Refining Phylogenetic Analyses

Author : Pablo A. Goloboff
Publisher : CRC Press
Page : 312 pages
File Size : 47,8 Mb
Release : 2022-07-22
Category : Science
ISBN : 9781000603989

Get Book

Refining Phylogenetic Analyses by Pablo A. Goloboff Pdf

This volume discusses the aspects of a phylogenetic analysis that go beyond basic calculation of most parsimonious trees. Practical application of all principles discussed is illustrated by reference to TNT, a freely available software package that can perform all the steps needed in a phylogenetic analysis. The first problem considered is how to summarize and compare multiple trees (including identification and handling wildcard taxa). Evaluation of the strength of support for groups, another critical component of any phylogenetic analysis, is given careful consideration. The different interpretations of measures of support are discussed and connected with alternative implementations. The book reviews rationales for estimating character reliability on the basis of homoplasy, with particular attention to morphological characters. The main methods for character weighting and their practical implementation, several of them unique to TNT, are discussed ad libitum. Also unique to TNT is the ability to directly analyze morphometric data (including landmarks), on the same footing as discrete characters. Finally, the scripting language of TNT is introduced. With scripting, it is possible to "program" TNT to create personalized routines and automate complex calculations, taking analyses to the next level and allowing exploration of new methods and ideas. Key Features Discusses the treatment of ambiguity in phylogenetic analyses in depth, for summarizing results or comparing trees Reviews literature on arguments and methods for weighting morphological characters and their practical application Describes theory and application of methods for evaluating strength of group support, based on either resampling or comparisons with suboptimal trees Discusses the use of morphometric characters in phylogenetic analysis Presents extensive information on commands and options of the TNT computer program, including the use and creation of scripts

Author : Pablo A. Goloboff
Publisher : CRC Press
Page : 307 pages
File Size : 48,9 Mb
Release : 2022-07-22
Category : Science
ISBN : 9781000604009

Get Book

Refining Phylogenetic Analyses by Pablo A. Goloboff Pdf

This volume discusses the aspects of a phylogenetic analysis that go beyond basic calculation of most parsimonious trees. Practical application of all principles discussed is illustrated by reference to TNT, a freely available software package that can perform all the steps needed in a phylogenetic analysis. The first problem considered is how to summarize and compare multiple trees (including identification and handling wildcard taxa). Evaluation of the strength of support for groups, another critical component of any phylogenetic analysis, is given careful consideration. The different interpretations of measures of support are discussed and connected with alternative implementations. The book reviews rationales for estimating character reliability on the basis of homoplasy, with particular attention to morphological characters. The main methods for character weighting and their practical implementation, several of them unique to TNT, are discussed ad libitum. Also unique to TNT is the ability to directly analyze morphometric data (including landmarks), on the same footing as discrete characters. Finally, the scripting language of TNT is introduced. With scripting, it is possible to "program" TNT to create personalized routines and automate complex calculations, taking analyses to the next level and allowing exploration of new methods and ideas. Key Features Discusses the treatment of ambiguity in phylogenetic analyses in depth, for summarizing results or comparing trees Reviews literature on arguments and methods for weighting morphological characters and their practical application Describes theory and application of methods for evaluating strength of group support, based on either resampling or comparisons with suboptimal trees Discusses the use of morphometric characters in phylogenetic analysis Presents extensive information on commands and options of the TNT computer program, including the use and creation of scripts

Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
Page : 401 pages
File Size : 47,5 Mb
Release : 2011-11-06
Category : Science
ISBN : 9781461417439

Get Book

Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis Pdf

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.

Author : Pablo A. Goloboff
Publisher : CRC Press
Page : 289 pages
File Size : 46,6 Mb
Release : 2022-07-22
Category : Science
ISBN : 9781000550061

Get Book

From Observations to Optimal Phylogenetic Trees by Pablo A. Goloboff Pdf

Taxonomists specializing in different groups once based phylogenetic analysis only on morphological data; molecular data was used more rarely. Although molecular systematics is routine today, the use of morphological data continues to be important, especially for phylogenetic placement of many taxa known only from fossils and rare or difficult to collect species. In addition, morphological analyses help identify potential biases in molecular analyses. And finally, scenarios with respect to morphology continue to motivate biologists: the beauty of a cheetah or a baobab does not lie in their DNA sequence, but instead on what they are and do! This book is an up-to-date revision of methods and principles of phylogenetic analysis of morphological data. It is also a general guide for using the computer program TNT in the analysis of such data. The book covers the main aspects of phylogenetic analysis and general methods to compare classifications derived from molecules and morphology. The basic aspects of molecular analysis are covered only as needed to highlight the differences with methods and assumptions for analysis of morphological datasets.

