Phylogenomic Data Acquisition

Author : W. Bryan Jennings
Publisher : CRC Press
Page : 345 pages
File Size : 54,8 Mb
Release : 2016-12-12
Category : Science
ISBN : 9781351722230

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Phylogenomic Data Acquisition by W. Bryan Jennings Pdf

Phylogenomics is a rapidly growing field of study concerned with using genome-wide data—usually in the form of DNA sequence loci—to infer the evolution of genes, genomes, and the Tree of Life. Accordingly, this discipline connects many areas in biology including molecular and genomic evolution, systems biology, molecular systematics, phylogeography, conservation genetics, DNA barcoding, and others. With the advent of Next Generation Sequencing in addition to advances in computer hardware and software over the past decade, researchers can now generate unparalleled phylogenomic datasets that are helping to illuminate many areas in the life sciences. This book is an introduction to the principles and practices of gathering these data. Phylogenomic Data Acquisition: Principles and Practice is intended for a broad cross-section of biologists and anyone else interested in learning how to obtain phylogenomic data using the latest methods.

Author : Rob DeSalle,Gonzalo Giribet,Ward Wheeler
Publisher : Birkhäuser
Page : 414 pages
File Size : 42,9 Mb
Release : 2013-12-01
Category : Science
ISBN : 9783034881258

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Techniques in Molecular Systematics and Evolution by Rob DeSalle,Gonzalo Giribet,Ward Wheeler Pdf

The amount of information that can be obtained by using molecular techniques in evolution, systematics and ecology has increased exponentially over the last ten years. The need for more rapid and efficient methods of data acquisition and analysis is growing accordingly. This manual presents some of the most important techniques for data acquisition developed over the last years. The choice and justification of data analysis techniques is also an important and critical aspect of modern phylogenetic and evolutionary analysis and so a considerable part of this volume addresses this important subject. The book is mainly written for students and researchers from evolutionary biology in search for methods to acquire data, but also from molecular biology who might be looking for information on how data are analyzed in an evolutionary context. To aid the user, information on web-located sites is included wherever possible. Approaches that will push the amount of information which systematics will gather in the

Author : Michael M. Miyamoto,Joel Cracraft
Publisher : Oxford University Press
Page : 369 pages
File Size : 55,7 Mb
Release : 1991-11-14
Category : Science
ISBN : 9780195361971

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Phylogenetic Analysis of DNA Sequences by Michael M. Miyamoto,Joel Cracraft Pdf

With increasing frequency, systematic and evolutionary biologists have turned to the techniques of molecular biology to complement their traditional morphological and anatomical approaches to questions of the historical relationship and descent among groups of animals and plants. In particular, the comparative analysis of DNA sequences is becoming a common and important focus of research attention today. The objective of this volume is to survey the emerging field of molecular systematics of DNA sequences, and to appraise the strengths and limitations of the different approaches yielded by these techniques. The contributors are an internationally recognized group of investigators from different schools and disciplines who critically address a diversity of crucial questions about DNA systematics, including DNA sequence data acquisition, phylogenetic inference, congruence and consensus problems, limitations of molecular data, and the integration of molecular and morphological data sets. The work will interest all botanists and zoologists involved in systematics, taxonomy, and evolution.

Author : Michael M. Miyamoto,Joel Cracraft
Publisher : Unknown
Page : 0 pages
File Size : 48,8 Mb
Release : 2023
Category : DNA
ISBN : 0197701825

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Phylogenetic Analysis of DNA Sequences by Michael M. Miyamoto,Joel Cracraft Pdf

The objective of this volume is to survey the emerging field of molecular systematics of DNA sequences. It focuses on the topics of DNA sequence data acquisition, phylogenetic inference, congruence and consensus problems, limitations of molecular data and integration of molecular data sets.

