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: 923

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

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: 927

Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.
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: 853

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

PHYLOGENETIC ANALYSIS MORPHOLO

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
 ...

Author: WIENS JOHN J

Publisher: Smithsonian

ISBN: 156098841X

Category: Morphology

Page: 220

View: 457

Categories: Morphology

Insect Systematics Evolution

Insect Systematics   Evolution

Birkhauser Verlag , Basel . Baker , R. H. , Yu , X. & DeSalle , R. ( 1998 )
Assessing the relative contribution of molecular and morphological characters in
simultaneous analysis trees . Molecular Phylogenetics and Evolution 9 : 427-436
.

Author:

Publisher:

ISBN: MINN:31951P01040046N

Category: Electronic journals

Page:

View: 168

An international journal of systematic entomology.
Categories: Electronic journals

Proceedings

Proceedings

( doi : 10.2307 / 2407408 ) Herron , M. D. , Castoe , T. A. & Parkinson , C. L. 2004
Sciurid phylogeny and the paraphyly of ... Rhein , R. , Dutheil , J. , Noel , Y. &
Bolker , B. 2005 APE : analyses of phylogenetics and evolution , R package v .
1.6 .

Author:

Publisher:

ISBN: UCSD:31822020764056

Category: Biology

Page:

View: 354

Categories: Biology

Australian Journal of Zoology

Australian Journal of Zoology

Macey , J . R . , and Verma , A . ( 1997 ) . Homology in phylogenetic analysis :
alignment of transfer RNA genes and the phylogenetic position of snakes .
Molecular Phylogenetics and Evolution 7 , 272 – 279 . doi : 10 . 1006 / mpev .
1997 .

Author:

Publisher:

ISBN: UOM:39015068696643

Category: Zoology

Page:

View: 736

Categories: Zoology

Herpetology

Herpetology

The value of the M . Depressor Mandibulae in phylogenetic hypotheses for
Eleutherodactylus and its allies ( Amphibia : Leptodactylidae ) . ... The
Behavioural Ecology of Humans and Other Mammals , edited by V . Standen and
R . A . Foley . ... Molecular phylogenetics , tRNA evolution , and historical
biogeography in anguid lizards and related taxonomic families . ... An integrative
analysis of phylogenetic relationships among newts of the genus Triturus ( family
Salamandridae ) , using ...

Author: F. Harvey Pough

Publisher: Pearson Education / Prentice Hall

ISBN: UOM:49015003470003

Category: Science

Page: 726

View: 927

For upper-level undergraduate courses in herpetology, this text emphasizes the integration of information to produce a picture of amphibians and their roles in ecosystems.
Categories: Science

Cichlid Research

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 ...

Author:

Publisher:

ISBN: UOM:39015051616681

Category: Cichlids

Page: 392

View: 834

Categories: Cichlids

Telopea

Telopea

Molecular Phylogenetics and Evolution 5 : 352 - 358 . ... Ellis , R . P . ( 1987 ) A
review of comparative leaf blade anatomy in the systematics of the Poaceae : the
past twenty - five years . ... Systematics of Gramineae : a cluster analysis study .

Author:

Publisher:

ISBN: CORNELL:31924084838758

Category: Botany

Page:

View: 944

Categories: Botany

Malacologia

Malacologia

Molecular Phylogenetics and Evolution , 22 : 399LITERATURE CITED ... W . E .
HOLZNAGEL , M . N . SCHNARE & R . R . GUTELL , 2000 , Phylogenetic
analysis of molluscan mitochondrial LSU rDNA sequences and secondary
structures .

Author:

Publisher:

ISBN: UVA:X006139355

Category: Mollusks

Page:

View: 962

Categories: Mollusks

D Elmo Hardy Memorial Volume

D  Elmo Hardy Memorial Volume

In : Molecular systematics and evolution : theory and practice ( DeSalle , R. ,
Giribet , G. & Wheeler , W. , eds . ) . Birkhauser ... Phylogeny of Drosophilidae (
Diptera ) , with comments on combined analysis and character support .
Molecular ...

Author: G. Allan Samuelson

Publisher:

ISBN: STANFORD:36105114400448

Category: Curculionidae

Page: 107

View: 238

Categories: Curculionidae

Major Transitions in Vertebrate Evolution

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 .

Author: Jason S. Anderson

Publisher: Life of the Past

ISBN: UOM:39015066901607

Category: Science

Page: 417

View: 161

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.
Categories: Science

Phylogeny and Classification of Neotropical Fishes

Phylogeny and Classification of Neotropical Fishes

Neotropical ichthyology: an overview; Fossils and geological evidence; The stage for neotropical fish diversification: a history of tropical south american rivers; The temporal context for the diversification of neotropical fishes; ...

