phylogenies in ecology a guide to concepts and methods

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Phylogenies In Ecology

Author : Marc W. Cadotte
ISBN : 9781400881192
Genre : Science
File Size : 61. 16 MB
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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.

Modern Phylogenetic Comparative Methods And Their Application In Evolutionary Biology

Author : László Zsolt Garamszegi
ISBN : 9783662435502
Genre : Science
File Size : 80. 93 MB
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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.

Functional And Phylogenetic Ecology In R

Author : Nathan G. Swenson
ISBN : 9781461495420
Genre : Computers
File Size : 55. 66 MB
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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.

Molecular Methods In Ecology

Author : Allan Baker
ISBN : 9781444311419
Genre : Science
File Size : 58. 22 MB
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The incorporation of molecular methods in ecological research has added an exciting new dimension to conventional studies, and opened windows into previously intractable areas of research, at the interface between ecology and genetics. Using these new methods it has now become routine to use genetic markers to study ecological phenomena, from molecular sexing of individuals and parentage of offspring, through to population structure of species and phylogenetic relationships of taxa. These methods have stimulated an explosion of empirical and analytical developments in molecular ecology, which have in turn, increasingly attracted students and professional biologists eager to employ them in their studies. Molecular Methods in Ecology traces the development of molecular ecology by reviewing basic molecular biological techniques and earlier methods such as protein electrophoresis, DNA-DNA hybridisation, restriction analysis of DNA, and DNA fingerprinting. Later chapters review methods using newer classes of markers such as microsatellites, introns, MHC, SSRs and AFLP markers in plants and molecular sexing in animals. The strengths and limitations of methods are discussed and guidance is provided in selecting the most appropriate methods for particular problems in ecology. This book will provide both postgraduates and researchers with a guide to choosing and employing appropriate methodologies for successful research in the field of molecular ecology. Provides up-to-date summaries of the latest molecular approaches in this rapidly expanding field. Gives guidance on the appropriate choice of methods for particular problems in ecology, and their strengths and limitations. Provides brief laboratory protocols for each molecular method and summaries of software available for analysis of data in molecular ecology. Outlines examples of the latest research results from studies of both plants and animals, integrated within the framework of molecular ecology.

An Introduction To Methods And Models In Ecology Evolution And Conservation Biology

Author : Stanton Braude
ISBN : 1400835453
Genre : Science
File Size : 79. 78 MB
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This unique textbook introduces undergraduate students to quantitative models and methods in ecology, behavioral ecology, evolutionary biology, and conservation. It explores the core concepts shared by these related fields using tools and practical skills such as experimental design, generating phylogenies, basic statistical inference, and persuasive grant writing. And contributors use examples from their own cutting-edge research, providing diverse views to engage students and broaden their understanding. This is the only textbook on the subject featuring a collaborative "active learning" approach that emphasizes hands-on learning. Every chapter has exercises that enable students to work directly with the material at their own pace and in small groups. Each problem includes data presented in a rich array of formats, which students use to answer questions that illustrate patterns, principles, and methods. Topics range from Hardy-Weinberg equilibrium and population effective size to optimal foraging and indices of biodiversity. The book also includes a comprehensive glossary. In addition to the editors, the contributors are James Beck, Cawas Behram Engineer, John Gaskin, Luke Harmon, Jon Hess, Jason Kolbe, Kenneth H. Kozak, Robert J. Robertson, Emily Silverman, Beth Sparks-Jackson, and Anton Weisstein. Provides experience with hypothesis testing, experimental design, and scientific reasoning Covers core quantitative models and methods in ecology, behavioral ecology, evolutionary biology, and conservation Turns "discussion sections" into "thinking labs" Professors: A supplementary Instructor's Manual is available for this book. It is restricted to teachers using the text in courses. For information on how to obtain a copy, refer to: http://press.princeton.edu/class_use/solutions.html

