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 ...

Analysis of Phylogenetics and Evolution with R

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 1461417430

Page: 386

View: 306

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.

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.

Analysis of Phylogenetics and Evolution with R

Author: Alexander Lattermann

Publisher: Springer

ISBN:

Page: 200

View: 128

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.

PHYLOGENETIC ANALYSIS MORPHOLO

Maddison , W . P . , and D . R . Maddison . 1992 . MacClade : Analysis of
Phylogeny and Character Evolution . Sinauer , Sunderland , Mass . Martins , E . P
. 1996 . Conducting phylogenetic comparative studies when the phylogeny is not
 ...

PHYLOGENETIC ANALYSIS MORPHOLO

Author: WIENS JOHN J

Publisher: Smithsonian

ISBN: 9781560988410

Page: 220

View: 986

Bayesian Evolutionary Analysis with BEAST

These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics.

Bayesian Evolutionary Analysis with BEAST

Author: Alexei J. Drummond

Publisher: Cambridge University Press

ISBN: 1316298345

Page:

View: 371

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.

Australian Journal of Zoology

Ecomorphology , performance capability and scaling in West Indian Anolis : an
evolutionary analysis . ... Nature 387 , 70-72 . doi : 10.1038 / 387070a0 Losos ,
J. B. , Creer , D. A. , Glossip , D. , Goellner , R. , Hampton , A. , Roberts , G. ,
Haskell , N. ... Molecular Phylogenetics and Evolution 27 , 384–397 . doi :
10.1016 / S1055-7903 ( 02 ) 00448-7 Ricklefs , R. E. , Cochran , D. , and Pianka ,
E. R. ( 1981 ) .

Australian Journal of Zoology

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Cichlid Research

Phylogenetic study of cichlid fishes in Lake Tanganyika : a lepidological
approach . ... Lowe - McConnell , R . H . 1959 . ... Evolution of MacClade :
Analysis of Phylogeny and Character NADH dehydrogenase subunit 2 in East
African Evolution ...

Cichlid Research

Author:

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ISBN:

Page: 392

View: 561

Proceedings of the National Academy of Sciences of the United States of America

EVOLUTION Multicellularity and the functional interdependence of motility and
molecular transport. masses rather than ... As in any large phylogenetic analysis ,
there are surely uncertainties and inaccuracies in the final hypothesis of
relationships . However , it is ... The GEE comparative analysis used the
ANALYSES OF PHYLOGENETICS AND EVOLUTION package available for R (
53 ) . We thank R.

Proceedings of the National Academy of Sciences of the United States of America

Author: National Academy of Sciences (U.S.)

Publisher:

ISBN:

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Major Transitions in Vertebrate Evolution

San Mauro , D . , D . J . Gower , O . V . Oommen , M . Wilkinson , and R . Zardoya .
... Molecular Phylogenetics and Evolution 33 : 413 - 427 . ... Skeleton formation in
the Branchiosauridae : a case study in comparing ontogenetic trajectories .

Major Transitions in Vertebrate Evolution

Author: Jason S. Anderson

Publisher: Life of the Past

ISBN:

Page: 417

View: 331

New discoveries of ancient vertebrates, filling in gaps in the fossil record, are quickly eroding the traditionally recognized differences between the principal groups of vertebrates—for example, between dinosaurs and birds—and radically changing our understanding of the evolutionary history of the major group of animals to which our species belongs. This book describes this changing scientific landscape and contributes to the revolution in our knowledge of the developmental mechanisms that underlie evolutionary transformation.

Steenstrupia

Pp . 261–264 in G. Grigg , R. Shine & H. Ehmann ( eds ) : Biology of Australian
Frogs and Reptiles . ... Serological relationships of sea snakes and their
evolutionary implication . ... Inferring species trees from gene trees : a
phylogenetic analysis of the Elapidae ( Serpentes ) based on the amino acid
sequences of venom ...

Steenstrupia

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The Veliger

We also thank the following institutions ( and collections personnel ) for loaning
material utilized in this study : Academy of ... Use of formalin - preserved samples
for molecular analysis . ... Molecular Phylogenetics and Evolution 13 : 377 – 391 .
... Pp . 381 - 424 in M . F . Claridge , H . A . Dawah & and M . R . Wilson ( eds . ) ...

The Veliger

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Australian Mammalogy

Molecular Biology and Evolution 10 : 1170 - 1195 . FARRIS JS ... Phylogenetic
relationships within the class Mammalia : a study using mitochondrial 125 RNA
sequences . Journal of ... LAPOINTE FJ , KIRSCH JAW AND BLEIWEISS R ,
1994 .

Australian Mammalogy

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Philosophical Transactions of the Royal Society of London

Su , B. , Wang , Y.-X. , Lan , H. , Wang , W. & Zhang , Y.-P. 1999 Phylogenetic
study of complete cytochrome b genes in ... 1016 / j.ympev.2003.08.015 )
Whitfield , L. S. , Lovell - Badge , R. & Goodfellow , P. N. 1993 Rapid sequence
evolution of ...

Philosophical Transactions of the Royal Society of London

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Each issue of Transactions B is devoted to a specific area of the biological sciences, including clinical science. All papers are peer reviewed and edited to the highest standards. Published on the 29th of each month, Transactions B is essential reading for all biologists.

Journal of the American Statistical Association

... and Cunningham , C. W. ( 1996 ) , “ Combining Data in Phylogenetic Analysis ,
” Trends in Ecology and Evolution , 11 ... Dashwood , W. M. , Hoffmann , P. R. ,
Yin , C. , Morens , D. M. , Kaplan , A. H. , Detels , R. , and Yanagihara , R. ( 1996 )
 ...

Journal of the American Statistical Association

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Human Evolution

In Molecular Anthropology ( M . Goodman and R . E . Tashian , eds ) , pp . 321 -
353 . New York ... Molecular Phylogenetics and Evolution 9 , 585 - 598 . Goren -
Inbar , N ... Analysis of one million base pairs of Neanderthal DNA . Nature , 444
 ...

Human Evolution

Author: Camilo J. Cela-Conde

Publisher: Oxford University Press

ISBN:

Page: 437

View: 183

This book is intended as a comprehensive overview of hominid evolution, synthesising data and approaches from physical anthropology, genetics, archaeology, psychology and philosophy. Human evolution courses are now widespread and this book has the potential to satisfy the requirements of most, particularly at the advanced undergraduate and graduate level. It is based on a translation, albeit with substantial modification, of a successful Spanish language book.

Exploring Evolutionary Biology

Species concepts and speciation analysis . In Current Ornithology , vol . 1 , ed . R
. F . Johnston . Plenum . _ . In press b . The significance of phylogenetic
classifications for systematic and evolutionary biology . Proc . NATO Advanced
Study ...

Exploring Evolutionary Biology

Author: Montgomery Slatkin

Publisher: Sinauer Associates, Incorporated

ISBN:

Page: 305

View: 719

Featuring a collection of articles from American Scientist between 1983 and 1995, this book is intended to serve as supplementary reading in evolutionary biology and to introduce the reader to modern research topics in the field. The articles are by leading research scientists and illustrate the diversity of problems that evolutionary biologists encounter along the way to understanding the history of living things and the processes that govern evolutionary change.

American Journal of Botany

Chloroplast DNA variation and evolution in Pisum : patterns of change and
phylogenetic analysis . Genetics 109 : 195 – 213 . , C . R SHIELDS , D . B .
COHEN , AND T . J . ORTON . 1983a . Chloroplast DNA evolution and the origin
of ...

American Journal of Botany

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