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Phylogenies in Ecology

Author: Marc W. Cadotte

Publisher: Princeton University Press

Published: 2016-08-09

Total Pages: 264

ISBN-13: 0691157685

Phylogenies in Ecology is the first book to critically review the application of phylogenetic methods in ecology, and it serves as a primer to working ecologists and students of ecology wishing to understand these methods. This book demonstrates how phylogenetic information is transforming ecology by offering fresh ways to estimate the similarities and differences among species, and by providing deeper, evolutionary-based insights on species distributions, coexistence, and niche partitioning. Marc Cadotte and Jonathan Davies examine this emerging area's explosive growth, allowing for this new body of hypotheses testing. Cadotte and Davies systematically look at all the main areas of current ecophylogenetic methodology, testing, and inference. Each chapter of their book covers a unique topic, emphasizes key assumptions, and introduces the appropriate statistical methods and null models required for testing phylogenetically informed hypotheses. The applications presented throughout are supported and connected by examples relying on real-world data that have been analyzed using the open-source programming language, R. Showing how phylogenetic methods are shedding light on fundamental ecological questions related to species coexistence, conservation, and global change, Phylogenies in Ecology will interest anyone who thinks that evolution might be important in their data.

Phylogenetic Ecology

Author: Nathan G. Swenson

Publisher: University of Chicago Press

Published: 2019-11-20

Total Pages: 229

ISBN-13: 022667150X

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Over the past decade, ecologists have increasingly embraced phylogenetics, the study of evolutionary relationships among species. As a result, they have come to discover the field’s power to illuminate present ecological patterns and processes. Ecologists are now investigating whether phylogenetic diversity is a better measure of ecosystem health than more traditional metrics like species diversity, whether it can predict the future structure and function of communities and ecosystems, and whether conservationists might prioritize it when formulating conservation plans. In Phylogenetic Ecology, Nathan G. Swenson synthesizes this nascent field’s major conceptual, methodological, and empirical developments to provide students and practicing ecologists with a foundational overview. Along the way, he highlights those realms of phylogenetic ecology that will likely increase in relevance—such as the burgeoning subfield of phylogenomics—and shows how ecologists might lean on these new perspectives to inform their research programs.

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Author: László Zsolt Garamszegi

Publisher: Springer

Published: 2014-07-29

Total Pages: 552

ISBN-13: 3662435500

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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.

Handbook of Trait-Based Ecology

Author: Francesco de Bello

Publisher: Cambridge University Press

Published: 2021-03-11

Total Pages: 311

ISBN-13: 1108472915

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Trait-based ecology is rapidly expanding. This comprehensive and accessible guide covers the main concepts and tools in functional ecology.

Inferring Phylogenies

Author: Joseph Felsenstein

Publisher: Sinauer Associates Incorporated

Published: 2004-01

Total Pages: 664

ISBN-13: 9780878931774

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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.

Biodiversity Conservation and Phylogenetic Systematics

Author: Roseli Pellens

Publisher: Springer

Published: 2016-02-24

Total Pages: 390

ISBN-13: 3319224611

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This book is about phylogenetic diversity as an approach to reduce biodiversity losses in this period of mass extinction. Chapters in the first section deal with questions such as the way we value phylogenetic diversity among other criteria for biodiversity conservation; the choice of measures; the loss of phylogenetic diversity with extinction; the importance of organisms that are deeply branched in the tree of life, and the role of relict species. The second section is composed by contributions exploring methodological aspects, such as how to deal with abundance, sampling effort, or conflicting trees in analysis of phylogenetic diversity. The last section is devoted to applications, showing how phylogenetic diversity can be integrated in systematic conservation planning, in EDGE and HEDGE evaluations. This wide coverage makes the book a reference for academics, policy makers and stakeholders dealing with biodiversity conservation.

Phylogenetics and Ecology

Author: Paul Eggleton

Publisher: Academic Press

Published: 1994-11-10

Total Pages: 400

ISBN-13:

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The relationship between systematics and ecology has recently been invigorated, and developed a long way from the "old" field of comparative biology. This change has been two-fold. Advances in phylogenetic research have allowed explicit phylogenetic hypotheses to be constructed for a range of different groups of organisms, and ecologists are now more aware that organism traits are influenced by the interaction of past and present. This volume discusses the impact of these modern phylogenetic methods on ecology, especially those using comparative methods. Although unification of these areas has proved difficult, a number of conclusions can be drawn from the text. These include the need for a "working" bridge between evolutionary biologists using logic-based cladistic methods and those using probability-based statistical methods, for care in the selection of tree types for comparative studies and for systematists to attempt to analyse ecologically important groups. Comparative ecologists and systematists need to come together to develop these ideas further, but this volume presents a very useful starting point for all those interested in systematics and ecology.

Phylogeny, Ecology, and Behavior

Author: Daniel R. Brooks

Publisher: University of Chicago Press

Published: 1991

Total Pages: 456

ISBN-13: 9780226075716

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"The merits of this work are many. A rigorous integration of phylogenetic hypotheses into studies of adaptation, adaptive radiation, and coevolution is absolutely necessary and can change dramatically our collective 'gestalt' about much in evolutionary biology. The authors advance and illustrate this thesis beautifully. The writing is often lucid, the examples are plentiful and diverse, and the juxtaposition of examples from different biological systems argues forcefully for the validity of the thesis. Many new insights are offered here, and the work is usually accessible to both the practiced phylogeneticist and the naive ecologist."—Joseph Travis, Florida State University "[Phylogeny, Ecology, and Behavior] presents its arguments forcefully and cogently, with ample . . .support. Brooks and McLennan conclude as they began, with the comment that evolution is a result, not a process, and that it is the result of an interaction of a variety of processes, environmental and historical. Evolutionary explanations must consider all these components, else they are incomplete. As Darwin's explanations of descent with modification integrated genealogical and ecological information, so must workers now incorporate historical and nonhistorical, and biological and nonbiological, processes in their evolutionary perspective."—Marvalee H. Wake, Bioscience "This book is well-written and thought-provoking, and should be read by those of us who do not routinely turn to phylogenetic analysis when investigating adaptation, evolutionary ecology and co-evolution."—Mark R. MacNair, Journal of Natural History

Functional and Phylogenetic Ecology in R

Author: Nathan G. Swenson

Publisher: Springer Science & Business Media

Published: 2014-03-26

Total Pages: 217

ISBN-13: 1461495423

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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.

Phylogenies in Ecology

Author: Marc W. Cadotte

Publisher: Princeton University Press

Published: 2016-08-09

Total Pages: 264

ISBN-13: 1400881196

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