSalle, Bernd Schierwater. Nixon , K. C. ... Nixon , K. C. and Davis , J. I. (
1991 ) Polymorphic taxa , missing values and cladistic analysis . ... The Origin of
Biodiversity in Insects : Phylogenetic tests of Evolutionary Scenarios , Mem . Mus
.

Author: R. deSalle

Publisher: Springer Science & Business Media

ISBN: 3764357258

Category: Medical

Page: 364

View: 782

Four years ago we edited a volume of 36 papers entitled Molecular Approaches to Ecology and Evolution (Schierwater et ai. , 1994), in which we attempted to put to gether a diverse array of papers that demonstrated the impact that the technologi cal revolution ofmolecular biology has had on the field ofevolutionary biologyand ecology. The present volume borrows from that theme but attempts to focus more sharply on the impact that molecular biology has had on our understanding of dif ferent hierarchical levels important in evolutionary and ecological studies. Because DNA sequence variation is at the heart ofeverypaper in the present volume, we feel it necessary to examine how DNA has affected study at various levels of biological organization. The majority of the chapters in the present volume follow themes es tablished in the earlier volume; all chapters by authors in the previous volume are either fully updated or entirely new and expand into areas that we felt were impor tant for a more complete understanding of the impact of DNA technology on ecol ogy and evolution. The collection of papers in this volume cover a diverse array of ecological and evolutionary questions and demonstrates the breadth of coverage molecular tech nology has imparted on modern evolutionary biology. There are also a broad range of hierarchical questions approached by the 17 papers in this volume.
Categories: Medical

Genetics and Evolution of Infectious Diseases

Genetics and Evolution of Infectious Diseases

The role of models in reconstructing evolutionary trees. In: Scotland, R.W. ...
Peplies, J., Kottmann, R., Ludwig, W., Glo ̈ckner, F.O., 2008. A standard
operating ... Cladistic methods in textual, linguistic, and phylogenetic analysis.
Syst. Biol.

Author: Michel Tibayrenc

Publisher: Elsevier

ISBN: 0123848903

Category: Medical

Page: 749

View: 674

This multidisciplinary book is at the crossroads between two major scientific fields of the 21st century: evolutionary biology and infectious diseases. The genomic revolution has upset modern biology and has revolutionized our approach to ancient disciplines such as evolutionary studies. In particular, this revolution is profoundly changing our view on genetically driven human phenotypic diversity, and this is especially true in disease genetic susceptibility. Infectious diseases are indisputably the major challenge of medicine. When looking globally, they are the number one killer of humans and therefore the main selective pressure exerted on our species. Even in industrial countries, infectious diseases are now far less under control than 20 years ago. The first part of this book covers the main features and applications of modern technologies in the study of infectious diseases. The second part provides detailed information on a number of the key infectious diseases such as malaria, SARS, avian flu, HIV, tuberculosis, nosocomial infections and a few other pathogens that will be taken as examples to illustrate the power of modern technologies and the value of evolutionary approaches. Takes an integrated approach to infectious diseases Includes contributions from leading authorities Provides the latest developments in the field
Categories: Medical

Animal Evolution

Animal Evolution

Helaers, R., Tzika, A.C., van de Peer, Y., and Milinkovitch, M. (2008) MANTIS, a
phylogenetic framework for multi-species genome comparisons. ... Hendy, M.D.
and Penny, D. (1989) A framework for the quantitative study of evolutionary trees.

Author: Maximilian J. Telford

Publisher: Oxford University Press

ISBN: 9780199549429

Category: Language Arts & Disciplines

Page: 245

View: 747

Describing and understanding the evolution of the diversity of bodyplans is a major goal of evolutionary biology. Taking a modern, integrated approach to this question, a group of leading researchers describe how modern techniques and disciplines have been combined, resulting in a dramatic renaissance in the study of animal evolution.
Categories: Language Arts & Disciplines

Population Genomics with R

Population Genomics with R

10.1.2 for an application in the analysis of selection) as well as a complete set of
tools to handle and analyze phylogenetic networks [reviewed in 124, 192].
Phylogenetic trees are appropriate to study evolution over long times (i.e., when
the ...

