Functional And Phylogenetic Ecology In R
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Functional And Phylogenetic Ecology In R
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Author : Nathan G. Swenson
language : en
Publisher: Springer Science & Business Media
Release Date : 2014-03-26
Functional And Phylogenetic Ecology In R written by Nathan G. Swenson and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-03-26 with Computers categories.
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 Ecology
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Author : Nathan G. Swenson
language : en
Publisher: University of Chicago Press
Release Date : 2019-11-20
Phylogenetic Ecology written by Nathan G. Swenson and has been published by University of Chicago Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-11-20 with Science categories.
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.
Phylogenetic Ecology
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Author : Nathan G. Swenson
language : en
Publisher: University of Chicago Press
Release Date : 2019-11-22
Phylogenetic Ecology written by Nathan G. Swenson and has been published by University of Chicago Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-11-22 with Science categories.
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.
Handbook Of Trait Based Ecology
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Author : Francesco de Bello
language : en
Publisher: Cambridge University Press
Release Date : 2021-03-11
Handbook Of Trait Based Ecology written by Francesco de Bello and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-03-11 with Nature categories.
Trait-based ecology is rapidly expanding. This comprehensive and accessible guide covers the main concepts and tools in functional ecology.
Phylogenetic Diversity
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Author : Rosa A. Scherson
language : en
Publisher: Springer
Release Date : 2018-08-31
Phylogenetic Diversity written by Rosa A. Scherson and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-08-31 with Science categories.
“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.
Phylogenies In Ecology
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Author : Marc W. Cadotte
language : en
Publisher: Princeton University Press
Release Date : 2016-08-09
Phylogenies In Ecology written by Marc W. Cadotte and has been published by Princeton University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-08-09 with Science categories.
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.
Analysis Of Phylogenetics And Evolution With R
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Author : Emmanuel Paradis
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-11-06
Analysis Of Phylogenetics And Evolution With R written by Emmanuel Paradis and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-11-06 with Science categories.
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.
Phylogenetic Comparative Methods In R
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Author : Liam J. Revell
language : en
Publisher: Princeton University Press
Release Date : 2022-09-06
Phylogenetic Comparative Methods In R written by Liam J. Revell and has been published by Princeton University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-09-06 with Science categories.
An authoritative introduction to the latest comparative methods in evolutionary biology Phylogenetic comparative methods are a suite of statistical approaches that enable biologists to analyze and better understand the evolutionary tree of life, and shed vital new light on patterns of divergence and common ancestry among all species on Earth. This textbook shows how to carry out phylogenetic comparative analyses in the R statistical computing environment. Liam Revell and Luke Harmon provide an incisive conceptual overview of each method along with worked examples using real data and challenge problems that encourage students to learn by doing. By working through this book, students will gain a solid foundation in these methods and develop the skills they need to interpret patterns in the tree of life. Covers every major method of modern phylogenetic comparative analysis in RExplains the basics of R and discusses topics such as trait evolution, diversification, trait-dependent diversification, biogeography, and visualizationFeatures a wealth of exercises and challenge problemsServes as an invaluable resource for students and researchers, with applications in ecology, evolution, anthropology, disease transmission, conservation biology, and a host of other areasWritten by two of today’s leading developers of phylogenetic comparative methods
The Nature Of Diversity
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Author : Daniel R. Brooks
language : en
Publisher: University of Chicago Press
Release Date : 2002-05-01
The Nature Of Diversity written by Daniel R. Brooks and has been published by University of Chicago Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2002-05-01 with Science categories.
All living things on earth—from individual species to entire ecosystems—have evolved through time, and evolution is the acknowledged framework of modern biology. Yet many areas of biology have moved from a focus on evolution to much narrower perspectives. Daniel R. Brooks and Deborah A. McLennan argue that it is impossible to comprehend the nature of life on earth unless evolution—the history of organisms—is restored to a central position in research. They demonstrate how the phylogenetic approach can be integrated with ecological and behavioral studies to produce a richer and more complete picture of evolution. Clearly setting out the conceptual, methodological, and empirical foundations of their research program, Brooks and McLennan show how scientists can use it to unravel the evolutionary history of virtually any characteristic of any living thing, from behaviors to ecosystems. They illustrate and test their approach with examples drawn from a wide variety of species and habitats. The Nature of Diversity provides a powerful new tool for understanding, documenting, and preserving the world's biodiversity. It is an essential book for biologists working in evolution, ecology, behavior, conservation, and systematics. The argument in The Nature of Diversity greatly expands upon and refines the arguments made in the authors' previous book Phylogeny, Ecology, and Behavior.
Ecology And Recovery Of Eastern Old Growth Forests
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Author : Andrew M. Barton
language : en
Publisher: Island Press
Release Date : 2018-11-08
Ecology And Recovery Of Eastern Old Growth Forests written by Andrew M. Barton and has been published by Island Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-11-08 with Nature categories.
The landscapes of North America, including eastern forests, have been shaped by humans for millennia, through fire, agriculture, hunting, and other means. But the arrival of Europeans on America’s eastern shores several centuries ago ushered in the rapid conversion of forests and woodlands to other land uses. By the twentieth century, it appeared that old-growth forests in the eastern United States were gone, replaced by cities, farms, transportation networks, and second-growth forests. Since that time, however, numerous remnants of eastern old growth have been discovered, meticulously mapped, and studied. Many of these ancient stands retain surprisingly robust complexity and vigor, and forest ecologists are eager to develop strategies for their restoration and for nurturing additional stands of old growth that will foster biological diversity, reduce impacts of climate change, and serve as benchmarks for how natural systems operate. Forest ecologists William Keeton and Andrew Barton bring together a volume that breaks new ground in our understanding of ecological systems and their importance for forest resilience in an age of rapid environmental change. This edited volume covers a broad geographic canvas, from eastern Canada and the Upper Great Lakes states to the deep South. It looks at a wide diversity of ecosystems, including spruce-fir, northern deciduous, southern Appalachian deciduous, southern swamp hardwoods, and longleaf pine. Chapters authored by leading old-growth experts examine topics of contemporary forest ecology including forest structure and dynamics, below-ground soil processes, biological diversity, differences between historical and modern forests, carbon and climate change mitigation, management of old growth, and more. This thoughtful treatise broadly communicates important new discoveries to scientists, land managers, and students and breathes fresh life into the hope for sensible, effective management of old-growth stands in eastern forests.