Author : Kurt Enslein,John F. Kinslow
Publisher : Unknown
Page : 252 pages
File Size : 43,8 Mb
Release : 1968
Category : Electronic
ISBN : OCLC:1198082489

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Data Acquisition and Processing in Biology and Medicine by Kurt Enslein,John F. Kinslow Pdf

Author : Rob DeSalle,Michael Tessler,Jeffrey Rosenfeld
Publisher : CRC Press
Page : 401 pages
File Size : 51,7 Mb
Release : 2020-08-18
Category : Computers
ISBN : 9781000080353

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Phylogenomics by Rob DeSalle,Michael Tessler,Jeffrey Rosenfeld Pdf

Phylogenomics: A Primer, Second Edition is for advanced undergraduate and graduate biology students studying molecular biology, comparative biology, evolution, genomics, and biodiversity. This book explains the essential concepts underlying the storage and manipulation of genomics level data, construction of phylogenetic trees, population genetics, natural selection, the tree of life, DNA barcoding, and metagenomics. The inclusion of problem-solving exercises in each chapter provides students with a solid grasp of the important molecular and evolutionary questions facing modern biologists as well as the tools needed to answer them.

Author : Paul A. Hohenlohe,Om P. Rajora
Publisher : Springer Nature
Page : 559 pages
File Size : 54,7 Mb
Release : 2020-12-09
Category : Science
ISBN : 9783030634896

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Population Genomics: Wildlife by Paul A. Hohenlohe,Om P. Rajora Pdf

Population genomics is revolutionizing wildlife biology, conservation, and management by providing key and novel insights into genetic, population and landscape-level processes in wildlife, with unprecedented power and accuracy. This pioneering book presents the advances and potential of population genomics in wildlife, outlining key population genomics concepts and questions in wildlife biology, population genomics approaches that are specifically applicable to wildlife, and application of population genomics in wildlife population and evolutionary biology, ecology, adaptation and conservation and management. It is important for students, researchers, and wildlife professionals to understand the growing set of population genomics tools that can address issues from delineation of wildlife populations to assessing their capacity to adapt to environmental change. This book brings together leading experts in wildlife population genomics to discuss the key areas of the field, as well as challenges, opportunities and future prospects of wildlife population genomics.

Author : Scott Orland Rogers
Publisher : CRC Press
Page : 423 pages
File Size : 53,5 Mb
Release : 2022-07-11
Category : Science
ISBN : 9781000596410

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Molecular Analyses by Scott Orland Rogers Pdf

DNA and RNA extraction methods from a variety of tissues and samples are now routine, including extraction from single cells. Many methods are now automated. Sequencing efficiency has reached the point where it is now possible to obtain gigabases of data, both quickly and inexpensively. Such methods permit the identification of gene versions, including those associated with disease (e.g. small nucleotide polymorphism analyses, or SNPs). The general public as well as clinicians can now access a wide variety of literature on the molecular bases of diseases, allowing them to better assess disease risks and treatments. This volume concentrates on medically-focused methods, and therefore the major audience will be medical professionals, students, and those involved in medically-related research endeavors. There are also papers in this volume dealing specifically with methods developed to analyze large sequence data sets. Many methods reviewed herein are more broadly applicable to other fields in biology, chemistry, bioinformatics, and bioengineering, and are intended for a broad readership. Key Features Summarizes nucleic acid extractions from a wide variety of tissues and cells Describes processes of nucleic acid preservation Reviews forensic sampling, detection of nucleic acids, and delivery of nucleic acids to multicellular organisms Provides essential guidance for sequencing, sequence analysis, database searches, and phylogenetic analyses Includes additional methods useful for analysis of nucleic acids and proteins Related Titles DeSalle, et al. Phylogenomics: A Primer (ISBN 978-0-3670-2849-7). Jennings, W. B. Phylogenomic Data Acquisition: Principles and Practice (ISBN 978-0-3678-6980-9). Wang, X. Next-Generation Sequencing Data Analysis (ISBN 978-1-4822-1788-9) Sung, W.-K. Algorithms for Next-Generation Sequencing (ISBN 978-0-3676-5797-0)

Author : Rob DeSalle,Michael Tessler,Jeffrey Rosenfeld
Publisher : CRC Press
Page : 415 pages
File Size : 46,6 Mb
Release : 2020-08-18
Category : Computers
ISBN : 9781000080391

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Phylogenomics by Rob DeSalle,Michael Tessler,Jeffrey Rosenfeld Pdf

Phylogenomics: A Primer, Second Edition is for advanced undergraduate and graduate biology students studying molecular biology, comparative biology, evolution, genomics, and biodiversity. This book explains the essential concepts underlying the storage and manipulation of genomics level data, construction of phylogenetic trees, population genetics, natural selection, the tree of life, DNA barcoding, and metagenomics. The inclusion of problem-solving exercises in each chapter provides students with a solid grasp of the important molecular and evolutionary questions facing modern biologists as well as the tools needed to answer them.

