The Crown of Thorns

Author:

Publisher:Springer Science & Business Media

ISBN:1461417430

Total Pages:386

Viewed:1664

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Books 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.

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Phylogenetics

Author:E. O. Wiley,Bruce S. Lieberman

Publisher:John Wiley & Sons

ISBN:1118017870

Total Pages:424

Viewed:1907

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Books 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.

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Author:László Zsolt Garamszegi

Publisher:Springer

ISBN:3662435500

Total Pages:552

Viewed:1750

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Books Description:

Phylogenetic comparative approaches are powerful analytical tools for making evolutionary inferences from interspecific data and phylogenies. The phylogenetic toolkit available to evolutionary biologists is currently growing at an incredible speed, but most methodological papers are published in the specialized statistical literature and many are incomprehensible for the user community. This textbook provides an overview of several newly developed phylogenetic comparative methods that allow to investigate a broad array of questions on how phenotypic characters evolve along the branches of phylogeny and how such mechanisms shape complex animal communities and interspecific interactions. The individual chapters were written by the leading experts in the field and using a language that is accessible for practicing evolutionary biologists. The authors carefully explain the philosophy behind different methodologies and provide pointers – mostly using a dynamically developing online interface – on how these methods can be implemented in practice. These “conceptual” and “practical” materials are essential for expanding the qualification of both students and scientists, but also offer a valuable resource for educators. Another value of the book are the accompanying online resources (available at: http://www.mpcm-evolution.com), where the authors post and permanently update practical materials to help embed methods into practice.

Functional and Phylogenetic Ecology in R

Author:Nathan G. Swenson

Publisher:Springer Science & Business Media

ISBN:1461495423

Total Pages:212

Viewed:394

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Books Description:

Functional and Phylogenetic Ecology in R is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a unique approach through its focus on ecological analyses and not macroevolutionary analyses. The author provides his own code, so that the reader is guided through the computational steps to calculate the desired metrics. This guided approach simplifies the work of determining which package to use for any given analysis. Example datasets are shared to help readers practice, and readers can then quickly turn to their own datasets.

Phylogenetic Diversity

Author:Rosa A. Scherson,Daniel P Faith

Publisher:Springer

ISBN:3319931458

Total Pages:217

Viewed:765

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Books Description:

“Biodiversity” refers to the variety of life. It is now agreed that there is a “biodiversity crisis”, corresponding to extinction rates of species that may be 1000 times what is thought to be “normal”. Biodiversity science has a higher profile than ever, with the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services involving more than 120 countries and 1000s of scientists. At the same time, the discipline is re-evaluating its foundations – including its philosophy and even core definitions. The value of biodiversity is being debated. In this context, the tree of life (“phylogeny”) is emerging as an important way to look at biodiversity, with relevance cutting across current areas of concern – from the question of resilience within ecosystems, to conservation priorities for globally threatened species – while capturing the values of biodiversity that have been hard to quantify, including resilience and maintaining options for future generations. This increased appreciation of the importance of conserving “phylogenetic diversity”, from microbial communities in the human gut to global threatened species, has inevitably resulted in an explosion of new indices, methods, and case studies. This book recognizes and responds to the timely opportunity for synthesis and sharing experiences in practical applications. The book recognizes that the challenge of finding a synthesis, and building shared concepts and a shared toolbox, requires both an appreciation of the past and a look into the future. Thus, the book is organized as a flow from history, concepts and philosophy, through to methods and tools, and followed by selected case studies. A positive vision and plan of action emerges from these chapters, that includes coping with inevitable uncertainties, effectively communicating the importance of this “evolutionary heritage” to the public and to policy-makers, and ultimately contributing to biodiversity conservation policy from local to global scales.

Handbook of Statistical Genomics

Author:David J. Balding,Ida Moltke,John Marioni

Publisher:John Wiley & Sons

ISBN:1119429250

Total Pages:1224

Viewed:1942

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Books Description:

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.

Bioinformatics and Phylogenetics

Author:Tandy Warnow

Publisher:Springer

ISBN:3030108376

Total Pages:410

Viewed:1711

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Books Description:

This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.