Author : E. O. Wiley,Bruce S. Lieberman
Publisher : John Wiley & Sons
Page : 444 pages
File Size : 52,5 Mb
Release : 2011-06-07
Category : Science
ISBN : 9780470905968

Get Book

Phylogenetics by E. O. Wiley,Bruce S. Lieberman Pdf

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 : John S. Wilkins,Frank E. Zachos,Igor Ya. Pavlinov
Publisher : CRC Press
Page : 383 pages
File Size : 45,5 Mb
Release : 2022-06-14
Category : Science
ISBN : 9781000549799

Get Book

Species Problems and Beyond by John S. Wilkins,Frank E. Zachos,Igor Ya. Pavlinov Pdf

Species Problems and Beyond offers a collection of up-to-date essays discussing from an interdisciplinary perspective the many ramifications of the ‘Species Problem.’ The authors represent experts in the philosophy of biology, in species-level evolutionary investigations, and in biodiversity studies and conservation. Some of the topics addressed concern the context sensitivity of the term ‘species’; species as individuals, processes, natural kinds, or as ‘operative concepts’; species delimitation in the age of Big (genomic) Data; and taxonomic inflation and its consequences for conservation strategies. The carefully edited volume will be an invaluable resource for philosophers of biology and evolutionary biologists alike. – Olivier Rieppel, Rowe Family Curator of Evolutionary Biology, Negaunee Integrative Research Center, Field Museum, USA Species, or ‘the Species Problem’, is a topic in science, in the philosophy of science, and in general philosophy. In fact, it encompasses many aspects of the same problem, and these are dealt with in this volume. Species are often thought of as fundamental units of biological matter to be used in ecology, conservation, classification, and biodiversity. The chapters in this book present opposing views on the current philosophical and conceptual issues of the Species Problem in biology. Divided into four sections, Concepts and Theories, Practice and Methods, Ranks and Trees and Names, and Metaphysics and Epistemologies, the book is authored by biologists, philosophers, and historians, many leaders in their fields. Topics include ontology of species, definitions of both species category and units, species rank, speciation issues, nomenclature, ecology, and species conservation. Species Problems and Beyond aims to clarify the contemporary issues of the Species Problem. It is ideal for use in upper-level seminars and courses in Evolutionary Biology, Philosophy of Science, Philosophy of Biology, Systematics and Taxonomy, and Phylogenetics/Cladistics, and for any scholar in these fields.

Author : Stanton B. Gelvin
Publisher : Springer
Page : 509 pages
File Size : 54,6 Mb
Release : 2018-11-28
Category : Medical
ISBN : 9783030032579

Get Book

Agrobacterium Biology by Stanton B. Gelvin Pdf

This volume reviews various facets of Agrobacterium biology, from modern aspects of taxonomy and bacterial ecology to pathogenesis, bacterial cell biology, plant and fungal transformation, natural transgenics, and biotechnology. Agrobacterium-mediated transformation is the most extensively utilized platform for generating transgenic plants, but modern biotechnology applications derive from more than 40 years of intensive basic scientific research. Many of the biological principles established by this research have served as models for other bacteria, including human and animal pathogens. Written by leading experts and highlighting recent advances, this volume serves both as an introduction to Agrobacterium biology for students as well as a more comprehensive text for research scientists.

Author : E. O. Wiley
Publisher : Unknown
Page : 406 pages
File Size : 49,9 Mb
Release : 2008
Category : Electronic
ISBN : OCLC:884488883

Get Book

Phylogenetics by E. O. Wiley Pdf

Author : Christian Kop,Heinrich C. Mayr,John Mylopoulos,Óscar Pastor
Publisher : Springer Science & Business Media
Page : 513 pages
File Size : 46,8 Mb
Release : 2005-10-11
Category : Computers
ISBN : 9783540293897

Get Book

Conceptual Modeling - ER 2005 by Christian Kop,Heinrich C. Mayr,John Mylopoulos,Óscar Pastor Pdf

Conceptual modeling is fundamental to any domain where one must cope with complex real-world situations and systems because it fosters communication - tween technology experts and those who would bene?t from the application of those technologies. Conceptual modeling is the key mechanism for und- standing and representing the domains of information system and database - gineering but also increasingly for other domains including the new “virtual” e-environmentsandtheinformationsystemsthatsupportthem.Theimportance of conceptual modeling in software engineering is evidenced by recent interest in “model-drivenarchitecture”and“extremenon-programming”.Conceptualm- eling also plays a prominent rolein various technical disciplines and in the social sciences. The Annual International Conference on Conceptual Modeling (referred to as the ER Conference) provides a central forum for presenting and discussing current research and applications in which conceptual modeling is the major emphasis. In keeping with this tradition, ER 2005, the 24th ER Conference, spanned the spectrum of conceptual modeling including research and practice in areas such as theories of concepts and ontologies underlying conceptual m- eling, methods and tools for developing and communicating conceptual models, and techniques for transforming conceptual models into e?ective (information) system implementations. Moreover, new areas of conceptual modeling incl- ing Semantic Web services and the interdependencies of conceptual modeling with knowledge-based, logical and linguistic theories and approaches were also addressed.