Author: Emmanuel Paradis

Publisher: CRC Press

ISBN: 9780429882432

Category: Mathematics

Page: 378

View: 775

Population Genomics With R presents a multidisciplinary approach to the analysis of population genomics. The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. Several dozen R packages are examined and integrated to provide a coherent software environment with a wide range of computational, statistical, and graphical tools. Small examples are used to illustrate the basics and published data are used as case studies. Readers are expected to have a basic knowledge of biology, genetics, and statistical inference methods. Graduate students and post-doctorate researchers will find resources to analyze their population genetic and genomic data as well as help them design new studies. The first four chapters review the basics of population genomics, data acquisition, and the use of R to store and manipulate genomic data. Chapter 5 treats the exploration of genomic data, an important issue when analysing large data sets. The other five chapters cover linkage disequilibrium, population genomic structure, geographical structure, past demographic events, and natural selection. These chapters include supervised and unsupervised methods, admixture analysis, an in-depth treatment of multivariate methods, and advice on how to handle GIS data. The analysis of natural selection, a traditional issue in evolutionary biology, has known a revival with modern population genomic data. All chapters include exercises. Supplemental materials are available on-line (http://ape-package.ird.fr/PGR.html).
Categories: Mathematics

Evolutionary History of the Marsupials and an Analysis of Osteological Characters

Evolutionary History of the Marsupials and an Analysis of Osteological Characters

"This book is the only single-authored, comprehensive volume on the history of marsupials which deals with both the living and extinct groups, and will interest all paleontologists and biologists concerned with mammalian evolution.

Author: Frederick S. Szalay

Publisher: Cambridge University Press

ISBN: 0521441692

Category: Science

Page: 481

View: 531

"This book is the only single-authored, comprehensive volume on the history of marsupials which deals with both the living and extinct groups, and will interest all paleontologists and biologists concerned with mammalian evolution."--BOOK JACKET.
Categories: Science

Species Concepts and Phylogenetic Theory

Species Concepts and Phylogenetic Theory

Phylogenetics. The Theory and Practice of Phylogenetic Systematics. New York:
Wiley-Interscience. Wiley, E. O. 1981b. ... A study of the evolutionary relationships
of Fundulus topminnows (Teleostei: Fundulidae ). ... Willmann, R. 1981.

Author: Quentin D. Wheeler

Publisher: Columbia University Press

ISBN: 9780231506625

Category: Science

Page: 256

View: 656

No question in theoretical biology has been more perennially controversial or perplexing than "What is a species?" Recent advances in phylogenetic theory have called into question traditional views of species and spawned many concepts that are currently competing for general acceptance. Once the subject of esoteric intellectual exercises, the "species problem" has emerged as a critically important aspect of global environmental concerns. Completion of an inventory of biodiversity, success in conservation, predictive knowledge about life on earth, management of material resources, formulation of scientifically credible public policy and law, and more depend upon our adoption of the "right" species concept. Quentin D. Wheeler and Rudolf Meier present a debate among top systematic biology theorists to consider the strengths and weaknesses of five competing concepts. Debaters include (1) Ernst Mayr (Biological Species Concept), (2) Rudolf Meier and Rainer Willmann (Hennigian species concept), (3) Brent Mishler and Edward Theriot (one version of the Phylogenetic Species Concept), (4) Quentin Wheeler and Norman Platnick (a competing version of the Phylogenetic Species Concept), and (5) E. O. Wiley and Richard Mayden (the Evolutionary Species Concept). Each author or pair of authors contributes three essays to the debate: first, a position paper with an opening argument for their respective concept of species; second, a counterpoint view of the weakness of competing concepts; and, finally, a rebuttal of the attacks made by other authors. This unique and lively debate format makes the comparative advantages and disadvantages of competing species concepts clear and accessible in a single book for the first time, bringing to light numerous controversies in phylogenetic theory, taxonomy, and philosophy of science that are important to a wide audience. Species Concepts and Phylogenetic Theory will meet a need among scientists, conservationists, policy-makers, and students of biology for an explicit, critical evaluation of a large and complex literature on species. An important reference for professionals, the book will prove especially useful in classrooms and discussion groups where students may find a concise, lucid entrée to one of the most complex questions facing science and society.
Categories: Science