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Author : Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey
Publisher : Cambridge University Press
Page : 750 pages
File Size : 48,8 Mb
Release : 2009-03-26
Category : Science
ISBN : 9780521877107
A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.
Author : Marco Salemi,Anne-Mieke Vandamme
Publisher : Cambridge University Press
Page : 456 pages
File Size : 54,7 Mb
Release : 2003-08-27
Category : Computers
ISBN : 052180390X
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Author : Roderick D.M. Page,Edward C. Holmes
Publisher : John Wiley & Sons
Page : 352 pages
File Size : 48,5 Mb
Release : 2009-07-14
Category : Science
ISBN : 9781444313369
The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.
Author : Barry G. Hall
Publisher : Unknown
Page : 221 pages
File Size : 44,5 Mb
Release : 2004
Category : Phylogeny
ISBN : 0878933123
Author : E. O. Wiley,Bruce S. Lieberman
Publisher : John Wiley & Sons
Page : 444 pages
File Size : 45,7 Mb
Release : 2011-06-07
Category : Science
ISBN : 9780470905968
The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.
Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
Page : 221 pages
File Size : 53,5 Mb
Release : 2006-11-25
Category : Science
ISBN : 9780387351001
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.
Author : Francesco de Bello,Carlos P. Carmona,André T. C. Dias,Lars Götzenberger,Marco Moretti,Matty P. Berg
Publisher : Cambridge University Press
Page : 311 pages
File Size : 47,6 Mb
Release : 2021-03-11
Category : Nature
ISBN : 9781108472913
Trait-based ecology is rapidly expanding. This comprehensive and accessible guide covers the main concepts and tools in functional ecology.
Author : Trevor R. Hodkinson,John A.N. Parnell
Publisher : CRC Press
Page : 374 pages
File Size : 48,9 Mb
Release : 2006-12-26
Category : Mathematics
ISBN : 9781420009538
To document the world's diversity of species and reconstruct the tree of life we need to undertake some simple but mountainous tasks. Most importantly, we need to tackle species rich groups. We need to collect, name, and classify them, and then position them on the tree of life. We need to do this systematically across all groups of organisms and b
Author : Olivier Rieppel
Publisher : CRC Press
Page : 514 pages
File Size : 43,6 Mb
Release : 2016-07-06
Category : Nature
ISBN : 9781138032156
Phylogenetic Systematics: Haeckel to Hennig traces the development of phylogenetic systematics against the foil of idealistic morphology through 100 years of German biology. It starts with the iconic Ernst Haeckel-the German Darwin from Jena-and the evolutionary morphology he developed. It ends with Willi Hennig, the founder of modern phylogenetic
Author : Philippe Lemey,Marco Salemi,Anne-Mieke Vandamme
Publisher : Cambridge University Press
Page : 763 pages
File Size : 43,7 Mb
Release : 2009-03-26
Category : Science
ISBN : 9781139478618
The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including BLAST, FastA, Clustal, T-coffee, Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL, ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC, SplitsTree, and RDP. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students.
Author : Masatoshi Nei,Sudhir Kumar
Publisher : Oxford University Press
Page : 352 pages
File Size : 40,9 Mb
Release : 2000-07-27
Category : Science
ISBN : 9780199881222
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.
Author : Tandy Warnow
Publisher : Cambridge University Press
Page : 399 pages
File Size : 53,9 Mb
Release : 2017-11-02
Category : Computers
ISBN : 9781107184718
This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.
Author : Ziheng Yang
Publisher : Oxford University Press
Page : 374 pages
File Size : 42,8 Mb
Release : 2006-10-05
Category : Medical
ISBN : 9780198566991
This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.
Author : Alexei J. Drummond,Remco R. Bouckaert
Publisher : Cambridge University Press
Page : 263 pages
File Size : 46,5 Mb
Release : 2015-08-06
Category : Computers
ISBN : 9781107019652
Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.
Author : Liam J. Revell,Luke J. Harmon
Publisher : Princeton University Press
Page : 441 pages
File Size : 47,9 Mb
Release : 2022-07-12
Category : Science
ISBN : 9780691219042
An authoritative introduction to the latest comparative methods in evolutionary biology Phylogenetic comparative methods are a suite of statistical approaches that enable biologists to analyze and better understand the evolutionary tree of life, and shed vital new light on patterns of divergence and common ancestry among all species on Earth. This textbook shows how to carry out phylogenetic comparative analyses in the R statistical computing environment. Liam Revell and Luke Harmon provide an incisive conceptual overview of each method along with worked examples using real data and challenge problems that encourage students to learn by doing. By working through this book, students will gain a solid foundation in these methods and develop the skills they need to interpret patterns in the tree of life. Covers every major method of modern phylogenetic comparative analysis in R Explains the basics of R and discusses topics such as trait evolution, diversification, trait-dependent diversification, biogeography, and visualization Features a wealth of exercises and challenge problems Serves as an invaluable resource for students and researchers, with applications in ecology, evolution, anthropology, disease transmission, conservation biology, and a host of other areas Written by two of today’s leading developers of phylogenetic comparative methods
