Phylogenetic Diversity

“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.

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.

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.

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.

This book provides an up to date review of the methods of measuring and assessing biological diversity, together with their application.

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.

Documents in comprehensive detail a major environmental crisis: rapidly declining amphibian populations and the disturbing developmental problems that are increasingly prevalent within many amphibian species.

This volume tackles questions of cultural evolution empirically and quantitatively, using a range of case studies from Africa, the Pacific, Europe, Asia and America. Powerful theoretical tools developed in evolutionary biology are used to test detailed hypotheses about historical patterns and adaptive functions in cultural evolution.