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
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.
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
Authoritative reviews and focused case studies on the history and future of the fauna and flora of Southeast Asia.
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
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
Category: Electronic journals
An international journal of systematic entomology.
( 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 .
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 .
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
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.
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 ...
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 .
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
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 .
Combining data in phylogenetic analysis. Trends in Ecology and Evolution 11:
152-157. Jokerst, J.D. 1981. The reproductive ecology of ... Kato H., R. Terauchi,
F.H. Utech, and S. Kawano. 1995. Molecular systematics of the Trilliaceae ...
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
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.
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
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.
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
Category: Evolution (Biology)
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.
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 ...
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.
Author: American Statistical AssociationPublish On: 2003
... 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
"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 ...