Analysis of Phylogenetics and Evolution with R

Analysis. of. Macroevolution. with. Phylogenies. Reconstructing the history of
species is a necessary step in understanding the mechanisms of biological
evolution. Once a phylogeny has been estimated, a lot of questions on how
species have ...

Analysis of Phylogenetics and Evolution with R

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 1461417430

Page: 386

View: 633

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.

Phylogenetic Ecology

“Evidence for a time-integrated species-area effect on the latitudinal gradient in
tree diversity.” American ... Evolution 14:64–81. Fitch, W. M. 1977. ... risk analysis:
phylogenetic signal as a predictor of host range of plant pests and pathogens.

Phylogenetic Ecology

Author: Nathan G. Swenson

Publisher:

ISBN: 022667150X

Page: 240

View: 691

Over the past decade, ecologists have increasingly embraced phylogenetics, the study of evolutionary relationships among species. As a result, they have come to discover the field's power to illuminate present ecological patterns and processes. Ecologists are now investigating whether phylogenetic diversity is a better measure of ecosystem health than more traditional metrics like species diversity, whether it can predict the future structure and function of communities and ecosystems, and whether conservationists might prioritize it when formulating conservation plans. In Phylogenetic Ecology, Nathan G. Swenson synthesizes this nascent field's major conceptual, methodological, and empirical developments to provide students and practicing ecologists with a foundational overview. Along the way, he highlights those realms of phylogenetic ecology that will likely increase in relevance--such as the burgeoning subfield of phylogenomics--and shows how ecologists might lean on these new perspectives to inform their research programs.

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.

Ecological Statistics

Author: Gordon A. Fox

Publisher: OUP Oxford

ISBN: 0191652881

Page: 400

View: 532

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.

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 ...

Methods in Comparative Plant Population Ecology

Author: David Gibson

Publisher: Oxford University Press, USA

ISBN: 0199671478

Page: 320

View: 170

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.

Proceedings

Akaike's information criterion ( AIC ) values and Akaike weights ( w ; ) for the 12
simple statistical and evolutionary ... The PGLS approach was implemented in R (
Ihaka & Gentleman 1996 ) using the Analysis of Phylogenetics and Evolution ...

Proceedings

Author:

Publisher:

ISBN:

Page:

View: 840

Cumulated Index Medicus

Molecular evolutionary analyses of nuclear - encoded small 19 ( 1 ) : 7-15
Genetics 1995 Feb ; 139 ( 2 ) : 975-92 subunit ... FEBS Lett 1995 Mar 13 ; 361 ( 1
) : 17-21 Site of synthesis and phylogenetic distribution of a whitefly - transmitted
 ...

Cumulated Index Medicus

Author:

Publisher:

ISBN:

Page:

View: 488

Scientific and Technical Aerospace Reports

Laboratory mutants constitute a system of 60 stable and genetically determined
species . ... which have experienced a phylogenetic evolution to overcome the
effects of gravity , was studied to analyze the long term effects of weightlessness
 ...

Scientific and Technical Aerospace Reports

Author:

Publisher:

ISBN:

Page:

View: 310

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.

Metabolic Ecology

Author: Richard M. Sibly

Publisher: John Wiley & Sons

ISBN: 1119968518

Page: 256

View: 614

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.

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.

Molecular Evolution and Phylogenetics

Author: Masatoshi Nei

Publisher: Oxford University Press

ISBN: 9780195350517

Page: 352

View: 205

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.

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.

Animal Evolution

Author: Maximilian J. Telford

Publisher: Oxford University Press

ISBN: 0199549427

Page: 245

View: 539

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.

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).

Issues in Life Sciences  Molecular Biology  2011 Edition

Author:

Publisher: ScholarlyEditions

ISBN: 1464963495

Page: 3330

View: 889

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/.

Evolutionary Analysis

The evolution of human bipedality : Ecology and functional morphology . Journal
of ... Borowik , O . A . 1995 Coding chromosomal data for phylogenetic analysis :
Phylogenetic resolution of the Pan - Homo - Gorilla trichotomy . Systematic ...

