Download or read book From Observations to Optimal Phylogenetic Trees written by Pablo A. Goloboff and published by CRC Press. This book was released on 2022-07-22 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book From Observations to Optimal Phylogenetic Trees written by Pablo A. Goloboff and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 1. "This book outlines the steps in a phylogenetic analysis that follow the generation of most parsimonious trees. In addition, character reliability approaches and methods of analysis for morphometric characters are summarized. The algorithm used throughout the book is TNT, a freely available software package able to summarize and compare multiple trees produced by ambiguous datasets, or analyses of different datasets. Unstable taxa (wildcards or rogues), which may obscure the relationships of the other taxa, are discussed extensively, as well as their identification and handling with several options implemented in TNT"--
Download or read book From Observations to Optimal Phylogenetic Trees written by Pablo A. Goloboff and published by CRC Press. This book was released on 2022-07-22 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2006-11-25 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Foundations of Phylogenetic Systematics written by Johann Wolfgang Wägele and published by . This book was released on 2005 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogeny inference and the classification of organisms are indispensable for all fields of biology. On the basis of a well corroborated tree of life it is possible to understand the evolution of structure and function, of genomes, of gene families, of cascades of developmental genes, and the origin of genes of medical importance. Ecologists need a stable classification of organisms to identify organisms, to find their correct names and thus further information on relevant species. This book offers an introduction to the theory of Phylogenetic Systematics and is a companion for all biologists who want to analyze morphological or molecular data with classical methods or with modern computer programs. The first part of the book explains the epistemological basis that is independent of the type of method used to construct phylogenetic trees. Unlike other empirical sciences, the estimation of data quality in phylogenetics is still little developed and very often neglected. Here a theoretical basis is presented that enables the systematist to assess critically and objectively the quality of different data sets and to make statements on the plausibility of results. This requires a conception of the notions of information content, probability of homology, probability of cognition, probability of events, the principle of parsimony, the differentiation of phenomenological and modelling methods. Willi Hennig's original method is compared with modern numerical systematics and an updated Hennigian procedure of data analysis is discussed. The difference between phenetic and phylogenetic cladistics is explained. Popular tools for data evaluation implemented in computer programs are explained including their axiomatic assumptions, sources of error and possible applications. For the more common tools the mathematical background is explained in a simple, easy-to-understand way.Johann-Wolfgang Wagele was until recently head of the Department for Animal Systematics (Lehrstuhl fur Spezielle Zoologie) at the University of Bochum and is now director of the Museum Alexander Koenig in Bonn (Germany). His main research interests are the taxonomy, phylogeny and biodiversity of Isopoda, which implies observations of life history, biogeography and ecology in combination with phylogeny inference. Further subjects include arthropod phylogeny and tools for explorative data analyses. The author is president of the Gesellschaft fur Biologische Systematik, a Central European society of systematists, and he is actively promoting biodiversity research.
Download or read book Phylogenetics written by E. O. Wiley and published by John Wiley & Sons. This book was released on 2011-10-11 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Reconstructing the Tree of Life written by Trevor R. Hodkinson and published by CRC Press. This book was released on 2006-12-26 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Species Problems and Beyond written by John S. Wilkins and published by CRC Press. This book was released on 2022-06-14 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Inferring Phylogenies written by Joseph Felsenstein and published by Sinauer Associates Incorporated. This book was released on 2004-01 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.
Download or read book Phylogenetic Supertrees written by Olaf R.P. Bininda-Emonds and published by Springer Science & Business Media. This book was released on 2004-05-31 with total page 547 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first book on "phylogenetic supertrees", a recent, but controversial development for inferring evolutionary trees. Rather than analyze the combined primary character data directly, supertree construction proceeds by combining the tree topologies derived from those data. This difference in strategy has allowed for the exciting possibility of larger, more complete phylogenies than are otherwise currently possible, with the potential to revolutionize evolutionarily-based research. This book provides a comprehensive look at supertrees, ranging from the methods used to build supertrees to the significance of supertrees to bioinformatic and biological research. Reviews of many the major supertree methods are provided and four new techniques, including a Bayesian implementation of supertrees, are described for the first time. The far-reaching impact of supertrees on biological research is highlighted both in general terms and through specific examples from diverse clades such as flowering plants, even-toed ungulates, and primates. The book also critically examines the many outstanding challenges and problem areas for this relatively new field, showing the way for supertree construction in the age of genomics. Interdisciplinary contributions from the majority of the leading authorities on supertree construction in all areas of the bioinformatic community (biology, computer sciences, and mathematics) will ensure that this book is a valuable reference with wide appeal to anyone interested in phylogenetic inference.
Download or read book Maximum Likelihood Methods in Molecular Phylogenetics written by Korbinian Sebastian Strimmer and published by Herbert Utz Verlag. This book was released on 1997 with total page 76 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Tutorials in Mathematical Biosciences IV written by Avner Friedman and published by Springer. This book was released on 2008-04-26 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers an introduction to fast growing research areas in evolution of species, population genetics, ecological models, and population dynamics. It reviews the concept and methodologies of phylogenetic trees, introduces ecological models, examines a broad range of ongoing research in population dynamics, and deals with gene frequencies under the action of migration and selection. The book features computational schemes, illustrations, and mathematical theorems.
Download or read book Handbook of Paleoanthropology written by Winfried Henke and published by Springer Science & Business Media. This book was released on 2007-05-10 with total page 2057 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 3-volume handbook brings together contributions by the world ́s leading specialists that reflect the broad spectrum of modern palaeoanthropology, thus presenting an indispensable resource for professionals and students alike. Vol. 1 reviews principles, methods, and approaches, recounting recent advances and state-of-the-art knowledge in phylogenetic analysis, palaeoecology and evolutionary theory and philosophy. Vol. 2 examines primate origins, evolution, behaviour, and adaptive variety, emphasizing integration of fossil data with contemporary knowledge of the behaviour and ecology of living primates in natural environments. Vol. 3 deals with fossil and molecular evidence for the evolution of Homo sapiens and its fossil relatives.
Download or read book The Phylogenetic Handbook written by Marco Salemi and published by Cambridge University Press. This book was released on 2009-03-26 with total page 750 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.
Download or read book Refining Phylogenetic Analyses written by Pablo A. Goloboff and published by CRC Press. This book was released on 2022-07-22 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
Download or read book Introduction to Genomics written by Arthur Lesk and published by Oxford University Press, USA. This book was released on 2012 with total page 421 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the latest techniques that enable us to study the genome in detail, the book explores what the genome tells us about life at the level of the molecule, the cell, and the organism
