From Observations to Optimal Phylogenetic Trees Book

From Observations to Optimal Phylogenetic Trees


  • Author : Pablo A. Goloboff
  • Publisher : Unknown
  • Release Date : 2022
  • Genre: Cladistic analysis
  • Pages : null
  • ISBN 10 : 1032114878
  • Total Read : 61
  • File Size : 6,9 Mb

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From Observations to Optimal Phylogenetic Trees Summary:

"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"--

From Observations to Optimal Phylogenetic Trees Book

From Observations to Optimal Phylogenetic Trees


  • Author : Pablo A. Goloboff
  • Publisher : CRC Press
  • Release Date : 2022-07-08
  • Genre: Science
  • Pages : 298
  • ISBN 10 : 9781000550061
  • Total Read : 97
  • File Size : 14,5 Mb

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From Observations to Optimal Phylogenetic Trees Summary:

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.

Refining Phylogenetic Analyses Book

Refining Phylogenetic Analyses


  • Author : Pablo A. Goloboff
  • Publisher : CRC Press
  • Release Date : 2022-07-08
  • Genre: Science
  • Pages : 312
  • ISBN 10 : 9781000604009
  • Total Read : 93
  • File Size : 7,5 Mb

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Refining Phylogenetic Analyses Summary:

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

Species Problems and Beyond Book

Species Problems and Beyond


  • Author : John S. Wilkins
  • Publisher : CRC Press
  • Release Date : 2022-06-14
  • Genre: Science
  • Pages : 383
  • ISBN 10 : 9781000549799
  • Total Read : 66
  • File Size : 14,9 Mb

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Species Problems and Beyond Summary:

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 Taxono

Handbook of Paleoanthropology Book

Handbook of Paleoanthropology


  • Author : Winfried Henke
  • Publisher : Springer Science & Business Media
  • Release Date : 2007-05-10
  • Genre: Science
  • Pages : 2057
  • ISBN 10 : 9783540324744
  • Total Read : 75
  • File Size : 19,9 Mb

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Handbook of Paleoanthropology Summary:

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.

Evolutionary Genetics Book
Score: 5
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Evolutionary Genetics


  • Author : Charles W. Fox
  • Publisher : Oxford University Press
  • Release Date : 2006-04-27
  • Genre: Science
  • Pages : 618
  • ISBN 10 : 0199775044
  • Total Read : 66
  • File Size : 7,6 Mb

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Evolutionary Genetics Summary:

Charles Fox and Jason Wolf have brought together leading researchers to produce a cutting-edge primer introducing readers to the major concepts in modern evolutionary genetics. This book spans the continuum of scale, from studies of DNA sequence evolution through proteins and development to multivariate phenotypic evolution, and the continuum of time, from ancient events that lead to current species diversity to the rapid evolution seen over relatively short time scales in experimental evolution studies. Chapters are accessible to an audience lacking extensive background in evolutionaryy genetics but also current and in-depth enough to be of value to established researchers in evolution biology.

Analysis of Phylogenetics and Evolution with R Book

Analysis of Phylogenetics and Evolution with R


  • Author : Emmanuel Paradis
  • Publisher : Springer Science & Business Media
  • Release Date : 2011-11-06
  • Genre: Science
  • Pages : 386
  • ISBN 10 : 9781461417439
  • Total Read : 68
  • File Size : 12,7 Mb

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Analysis of Phylogenetics and Evolution with R Summary:

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.

Introduction to Genomics Book

Introduction to Genomics


  • Author : Arthur Lesk
  • Publisher : Oxford University Press
  • Release Date : 2012
  • Genre: Medical
  • Pages : 421
  • ISBN 10 : 9780199564354
  • Total Read : 67
  • File Size : 10,8 Mb

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Introduction to Genomics Summary:

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