The Phylogenetic System of Ephemeroptera

Author:Nikita Kluge

Publisher:Springer Science & Business Media

ISBN:9400708726

Total Pages:442

Viewed:1232

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Books Description:

The book has general biological significance due to usage of the new non-ranking nomenclature and the rational layout of taxonomic text, which can be qualified as post-Linnaean systematics. While after the works by Lameere and Hennig, non-ranking classifications became widely used, this book represents the first experience of consistently non-ranking classification, including taxa of low taxonomic level (i.e. taxa traditionally regarded as genera, families et al.). In contrast to other recent attempts to elaborate a non-ranking nomenclature not contradictory to the International Code of Zoological Nomenclature, this one appears to be successful and can be applied to any zoological taxa (although its application in botany could be possible only after further elaboration). Biology is currently going through a crisis, which causes some investigators to use such non-scientific methods of reconstructing phylogeny as parsimony analysis. The author believes that the new method of phylogeny description and reconstruction used in this book will help indicate a way out of this crisis.

Phylogenomics

Author:Christoph Bleidorn

Publisher:Springer

ISBN:3319540645

Total Pages:222

Viewed:1156

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Books Description:

This unique textbook provides a clear and concise overview of the key principles of the complex field of phylogenomics, with a particular focus on sequencing technologies that are crucial to studying and understanding interrelations in evolutionary genomics. It includes chapters dedicated to the analysis of nucleotide sequences using assembling and alignment methods and also discusses the main strategies for phylogenetic studies, systematic errors and their correction. This highly readable textbook is intended for graduate students and young researchers with an interest in phylogenetics and evolutionary developmental biology.

Evolution in the Dark

Author:Horst Wilkens,Ulrike Strecker

Publisher:Springer

ISBN:3662545128

Total Pages:217

Viewed:1298

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Books Description:

This book provides fascinating insights into the development and genetics of evolutionary processes on the basis of animals living in the dark, such as the Astyanax cave fish. Biologically functionless traits show high variability, which results from neutral deleterious mutations no longer being eliminated by natural selection, which normally acts to preserve functional capability. These negative mutations accumulate until the traits they are responsible for become rudimentary or even lost. The random genetic basis of regressive evolution is in accordance with Nei’s Neutral Theory of Molecular Evolution, which applies to the molecular level. Such processes are particularly conspicuous in species living in constant darkness, where, for example in Astyanax, all traits depending on the exposure to light, like eyes, pigmentation, visually triggered aggressive behaviour, negative phototaxis, and several peripheral outcomes of circadian rhythmicity, are useless and diminish. In compensation constructive traits like taste, olfaction or the lateral line senses are improved by selection and do not show variability. Regressive and constructive traits inherit independently, proving that the rudimentation process is not driven by pleiotropic linkage between them. All these traits are subject to mosaic evolution and exhibit unproportional epistatic gene effects, which play an important role in evolutionary adaptation and improvement. Offering valuable evolutionary insights and supplemented by a wealth of illustrations, this book will appeal to evolutionary and developmental biologists alike.

Molecular Evolution and Phylogenetics

Author:Masatoshi Nei,Sudhir Kumar

Publisher:Oxford University Press

ISBN:0199881227

Total Pages:352

Viewed:589

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Books Description:

During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.

Avian Ancestors

Author:Federico Agnolin,Fernando E. Novas

Publisher:Springer Science & Business Media

ISBN:9400756372

Total Pages:96

Viewed:614

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Books Description:

Although consensus exists among researchers that birds evolved from coelurosaurian theropods, paleontologists still debate the identification of the group of coelurosaurians that most closely approaches the common ancestor of birds. The last 20 years witnessed the discovery of a wide array of avian-like theropods that has considerably amplified the anatomical disparity among deinonychosaurians, some of which resemble Archaeopteryx more than Deinonychus. Among these newly discovered theropods that show remarkable bird-like characteristics are the four-winged theropods Microraptor and Anchiornis, and the unenlagiids Unenlagia, Buitreraptor, and Rahonavis. A bizarre group of minute-sized coelurosaurs, the Scansoriopterygidae, also exhibits some avian similarities that lead some authors to interpret them as more closely related to birds than other dinosaurs. With the aim to explore the phylogenetic relationships of these coelurosaurians and birds, we merged recently published integrative databases, resulting in significant changes in the topological distribution of taxa within Paraves. We present evidence that Dromaeosauridae, Microraptoria, Unenlagiidae, and Anchiornis + Xiaotingia form successive sister taxa of Aves, and that the Scansoriopterygidae are basal coelurosaurians not closely related to birds. The implications in the evolutionary sequence of anatomical characters leading to birds, including the origin of flight, are also considered in light of this new phylogenetic hypothesis.