Author: Luiz R. Malabarba

Publisher: Edipucrs

ISBN: UCSD:31822029670478

Category: Fishes

Page: 603

View: 325

Neotropical ichthyology: an overview; Fossils and geological evidence; The stage for neotropical fish diversification: a history of tropical south american rivers; The temporal context for the diversification of neotropical fishes; Phylogeny of fossil characiformes and paleobiogeography of the Tremembe formation, Sao Paulo; Brazil; Maastrichtian to early late paleocene freshwater osteichthyes of Bolivia: additions and comments; Characiformes; Higher lever phylogenetic concepts within characiforms (Ostariophysi), a historical review; Relationships of the characidiinae and phylogeny of characiform fishes (Teleostei: ostariophysi); Phylogenetic study of the hemiodontidae (Ostariophysi: characiformes); Perspectives about the phylogeny and classification of the chacidae (Teleostei: Characiformes); Relationships of the tribes and genera of the glandulocaudinae (Ostariophysi: characiformes: characidae) with a description of a New Genus, Chrysobrycon; Monophyly of the Cheirodontinae, characters and major clades (Ostariophysi: characidae); Sperm ultrastructure in characid fishes (Teleostei: ostariophysi); The genus Creagrutus (Teleostei: Characiformes: Characidae): monophyly, relationships, and undetected diversity; A phylogenetic analysis of Roestes Gunther and Gilbertolus Eigenmann, with a hypothesis on the relationships of the Cynodontidae and Acestrorhynchidae (Teleostei: Ostariophysi: Characiformes); Siluriformes; Phylogenetic relationships of neotropical siluriformes: historical overview and synthesis of hypotheses; Monophyly and interrelationships of the Centromochlinae (Siluriformes: Auchenipteridae); Systematics, biogeography, and the fossil record of the Callichthyidae: a review of the available data; Phylogenetic relationships of the Loricariidae (Siluriformes) based on mitochondrial rRNA gene sequences; Conflict and resolution: impact of new taxa on phylogenetic studies of the neotropical cascudinhos (Siluroidei: Loricariidae); Gymnotiformes; The Gymnotiform "Eels" of tropical America: a history of classification and phylogeny of the South American electric Knifefishes (Teleostei: Ostariophysi: Siluriphysi); Phylogenetic systematics of Gymnotiformes with diagnoses of 58 clades: a review of available data; The phylogenetic position of the South America Electric Fish genera Sternophygus and Archolaemus (Ostariophysi: Gymnotiformes) according to 12s and 16s mitochondrial DNA sequences; Perciformes; A phylogeny and classfication of the South American Cichlidae (Teleostei: Perciformes); Molecular phylogeny of neotropical cichlids: the relationships of Cichlasomines and heroines; Mitochondrial phylogenetics, biogeography, and evolution of parental care and mating systems in Gymnogeophagus (Perciformes: Cichlidae); Atherinomorpha; Phylogenetic systematics and historical biogeography of the neotropical silverside family Atheronopsidae (Teleostei: Atheriniformes); Phylogeny and classification of the Cyprinodontiformes (Euteleostei: Atherinomorpha): a reappraisal; Phylogeny and classification of the Anablepidae (Teleostei: Cyprinodontiformes); Cytogenetic markers; Cytogenetic markers in neotropical freshwater fishes.
Categories: Fishes

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: 482

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

Evolutionary Analysis

Evolutionary Analysis

Ribosomal RNA structure : Compensatory mutations and implications for
phylogenetic analysis . Molecular ... S . R . Palumbi . 1992 . Rates of
mitochondrial DNA evolution in sharks are slow compared with mammals .
Nature 357 : 153 – 155 .

Author: Scott Freeman

Publisher:

ISBN: UOM:39015049724803

Category: Evolution (Biology)

Page: 704

View: 698

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.
Categories: Evolution (Biology)

Philosophical Transactions of the Royal Society of London

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 ...

Author:

Publisher:

ISBN: CORNELL:31924101591349

Category: Biology

Page:

View: 845

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.
Categories: Biology

Journal of the American Statistical Association

Journal of the American Statistical Association

... and Cunningham , C . W . ( 1996 ) , “ Combining Data in Phylogenetic Analysis
, " Trends in Ecology and Evolution , 11 ... and McCabe , E . R . B . ( 2001 ) , “
Priamte DAXI , SRY , and SOX9 : Evolutionary Stratification of Sex Determination
 ...

Author: American Statistical Association

Publisher:

ISBN: UOM:39015057373519

Category: Statistics

Page:

View: 715

Categories: Statistics

Archives des sciences et compte rendu des s ances de la Soci t

Archives des sciences et compte rendu des s  ances de la Soci  t

"Calculation of evolutionary' tree-. from sequence data. ... "MacClade: Analysis of
phytogeny and character evolution. ... Inc. Nadot, S., Bittar. G.. Carter, L., Lacroix.
R. & Lfjeune. B. 1995. "A phylogenetic analyst ot monocotyledons based on the ...

Author:

Publisher:

ISBN: UCAL:B4402689

Category: Natural history

Page:

View: 419

Categories: Natural history