Author : Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey
Publisher : Cambridge University Press
Page : 750 pages
File Size : 45,6 Mb
Release : 2009-03-26
Category : Science
ISBN : 9780521877107

Get Book

The Phylogenetic Handbook by Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey Pdf

A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

Author : Muriel Gargaud,Hervé Martin,Philippe Claeys
Publisher : Springer Science & Business Media
Page : 680 pages
File Size : 43,6 Mb
Release : 2007-01-05
Category : Science
ISBN : 9783540336938

Get Book

Lectures in Astrobiology by Muriel Gargaud,Hervé Martin,Philippe Claeys Pdf

First comprehensive, beginning graduate level book on the emergent science of astrobiology.

Author : Marketa J. Zvelebil,Jeremy O. Baum
Publisher : Garland Science
Page : 804 pages
File Size : 40,9 Mb
Release : 2008
Category : Bioinformatics
ISBN : 0815340249

Get Book

Understanding Bioinformatics by Marketa J. Zvelebil,Jeremy O. Baum Pdf

Suitable for advanced undergraduates & postgraduates, this book provides a definitive guide to bioinformatics. It takes a conceptual approach & guides the reader from first principles through to an understanding of the computational techniques & the key algorithms.

Author : Richard H. Baltz,Arnold L. Demain,Julian E. Davies
Publisher : American Society for Microbiology Press
Page : 1894 pages
File Size : 41,9 Mb
Release : 2010-03-25
Category : Medical
ISBN : 9781555815127

Get Book

Manual of Industrial Microbiology and Biotechnology by Richard H. Baltz,Arnold L. Demain,Julian E. Davies Pdf

A rich array of methods and discussions of productive microbial processes. • Reviews of the newest techniques, approaches, and options in the use of microorganisms and other cell culture systems for the manufacture of pharmaceuticals, industrial enzymes and proteins, foods and beverages, fuels and fine chemicals, and other products. • Focuses on the latest advances and findings on the current state of the art and science and features a new section on the microbial production of biofuels and fine chemicals, as well as a stronger emphasis on mammalian cell culture methods. • Covers new methods that enhance the capacity of microbes used for a wide range of purposes, from winemaking to pharmaceuticals to bioremediation, at volumes from micro- to industrial scale.

Author : Muriel Gargaud,Philippe Claeys,Purificación López-García,Hervé Martin,Thierry Montmerle,Robert Pascal,Jacques Reisse
Publisher : Springer Science & Business Media
Page : 371 pages
File Size : 52,8 Mb
Release : 2007-07-05
Category : Science
ISBN : 9780387450834

Get Book

From Suns to Life: A Chronological Approach to the History of Life on Earth by Muriel Gargaud,Philippe Claeys,Purificación López-García,Hervé Martin,Thierry Montmerle,Robert Pascal,Jacques Reisse Pdf

This review gathers astronomers, geologists, biologists, and chemists around a common question: how did life emerge on Earth? The ultimate goal is to probe an even more demanding question: is life universal? This not-so linear account highlights problems, gaps, and controversies. Discussion covers the formation of the solar system; the building of a habitable planet; prebiotic chemistry, biochemistry, and the emergence of life; the early Earth environment, and much more.

Author : P. Ehrenfreund,W.M. Irvine,T. Owen,Luann Becker,Jen Blank,J.R. Brucato,Luigi Colangeli,Sylvie Derenne,Anne Dutrey,Didier Despois,Antonio Lazcano,Francois Robert
Publisher : Springer Science & Business Media
Page : 521 pages
File Size : 42,7 Mb
Release : 2006-03-05
Category : Science
ISBN : 9781402023057

Get Book

Astrobiology: Future Perspectives by P. Ehrenfreund,W.M. Irvine,T. Owen,Luann Becker,Jen Blank,J.R. Brucato,Luigi Colangeli,Sylvie Derenne,Anne Dutrey,Didier Despois,Antonio Lazcano,Francois Robert Pdf

Astrobiology, a new exciting interdisciplinary research field, seeks to unravel the origin and evolution of life wherever it might exist in the Universe. The current view of the origin of life on Earth is that it is strongly connected to the origin and evolution of our planet and, indeed, of the Universe as a whole. We are fortunate to be living in an era where centuries of speculation about the two ancient and fundamental problems: the origin of life and its prevalence in the Universe are being replaced by experimental science. The subject of Astrobiology can be approached from many different perspectives. This book is focused on abiogenic organic matter from the viewpoint of astronomy and planetary science and considers its potential relevance to the origins of life on Earth and elsewhere. Guided by the review papers in this book, the concluding chapter aims to identify key questions to motivate future research and stimulate astrobiological applications of current and future research facilities and space missions. Today’s rich array of new spacecraft, telescopes and dedicated scientists promises a steady flow of discoveries and insights that will ultimately lead us to the answers we seek.