Evolutionary Analysis

Author: Scott Freeman

Publisher:

ISBN:

Page: 704

View: 883

Designed to help readers learn how to "think" like evolutionary biologists, this 4-color book approaches evolutionary biology as a dynamic field of inquiry and as a "process." Using a theme-based approach, it illustrates the interplay between theory, observation, testing and interpretation. It offers commentary on strengths and weaknesses of data sets, gives detailed examples rather than a broad synoptic approach, includes many data graphics and boxes regarding both sides of controversies. Introduces each major organizing theme in evolution through a question--e.g., How has HIV become drug resistant? Why did the dinosaurs, after dominating the land vertebrates for 150 million years, suddenly go extinct? Are humans more closely related to gorillas or to chimpanzees? Focuses on many applied, reader-relevant topics--e.g., evolution and human health, the evolution of senescence, sexual selection, social behavior, eugenics, and biodiversity and conservation. Then develops the strategies that evolutionary biologists use for finding an answers to such questions. Then considers the observations and experiments that test the predictions made by competing hypotheses, and discusses how the data are interpreted. For anyone interested in human evolution, including those working in human and animal health care, environmental management and conservation, primary and secondary education, science journalism, and biological and medical research.

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
 ...

The Evolutionary Biology of Flies

Author: David K. Yeates

Publisher: Columbia University Press

ISBN: 0231501706

Page: 440

View: 380

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.

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
 ...

Evolution of the Vertebrate Auditory System

Author: Geoffrey A. Manley

Publisher: Springer Science & Business Media

ISBN: 9780387210896

Page: 416

View: 464

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.

Systematics Evolution and Biogeography of Compositae

Erythroseris , a new genus and the previously unknown sister group of Cichorium
( Cichorieae subtribe Cichoriinae ) . Willdenowia ... Phylogenetic and
evolutionary implications of interspecific chloroplast DNA variation in Krigia (
Asteraceae : Lactuceae ) . ... Phylogenetic analysis of chloroplast matk gene and
ITS of nrDNA sequences reveals polyphyly of the genus Sonchus ( Asteraceae :
Cichorieae ) .

Systematics  Evolution  and Biogeography of Compositae

Author: Vicki A. Funk

Publisher:

ISBN:

Page: 965

View: 265

"This spectacular book does full justice to the Compositae (Asteraceae), the largest and most successful flowering plant family with some 1700 genera and 24,000 species. It is an indispensable reference, providing the most up-to-date hypotheses of phylogenetic relationships in the family based on molecular and morphological characters, along with the corresponding subfamilial and tribal classification. The 2009 work not only integrates the extensive molecular phylogenetic analyses conducted in the last 25 years, but also uses these to produce a metatree for about 900 taxa of Compositae. The book contains 44 chapters, contributed by 80 authors, covering the history, economic importance, character variation, and systematic and phylogenetic diversity of the family. The emphasis of this work is phylogenetic; its chapters provide a detailed, current, and thoroughly documented presentation of the major (and not so major) clades in the family, citing some 2632 references. Like the Compositae, the book is massive, diverse, and fascinating. It is beautifully illustrated, with 170 figures, and an additional 108 cladograms (all consistently color-coded, based on the geographic range of the included taxa); within these figures are displayed 443 color photographs, clearly demonstrating the amazing array of floral and vegetative form expressed by members of the clade." --NHBS Environment Bookstore.

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 .

Flukes and Snails Revisited

Author: D. Rollinson

Publisher: Cambridge University Press

ISBN: 9780521891066

Page: 304

View: 877

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

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 ?

Molecular Approaches To Ecology And Evolution

Author: R. deSalle

Publisher: Springer Science & Business Media

ISBN: 9783764357252

Page: 364

View: 955

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.

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 ...

Species Concepts and Phylogenetic Theory

Author: Quentin D. Wheeler

Publisher: Columbia University Press

ISBN: 0231506627

Page: 256

View: 667

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.