Author : Anonim
Publisher : Academic Press
Page : 344 pages
File Size : 43,7 Mb
Release : 2017-11-17
Category : Science
ISBN : 9780128132623

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Fungal Phylogenetics and Phylogenomics by Anonim Pdf

Fungal Phylogenetics and Phylogenomics, Volume 99, the latest release in the Advances in Genetics series, presents users with new chapters that delve into such topics as the Advances of fungal phylogenomics and the impact on fungal systematics, Data crunching for fungal phylogenomics: insights into data collection and phylogenetic inference based on genome data for fungi, Genomic and epigenomic traits of emerging fungal pathogens, Advances in fungal gene cluster diversity and evolution, Phylogenomics of Fusarium oxysporum species complex, Phylogenomic analyses of pathogenic yeasts, and the Phylogenetics and phylogenomics of rust fungi. The series continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines, critically analyzing future directions. Critically analyzes future directions for the study of clinical genetics Written and edited by recognized leaders in the field Presents new medical breakthroughs that are occurring as a result of advances in our knowledge of genetics

Author : John S. Wilkins,Frank E. Zachos,Igor Ya. Pavlinov
Publisher : CRC Press
Page : 383 pages
File Size : 43,8 Mb
Release : 2022-06-14
Category : Science
ISBN : 9781000549799

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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 : J. Wolfgang Wägele,Thomas Bartolomaeus
Publisher : Walter de Gruyter
Page : 761 pages
File Size : 55,6 Mb
Release : 2014-02-27
Category : Science
ISBN : 9783110277524

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Deep Metazoan Phylogeny: The Backbone of the Tree of Life by J. Wolfgang Wägele,Thomas Bartolomaeus Pdf

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 comprehensiveoverview available of the state of the art in this exciting field of evolutionary research.

Author : Laura Kubatko,L. Lacey Knowles
Publisher : Princeton University Press
Page : 352 pages
File Size : 47,9 Mb
Release : 2023-03-14
Category : Science
ISBN : 9780691245157

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Species Tree Inference by Laura Kubatko,L. Lacey Knowles Pdf

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 : Calyampudi Radhakrishna Rao
Publisher : World Scientific
Page : 213 pages
File Size : 44,8 Mb
Release : 1997
Category : Mathematics
ISBN : 9789810231118

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Statistics and Truth by Calyampudi Radhakrishna Rao Pdf

Written by one of the top most statisticians with experience in diverse fields of applications of statistics, the book deals with the philosophical and methodological aspects of information technology, collection and analysis of data to provide insight into a problem, whether it is scientific research, policy making by government or decision making in our daily lives.The author dispels the doubts that chance is an expression of our ignorance which makes accurate prediction impossible and illustrates how our thinking has changed with quantification of uncertainty by showing that chance is no longer the obstructor but a way of expressing our knowledge. Indeed, chance can create and help in the investigation of truth. It is eloquently demonstrated with numerous examples of applications that statistics is the science, technology and art of extracting information from data and is based on a study of the laws of chance. It is highlighted how statistical ideas played a vital role in scientific and other investigations even before statistics was recognized as a separate discipline and how statistics is now evolving as a versatile, powerful and inevitable tool in diverse fields of human endeavor such as literature, legal matters, industry, archaeology and medicine.Use of statistics to the layman in improving the quality of life through wise decision making is emphasized.

Author : Rob Desalle,Bernd Schierwater
Publisher : CRC Press
Page : 446 pages
File Size : 44,6 Mb
Release : 2010-12-07
Category : Science
ISBN : 9781439854020

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Key Transitions in Animal Evolution by Rob Desalle,Bernd Schierwater Pdf

Tackling one of the most difficult and delicate of the evolutionary questions, this challenging book summarizes the more recent results in phylogenetics and developmental biology that address the evolution of key innovations in metazoans. Divided into three sections, the first considers the phylogenetic issues involving this area of the tree of life and the elucidation of those relationships that continue to trouble taxonomists. The second section considers the developmental biology of metazoan evolution including the development of the nervous system, sensory organs, and physiological maturation. Part three focuses on the evolution of pattern and process in the Metazoa.