Landscape Genetics

Author : Niko Balkenhol
ISBN : 9781118525241
Genre : Science
File Size : 82. 37 MB
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Despite the substantial interest in landscape genetics from the scientific community, learning about the concepts and methods underlying the field remains very challenging. The reason for this is the highly interdisciplinary nature of the field, which combines population genetics, landscape ecology, and spatial statistics. These fields have traditionally been treated separately in classes and textbooks, and very few scientists have received the interdisciplinary training necessary to efficiently teach or apply the diversity of techniques encompassed by landscape genetics. To address the current knowledge gap, this book provides the first in depth treatment of landscape genetics in a single volume. Specifically, this book delivers fundamental concepts and methods underlying the field, covering particularly important analytical methods in detail, and presenting empirical and theoretical applications of landscape genetics for a variety of environments and species. Consistent with the interdisciplinary nature of landscape genetics, the book combines an introductory, textbook like section with additional sections on advanced topics and applications that are more typical of edited volumes. The chapter topics and the expertise of the authors and the editorial team make the book a standard reference for anyone interested in landscape genetics. The book includes contributions from many of the leading researchers in landscape genetics. The group of scientists we have assembled has worked on several collaborative projects over the last years, including a large number of peer reviewed papers, several landscape genetics workshops at international conferences, and a distributed graduate seminar on landscape genetics. Based on the experiences gained during these collaborative teaching and research activities, the book includes chapters that synthesize fundamental concepts and methods underlying landscape genetics (Part 1), chapters on advanced topics that deserve a more in depth treatment (Part 2), and chapters illustrating the use of concepts and methods in empirical applications (Part 3). This structure ensures a high usefulness of the book for beginning landscape geneticists and experienced researchers alike, so that it has a broad target audience. At least one of the four co editors is involved in almost every chapter of the book, thereby ensuring a high consistency and coherency among chapters.

Learning Landscape Ecology

Author : Sarah E. Gergel
ISBN : 9781493963744
Genre : Science
File Size : 87. 43 MB
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This title meets a great demand for training in spatial analysis tools accessible to a wide audience. Landscape ecology continues to grow as an exciting discipline with much to offer for solving pressing and emerging problems in environmental science. Much of the strength of landscape ecology lies in its ability to address challenges over large areas, over spatial and temporal scales at which decision-making often occurs. As the world tackles issues related to sustainability and global change, the need for this broad perspective has only increased. Furthermore, spatial data and spatial analysis (core methods in landscape ecology) are critical for analyzing land-cover changes world-wide. While spatial dynamics have long been fundamental to terrestrial conservation strategies, land management and reserve design, mapping and spatial themes are increasingly recognized as important for ecosystem management in aquatic, coastal and marine systems. This second edition is purposefully more applied and international in its examples, approaches, perspectives and contributors. It includes new advances in quantifying landscape structure and connectivity (such as graph theory), as well as labs that incorporate the latest scientific understanding of ecosystem services, resilience, social-ecological landscapes, and even seascapes. Of course, as before, the exercises emphasize easy-to-use, widely available software.

The Phylogenetic Handbook

Author : Philippe Lemey
ISBN : 9780521877107
Genre : Science
File Size : 69. 89 MB
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A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

Plant Functional Diversity

Author : Eric Garnier
ISBN : 9780198757368
Genre : Plant diversity
File Size : 71. 38 MB
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Biological diversity, the variety of living organisms on Earth, is traditionally viewed as the diversity of taxa, and species in particular. However, other facets of diversity also need to be considered for a comprehensive understanding of evolutionary and ecological processes. This novel book demonstrates the advantages of adopting a functional approach to diversity in order to improve our understanding of the functioning of ecological systems and their components. The focus is on plants, which are major components of these systems, and for which the functional approach has led to major scientific advances over the last 20 years. Plant Functional Diversity presents the rationale for a trait-based approach to functional diversity in the context of comparative plant ecology and agroecology. It demonstrates how this approach can be used to address a number of highly debated questions in plant ecology pertaining to plant responses to their environment, controls on plant community structure, ecosystem properties, and the services these deliver to human societies. This research level text will be of particular relevance and use to graduate students and professional researchers in plant ecology, agricultural sciences and conservation biology.

Handbook Of Meta Analysis In Ecology And Evolution

Author : Julia Koricheva
ISBN : 9781400846184
Genre : Science
File Size : 88. 36 MB
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Meta-analysis is a powerful statistical methodology for synthesizing research evidence across independent studies. This is the first comprehensive handbook of meta-analysis written specifically for ecologists and evolutionary biologists, and it provides an invaluable introduction for beginners as well as an up-to-date guide for experienced meta-analysts. The chapters, written by renowned experts, walk readers through every step of meta-analysis, from problem formulation to the presentation of the results. The handbook identifies both the advantages of using meta-analysis for research synthesis and the potential pitfalls and limitations of meta-analysis (including when it should not be used). Different approaches to carrying out a meta-analysis are described, and include moment and least-square, maximum likelihood, and Bayesian approaches, all illustrated using worked examples based on real biological datasets. This one-of-a-kind resource is uniquely tailored to the biological sciences, and will provide an invaluable text for practitioners from graduate students and senior scientists to policymakers in conservation and environmental management. Walks you through every step of carrying out a meta-analysis in ecology and evolutionary biology, from problem formulation to result presentation Brings together experts from a broad range of fields Shows how to avoid, minimize, or resolve pitfalls such as missing data, publication bias, varying data quality, nonindependence of observations, and phylogenetic dependencies among species Helps you choose the right software Draws on numerous examples based on real biological datasets

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