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: 390

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

Biotic Evolution and Environmental Change in Southeast Asia

Biotic Evolution and Environmental Change in Southeast Asia

Paralogy in cladistic biogeography and analysis ofparalogy-free subtrees.
American Museum Novitates, 3167, 1-58. Paradis, E. (2004). APE: analyses of
phylogenetics and evolution in R language. Bioinformatics, 20, 289-90. Pfeil,
B. E. and ...

Author: David Gower

Publisher: Cambridge University Press

ISBN: 9781107001305

Category: Nature

Page: 475

View: 125

Authoritative reviews and focused case studies on the history and future of the fauna and flora of Southeast Asia.
Categories: Nature

Ecological Statistics

Ecological Statistics

Contemporary theory and application Gordon A. Fox, Simoneta Negrete-
Yankelevich, Vinicio J. Sosa ... Evolutionary Inferences from Phylogenies: A
Review of Methods. Annual ... Analysis of Phylogenetics and Evolution with R,
2nd ed.

Author: Gordon A. Fox

Publisher: OUP Oxford

ISBN: 9780191652882

Category: Science

Page: 400

View: 636

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: 369

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

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: 347

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

Scales and Hierarchies

Scales and Hierarchies

A Cross-Disciplinary Perspective Ina Bornkessel-Schlesewsky, Andrej
Malchukov, Marc D. Richards. package. Paradis, E., J. Claude, and K. Strimmer.
2004. APE: analyses of phylogenetics and evolution in R language.
Bioinformatics 20: ...

Author: Ina Bornkessel-Schlesewsky

Publisher: Walter de Gruyter GmbH & Co KG

ISBN: 9783110395006

Category: Language Arts & Disciplines

Page: 361

View: 223

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: 486

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

4: 11–17. Nagl, S., H. Tichy, W. E. Mayer, N. Takahata and J. Klein. (1998)
Persistence of neutral polymorphisms in ... 133–147, Oxford University Press,
Oxford, U.K. Nei, M. (1996) Phylogenetic analysis in molecular evolutionary
genetics.

Author: Masatoshi Nei

Publisher: Oxford University Press

ISBN: 0195350510

Category: Science

Page: 352

View: 806

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

Bioinformatics and Phylogenetics

Bioinformatics and Phylogenetics

HPC Wire 9, 47 (2000) 6. Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu,
C.H., Xie, D., Suchard, M.A., Rambaut, A., Drummond, A.J.: BEAST2: a software
platform for Bayesian evolutionary analysis. PLOS Comput. Biol. 10(4), 1–6 ...

Author: Tandy Warnow

Publisher: Springer

ISBN: 9783030108373

Category: Computers

Page: 410

View: 180

This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.
Categories: Computers

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: 120

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

Issues in Life Sciences Molecular Biology 2011 Edition

Issues in Life Sciences  Molecular Biology  2011 Edition

... their study in Molecular Phylogenetics and Evolution (How stable is the “
Polyphyly of Lice” hypothesis (Insecta: Psocodea)?: a comparison of
phylogenetic signal in multiple genes Molecular Phylogenetics and Evolution,
2010;55(3):939-51).

Author:

Publisher: ScholarlyEditions

ISBN: 9781464963490

Category: Science

Page: 3330

View: 709

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

Natural History and Applied Ecology of Carabid Beetles

Natural History and Applied Ecology of Carabid Beetles

Cavalli - Sforza , L . L . & Edwards , A . W . F . 1967 : Phylogenetics analysis :
models and estimation procedures .American Journal of Human Genetics ...
Molecular Phylogenetics and Evolution 4 : 433 - 477 . Estoup , A . , Solignac , M .
, Harry ...

Author: Pietro Brandmayr

Publisher: Pensoft Publishers

ISBN: 9546421006

Category: Science

Page: 304

View: 976

Categories: Science

The Evolutionary Biology of Flies

The Evolutionary Biology of Flies

Fossil history and the evolution of hexapod structures. In CSIRO,The Insects of
Australia, pp. 141–179. Carlton: Melbourne University Press. Laamanen, T. R., R.
Meier, M. A. Miller, A. Hille, and B. M. Wiegmann. 2005. Phylogenetic analysis of
 ...

Author: David K. Yeates

Publisher: Columbia University Press

ISBN: 9780231501705

Category: Science

Page: 440

View: 815

Flies (Dipteria) have had an important role in deepening scientists'understanding of modern biology and evolution. The study of flies has figured prominently in major advances in the fields of molecular evolution, physiology, genetics, phylogenetics, and ecology over the last century. This volume, with contributions from top scientists and scholars in the field, brings together diverse aspects of research and will be essential reading for entomologists and fly researchers.
Categories: Science

Evolution of the Vertebrate Auditory System

Evolution of the Vertebrate Auditory System

With this background information , the reader should be better able to fit the
themes being discussed into their relevant place in the context of vertebrates as a
whole . 1. The Phylogenetic Framework No evolutionary analysis can take place
 ...