Handbook of Milk Composition

Author:Gerard Meurant

Publisher:Elsevier

ISBN:0080533116

Total Pages:919

Viewed:1272

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Books Description:

This informative treatise offers a concise collection of existing, expert data summarizing the composition of milk. The Handbook of Milk Composition summarizes current information on all aspects of human and bovine milk, including: sampling, storage, composition, as well as specific chapters on major and minor components such as protein, carbohydrates, lipids, electrolytes, minerals, vitamins and hormones. The book also features comprehensive coverage of compartmentation, host-defense components, factors affecting composition, composition of commercial formulas, and contaminants. * Reliable data on the composition of human and bovine milks. * Discusses the many factors affecting composition. * Composition tables make up 25-30% of the total book. * Problems concerning sampling and analysis are described. * Should appeal equally to industry and academia. * Also of interest to developing countries in need of information on infant nutrition and agricultural development

Microbial Diversity

Author:Oladele Ogunseitan

Publisher:John Wiley & Sons

ISBN:1405144483

Total Pages:312

Viewed:1226

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Books Description:

This book offers the first comprehensive, in-depth treatment of microbial diversity for undergraduate and graduate students. Using a global approach, Microbial Diversity illustrates the impact of microorganisms on ecological and Earth system phenomena. Accompanied by a devoted website with resources for both instructors and students: www.blackwellpublishing.com/ogunseitan Uses key ecological and global phenomena to show the continuity of microbial contribution. Illustrates the importance of microbial diversity for the understanding of global physiochemical and biological processes. Presents analyses of microscopic, culture, molecular, and phylogenetic systematic methods. Shows the relevance of microbial diversity to global environmental problems, such as climate change and ozone depletion. Features numerous illustrations, including over 60 4-color photographs of microbes.

The Evolution of Phylogenetic Systematics

Author:Andrew Hamilton

Publisher:Univ of California Press

ISBN:0520956753

Total Pages:314

Viewed:1939

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Books Description:

The Evolution of Phylogenetic Systematics aims to make sense of the rise of phylogenetic systematics—its methods, its objects of study, and its theoretical foundations—with contributions from historians, philosophers, and biologists. This volume articulates an intellectual agenda for the study of systematics and taxonomy in a way that connects classification with larger historical themes in the biological sciences, including morphology, experimental and observational approaches, evolution, biogeography, debates over form and function, character transformation, development, and biodiversity. It aims to provide frameworks for answering the question: how did systematics become phylogenetic?

Darwinian Evolution of Molecules

Author:Hiromoto Nakazawa

Publisher:Springer

ISBN:9811087245

Total Pages:143

Viewed:1856

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Books Description:

On the basis of thermodynamic considerations and the Earth’s historical processes, this book argues the physical inevitability of life’s generation and evolution, i.e., Why did life generate? Why does life evolve? Following an introduction to the problem, the hypothesis “Darwinian Evolution of Molecules” is proposed, which explains how, when, and where life was instigated through successive chemical reactions and the survival of selected molecules. The individual processes described are all scientifically reasonable, being verifiable by experiment. The hypothesis is supported by extensive reference to the scientific literature published in academic journals, including some experimental reports from the author’s own research group. The readers of this book will learn that the decreasing temperature of the early Earth led to a reduction in its entropy, inducing the Earth’s materials to order, which entailed ordering of the light elements as organic molecules with subsequent further ordering (i.e., evolution) to systems that can be considered alive (i.e., life). Researchers and students, as well as the non-academic audience, interested in the interdisciplinary problem of the origin of life will find suggestions and possible approaches to the scientific and conceptual problems they may be facing.

The Handbook of Historical Linguistics, Volume II

Author:Richard D. Janda,Brian D. Joseph,Barbara S. Vance

Publisher:John Wiley & Sons

ISBN:1118732308

Total Pages:640

Viewed:661

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Books Description:

An entirely new follow-up volume providing a detailed account of numerous additional issues, methods, and results that characterize current work in historical linguistics. This brand-new, second volume of The Handbook of Historical Linguistics is a complement to the well-established first volume first published in 2003. It includes extended content allowing uniquely comprehensive coverage of the study of language(s) over time. Though it adds fresh perspectives on several topics previously treated in the first volume, this Handbook focuses on extensions of diachronic linguistics beyond those key issues. This Handbook provides readers with studies of language change whose perspectives range from comparisons of large open vs. small closed corpora, via creolistics and linguistic contact in general, to obsolescence and endangerment of languages. Written by leading scholars in their respective fields, new chapters are offered on matters such as the origin of language, evidence from language for reconstructing human prehistory, invocations of language present in studies of language past, benefits of linguistic fieldwork for historical investigation, ways in which not only biological evolution but also field biology can serve as heuristics for research into the rise and spread of linguistic innovations, and more. Moreover, it: offers novel and broadened content complementing the earlier volume so as to provide the fullest available overview of a wholly engrossing field includes 23 all-new contributed chapters, treating some familiar themes from fresh perspectives but mostly covering entirely new topics features expanded discussion of material from language families other than Indo-European provides a multiplicity of views from numerous specialists in linguistic diachrony. The Handbook of Historical Linguistics, Volume II is an ideal book for undergraduate and graduate students in linguistics, researchers and professional linguists, as well as all those interested in the history of particular languages and the history of language more generally.

Insect Morphology and Phylogeny

Author:Rolf G. Beutel,Frank Friedrich,Xing-Ke Yang,Si-Qin Ge

Publisher:Walter de Gruyter

ISBN:3110264048

Total Pages:531

Viewed:874

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Books Description:

In the last decades a remarkable renaissance has materialized in insect morphology, mainly triggered by the development of new cutting-edge technologies. This is an exciting time for biological synthesis where the mysteries and data derived from genomes can be combined with centuries of data from morphology and development. And, now, more than ever, detailed knowledge of morphology is essential to understanding the evolution of all groups of organisms. In this “age of phylogenomics” researchers rely on morphological data to support molecular findings, test complex evolutionary scenarios, and for placing fossil taxa. This textbook provides an in-depth treatment of the structures and the phylogeny of the megadiverse Hexapoda. The first part presents an up-to-date overview of general insect morphology with detailed drawings, scanning electron micrographs, and 3-D reconstructions. Also included is a chapter covering innovative morphological techniques (e.g., μ-computer tomography, 3-D modeling), brief treatments of insect development and phylogenetic methods, and a comprehensive morphological glossary. The second part is of a modern synthesis of insect systematics that includes taxon-specific morphological information for all Orders. The work is an invaluable reference for students and researchers working in all facets of biology and is a must for evolutionary biologists. A detailed understanding of morphology is essential in unraveling phylogenetic relationships and developing complex evolutionary scenarios. Increasingly researchers in phylogenomics are re/turning to morphological data to support their findings, while the development of new cutting-edge technologies has further increased interest in this growing field. This definitive handbook provides an in-depth treatment of insect morphology. The first part presents an up-to-date overview of insect morphology with detailed drawings, brilliant scanning electron micrographs and 3-D reconstructions as interactive PDFs. Thisis complemented by a chapter on innovative morphological techniques (e.g., μ-computer tomography, 3-D modeling) and a comprehensive morphological glossary. The second part treats the state of the art in insect systematics and includes taxon-specific morphological information for all orders. Systematicsare treated formally, with for example the arguments for relationships (“apomorphies”) always listed explicitly. The work is a useful reference for students and researchers working in different fields of biology and a must for those dealing with insects from an evolutionary perspective.

The Insects

Author:P. J. Gullan,P. S. Cranston

Publisher:John Wiley & Sons

ISBN:9781444317671

Total Pages:584

Viewed:1934

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Books Description:

This established, popular textbook provides a stimulating andcomprehensive introduction to the insects, the animals thatrepresent over half of the planet's biological diversity. In thisnew fourth edition, the authors introduce the key features ofinsect structure, function, behavior, ecology and classification,placed within the latest ideas on insect evolution. Much of thebook is organised around major biological themes - living on theground, in water, on plants, in colonies, and as predators,parasites/parasitoids and prey. A strong evolutionary theme ismaintained throughout. The ever-growing economic importance ofinsects is emphasized in new boxes on insect pests, and in chapterson medical and veterinary entomology, and pest management. Updated'taxoboxes' provide concise information on all aspects of each ofthe 27 major groupings (orders) of insects. Key Features: All chapters thoroughly updated with the latest results frominternational studies Accompanying website with downloadable illustrations and linksto video clips All chapters to include new text boxes of topical issues andstudies Major revision of systematic and taxonomy chapter Still beautifully illustrated with more new illustrations fromthe artist, Karina McInnes A companion resources site is available at ahref="http://www.wiley.com/go/gullan/insects"target="_blank"www.wiley.com/go/gullan/insects/a. This siteincludes: Copies of the figures from the book for downloading, along witha PDF of the captions. Colour versions of key figures from the book A list of useful web links for each chapter, selected by theauthor.