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A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.
This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.
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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.
The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including BLAST, FastA, Clustal, T-coffee, Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL, ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC, SplitsTree, and RDP. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students.
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.
Nitrogen constitutes 78% of the Earth’s atmosphere and inevitably occupies a predominant role in marine and terrestrial nutrient biogeochemistry and the global climate. Callous human activities, like the excessive industrial nitrogen fixation and the incessant burning of fossil fuels, have caused a massive acceleration of the nitrogen cycle, which has, in turn, led to an increasing trend in eutrophication, smog formation, acid rain, and emission of nitrous oxide, which is a potent greenhouse gas, 300 times more powerful in warming the Earth’s atmosphere than carbon dioxide. This book comprehensively reviews the biotransformation of nitrogen, its ecological significance and the consequences of human interference. It will appeal to environmentalists, ecologists, marine biologists, and microbiologists worldwide, and will serve as a valuable guide to graduates, post-graduates, research scholars, scientists, and professors.
A collection of highly valuable statistical and computational approaches designed for developing powerful methods to analyze large-scale high-throughput data derived from studies of complex diseases. Such diseases include cancer and cardiovascular disease, and constitute the major health challenges in industrialized countries. They are characterized by the systems properties of gene networks and their interrelations, instead of individual genes, whose malfunctioning manifests in pathological phenotypes, thus making the analysis of the resulting large data sets particularly challenging. This is why novel approaches are needed to tackle this problem efficiently on a systems level. Written by computational biologists and biostatisticians, this book is an invaluable resource for a large number of researchers working on basic but also applied aspects of biomedical data analysis emphasizing the pathway level.
The Anthropology of Learning in Childhood offers a large, mural-like portrait of childhood across time, culture, species, and environment. Even a casual reading of the literature on childhood will persuade one that learning is a very important topic that commands the attention of tens of thousands of scholars and practitioners. Yet, anthropological research on children has exerted relatively little influence on this community. This book will change that. The book demonstrates that anthropologists studying childhood can offer a description and theoretically sophisticated account of children's learning and its role in their development, socialization, and enculturation. Further, it demonstrates the particular contribution that children's learning makes to the construction of society and culture as well as the role that culture-acquiring children play in human evolution. Chapters have been contributed in archaeology, primatology, biological and cultural anthropology, and cross-cultural psychology.