Author: Geoffrey A. Manley

Publisher: Springer Science & Business Media

ISBN: 038721089X

Category: Science

Page: 416

View: 756

The function of vertebrate hearing is served by a surprising variety of sensory structures in the different groups of fish, amphibians, reptiles, birds, and mammals. This book discusses the origin, specialization, and functional properties of sensory hair cells, beginning with environmental constraints on acoustic systems and addressing in detail the evolutionary history behind modern structure and function in the vertebrate ear. Taking a comparative approach, chapters are devoted to each of the vertebrate groups, outlining the transition to land existence and the further parallel and independent adaptations of amniotic groups living in air. The volume explores in depth the specific properties of hair cells that allowed them to become sensitive to sound and capable of analyzing sounds into their respective frequency components. Evolution of the Vertebrate Auditory System is directed to a broad audience of biologists and clinicians, from the level of advanced undergraduate students to professionals interested in learning more about the evolution, structure, and function of the ear.
Categories: Science

Contributions Celebrating Kumar Krishna

Contributions Celebrating Kumar Krishna

Constantino R (1997) Morphology of the digestive tube ofMacuxiterrnes and its
phylogenetic significance (Isoptera: ... P (2007) A comprehensive phylogenetic
analysis of termites (Isoptera) illuminates key aspects of their evolutionary
biology.

Author: Michael S. Engel

Publisher: PenSoft Publishers LTD

ISBN: 9789546426178

Category: Science

Page: 332

View: 223

The present issue of ZooKeys comprises a series of papers honoring Prof. Kumar Krishna, the leading au-thority on the systematics and biology of termites (Isoptera). After becoming exposed to termite systematics under the tutelage of Mittan L. Roonwal in India, Kumar received his doctoral training from the legendary termite systematist and evolutionary biologist Alfred E. Emerson at the University of Chicago. Subsequently, Kumar moved to the City University of New York and the American Museum of Natural History from where, even today, he has produced some of the most important contributions to the study of termites, most notably his two-volume set, Biology of Termites (1969?1970, Academic Press), and the forthcoming monumental Treatise on the Isoptera of the World (AMNH). Herein colleagues and friends recognize his lifetime of accomplishments in biological systematics by presenting original papers on insect lineages as diverse as termites and grasshoppers, and flies and bees, among others. A brief biographical account and list of his publications to date are provided.
Categories: Science

Flukes and Snails Revisited

Flukes and Snails Revisited

Privatety published in Danish with English summary ) . JOLLY ... Molecular
Phylogenetics and Evolution 4 , 314-330 . ... RNAdraw : an integrated program
for RNA secondary structure calculation and analysis under 32 - bit Microsoft
Windows .

Author: D. Rollinson

Publisher: Cambridge University Press

ISBN: 052189106X

Category: Science

Page: 304

View: 131

Summarises the current state of various studies investigating snail-parasite relationships.
Categories: Science

Molecular Approaches To Ecology And Evolution

Molecular Approaches To Ecology And Evolution

Nixon , K. C. and Carpenter , J. M. ( 1996a ) On simultaneous analysis . ... Nixon ,
K. C. and Davis , J. I. ( 1991 ) Polymorphic taxa , missing values and cladistic
analysis . ... Wenzel , J. W. ( 1997 ) When is a phylogenetic test good enough ?

Author: R. deSalle

Publisher: Springer Science & Business Media

ISBN: 3764357258

Category: Medical

Page: 364

View: 753

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

Functional and Phylogenetic Ecology in R

Functional and Phylogenetic Ecology in R

This book presents a unique approach through its focus on ecological analyses and not macroevolutionary analyses.

Author: Nathan G. Swenson

Publisher: Springer Science & Business Media

ISBN: 9781461495420

Category: Computers

Page: 212

View: 493

Functional and Phylogenetic Ecology in R is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a unique approach through its focus on ecological analyses and not macroevolutionary analyses. The author provides his own code, so that the reader is guided through the computational steps to calculate the desired metrics. This guided approach simplifies the work of determining which package to use for any given analysis. Example datasets are shared to help readers practice, and readers can then quickly turn to their own datasets.
Categories: Computers

Species Concepts and Phylogenetic Theory

Species Concepts and Phylogenetic Theory

In: I. Cracraft and N. Eldredge, eds. Phylogenetic Analysis and Paleontology, pp.
211—225. New York: Columbia University Press. Wiley, E. O. 1980a. Is the
evolutionary species fictionP—A consideration of classes, individuals and
historical ...

Author: Quentin D. Wheeler

Publisher: Columbia University Press

ISBN: 9780231506625

Category: Science

Page: 256

View: 915

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

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

The widely used phylogenetic generalised least square (PGLS) can be seen as a
special case of PGLMM. ... (2) phylogenetic meta-analysis, (3) non-Gaussian
traits analysis, and (4) missing values and data augmentation. ... Modern
Phylogenetic Comparative Methods and Their Application in Evolutionary
Biology, DOI: ...

Author: László Zsolt Garamszegi

Publisher: Springer

ISBN: 9783662435502

Category: Science

Page: 552

View: 898

Phylogenetic comparative approaches are powerful analytical tools for making evolutionary inferences from interspecific data and phylogenies. The phylogenetic toolkit available to evolutionary biologists is currently growing at an incredible speed, but most methodological papers are published in the specialized statistical literature and many are incomprehensible for the user community. This textbook provides an overview of several newly developed phylogenetic comparative methods that allow to investigate a broad array of questions on how phenotypic characters evolve along the branches of phylogeny and how such mechanisms shape complex animal communities and interspecific interactions. The individual chapters were written by the leading experts in the field and using a language that is accessible for practicing evolutionary biologists. The authors carefully explain the philosophy behind different methodologies and provide pointers – mostly using a dynamically developing online interface – on how these methods can be implemented in practice. These “conceptual” and “practical” materials are essential for expanding the qualification of both students and scientists, but also offer a valuable resource for educators. Another value of the book are the accompanying online resources (available at: http://www.mpcm-evolution.com), where the authors post and permanently update practical materials to help embed methods into practice.
Categories: Science