Author: Karen Y. Siu Ting Salvatierra
Publisher:
ISBN:
Category : Biology Theses
Languages : en
Pages : 0

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Author:
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Author: Trevor R. Hodkinson
Publisher: CRC Press
ISBN: 1420009532
Category : Mathematics
Languages : en
Pages : 374

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Book Description
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: Emmanuel Paradis
Publisher: Springer Science & Business Media
ISBN: 1461417430
Category : Science
Languages : en
Pages : 401

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Book Description
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: Olaf R.P. Bininda-Emonds
Publisher: Springer Science & Business Media
ISBN: 1402023308
Category : Science
Languages : en
Pages : 547

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Book Description
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.

Author: E. O. Wiley
Publisher: John Wiley & Sons
ISBN: 0470905964
Category : Science
Languages : en
Pages : 444

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Book Description
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: Tommy Rodriguez
Publisher: iUniverse
ISBN: 1663206481
Category : Science
Languages : en
Pages : 75

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Book Description
Want to build an evolutionary tree? Here’s your chance to learn how. The field of bioinformatics was born out of the need to manage, analyze, and examine raw genomic data in meaningful and exciting ways, such as the discipline of computational phylogenetics would provide. The evolutionary inferences reached among the several peer-reviewed articles contained in this book are neither novel nor breakthrough. However, it is in the application of computational techniques, experiment design, and probabilistic models where this research finds a stronghold. As a matter of practicality, the original manuscripts have been edited for a broader audience due to its highly technical language. The essays compiled in these pages have undergone a facelift, from their original scientific format into a more reader-friendly layout, as to better accommodate two different perspectives – both experts and non-experts alike.

Author: Laura Kubatko
Publisher: Princeton University Press
ISBN: 0691245150
Category : Science
Languages : en
Pages : 352

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Book Description
An up-to-date reference book on phylogenetic methods and applications for evolutionary biologists The increasingly widespread availability of genomic data is transforming how biologists estimate evolutionary relationships among organisms and broadening the range of questions that researchers can test in a phylogenetic framework. Species Tree Inference brings together many of today’s leading scholars in the field to provide an incisive guide to the latest practices for analyzing multilocus sequence data. This wide-ranging and authoritative book gives detailed explanations of emerging new approaches and assesses their strengths and challenges, offering an invaluable context for gauging which procedure to apply given the types of genomic data and processes that contribute to differences in the patterns of inheritance across loci. It demonstrates how to apply these approaches using empirical studies that span a range of taxa, timeframes of diversification, and processes that cause the evolutionary history of genes across genomes to differ. By fully embracing this genomic heterogeneity, Species Tree Inference illustrates how to address questions beyond the goal of estimating phylogenetic relationships of organisms, enabling students and researchers to pursue their own research in statistically sophisticated ways while charting new directions of scientific discovery.

Author: J. Wolfgang Wägele
Publisher: Walter de Gruyter GmbH & Co KG
ISBN: 3110372967
Category : Science
Languages : en
Pages : 770

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Book Description
The growing success of molecular methods has challenged traditional views of animal evolution and a large number of alternative hypotheses are hotly debated today. For the deep metazoan phylogeny project, data sets of hitherto unmatched quality and quantity were compiled and analysed with innovative bioinformatics tools. The book begins at the base of the tree of life to discuss the origin of animals and early branches of the phylogenetic tree. The following section presents special data sets gained from mitochondrial genomes and from morphology, with a focus on nervous systems. The final section is dedicated to theoretical aspects of data analysis and new bioinformatics tools. The book closes with a unique general discussion of all hypotheses contained in previous chapters. This work provides the most comprehensive overview available of the state of the art in this exciting field of evolutionary research.

Author: Charles Semple
Publisher: Oxford University Press on Demand
ISBN: 9780198509424
Category : Computers
Languages : en
Pages : 258

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Book Description
'Phylogenetics' is the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics. It is a flourishing area of intereaction between mathematics, statistics, computer science and biology.The main role of phylogenetic techniques lies in evolutionary biology, where it is used to infer historical relationships between species. However, the methods are also relevant to a diverse range of fields including epidemiology, ecology, medicine, as well as linguistics and cognitive psychologyThis graduate-level book, based on the authors lectures at The University of Canterbury, New Zealand, focuses on the mathematical aspects of phylogenetics. It brings together the central results of the field (providing proofs of the main theorem), outlines their biological significance,and indicateshow algorithms may be derived. The presentation is self-contained and relies on discrete mathematics with some probability theory. A set of exercises and at least one specialist topic ends each chapter.This book is intended for biologists interested in the mathematical theory behind phylogenetic methods, and for mathematicians, statisticians, and computer scientists eager to learn about this emerging area of discrete mathematics.'Phylogenetics' in the 24th volume in the Oxford Lecture Series in Mathematics and its Applications. This series contains short books suitable for graduate students and researchers who want a well-written account of mathematics that is fundamental to current to research. The series emphasises futuredirections of research and focuses on genuine applications of mathematics to finance, engineering and the physical and biological sciences.