Download or read book Timetrees Incorporating Fossils and Molecules 2nd edition written by Michel Laurin and published by Frontiers Media SA. This book was released on 2022-09-15 with total page 194 pages. Available in PDF, EPUB and Kindle. Book excerpt: Calibrating phylogenies to time is central to addressing many questions in evolutionary biology and macroevolution. The fossil record once provided our only source for establishing a timeline for evolution. However, the incompleteness of the fossil record and the non-uniformity of fossil recovery rate make it challenging to obtain precise estimates of divergence times from fossil evidence alone. Molecular dating, which combines evidence from the geological and molecular records, enables us to generate a much more complete and precise timeline of events. The molecular clock can be time-calibrated using temporal evidence from fossils and used to estimate divergence times based on the assumption that the rate of sequence evolution will be approximately constant over time and among lineages. Methodological challenges to applying this concept in practice have been to relax the assumption of constant evolutionary rates and to model the uncertainty associated with paleontological and geological calibrations. To this end, available statistical methods have become increasingly complex in order to capture key features of empirical data. These are typically applied using Bayesian inference, which provides a powerful framework for incorporating multiple sources of uncertainty. Although overall more effort has been expended in developing models of molecular sequence evolution, critical advances have also included approaches to modeling taxonomic diversification and fossilization. In particular, recent advances in birth-death process models have allowed for continuous sampling along lineages, enabling more information from the fossil record to be incorporated into dating analyses in a statistically coherent way. In addition, available dating methods can now be applied to scenarios in which no molecular data may be available, allowing for novel insights into the evolution of entirely extinct clades. Other recent innovations enable us to date divergence times among taxa that have no fossil record, including the use of gene duplication events or biogeographic evidence. Furthermore, time-calibrated trees are necessary for obtaining phylogenetic estimates of taxonomic diversification and extinction rates, which can now be jointly inferred along with lineage divergence times. These approaches offer an exciting opportunity to understand the evolution of life in deep time, although key challenges remain, especially with regards to modeling the processes of genome evolution, taxonomic diversification and fossil recovery. In this Research Topic, we focus on recent advances in methodology, outstanding challenges, and the application of molecular and paleontological dating methods to empirical case studies across the Tree of Life.

Download or read book The Timetree of Life written by S. Blair Hedges and published by OUP Oxford. This book was released on 2009-04-23 with total page 1237 pages. Available in PDF, EPUB and Kindle. Book excerpt: The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrialimpacts, and other features.The Timetree of Life is the first reference book to synthesize the wealth of information relating to the temporal component of phylogenetic trees. In the past, biologists have relied exclusively upon the fossil record to infer an evolutionary timescale. However, recent revolutionary advances in molecular biology have made it possible to not only estimate the relationships of many groups of organisms, but also to estimate their times of divergence with molecular clocks. The routineestimation and utilization of these so-called 'time-trees' could add exciting new dimensions to biology including enhanced opportunities to integrate large molecular data sets with fossil and biogeographic evidence (and thereby foster greater communication between molecular and traditional systematists). Theycould help estimate not only ancestral character states but also evolutionary rates in numerous categories of organismal phenotype; establish more reliable associations between causal historical processes and biological outcomes; develop a universally standardized scheme for biological classifications; and generally promote novel avenues of thought in many arenas of comparative evolutionary biology.This authoritative reference work brings together, for the first time, experts on all major groups of organisms to assemble a timetree of life. The result is a comprehensive resource on evolutionary history which will be an indispensable reference for scientists, educators, and students in the life sciences, earth sciences, and molecular biology. For each major group of organism, a representative is illustrated and a timetree of families and higher taxonomic groups is shown. Basic aspects ofthe evolutionary history of the group, the fossil record, and competing hypotheses of relationships are discussed. Details of the divergence times are presented for each node in the timetree, and primary literature references are included. The book is complemented by an online database(www.timetree.net) which allows researchers to both deposit and retrieve data.

Download or read book The Molecular Evolutionary Clock written by Simon Y. W. Ho and published by Springer Nature. This book was released on 2021-01-18 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents coverage of the principles and practice of molecular clocks, which have provided fascinating and unprecedented insights into the evolutionary timescale of life on earth. It begins by following the early development of the molecular evolutionary clock in the 1960s, and leads to the complex statistical approaches that are now used to analyse genome sequences. The chapters of this book have been contributed by leading experts in the field and address the important issues of evolutionary rates, molecular dating, and phylogenomic analysis. This is the first time that these different aspects of the molecular clock have been brought together in a single, comprehensive volume. It is an invaluable reference for students and researchers interested in evolutionary biology, genetic analysis, and genomic evolution.

Download or read book Phylonyms written by Kevin de Queiroz and published by CRC Press. This book was released on 2020-04-30 with total page 1030 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylonyms is an implementation of PhyloCode, which is a set of principles, rules, and recommendations governing phylogenetic nomenclature. Nearly 300 clades - lineages of organisms - are defined by reference to hypotheses of phylogenetic history rather than by taxonomic ranks and types. This volume will document the Real World uses of PhyloCode and will govern and apply to the names of clades, while species names will still be governed by traditional codes. Key Features Provides clear regulations for implementing new guidelines for naming lineages of organisms incorporates expressly evolutionary and phylogenetic principles Works with existing codes of nomenclature Eliminates the reliance on rank-based classification in favor of phylogenetic relationships Related Titles: Rieppel, O. Phylogenetic Systematics: Haeckel to Hennig (ISBN 978-1-4987-5488-0) Cantino, P. D. and de Queiroz, K. International Code of Phylogenetic Nomenclature (PhyloCode) (ISBN 978-1-138-33282-9).

Download or read book Mammals from the Age of Dinosaurs written by Zofia Kielan-Jaworowska and published by Columbia University Press. This book was released on 2005-02-05 with total page 649 pages. Available in PDF, EPUB and Kindle. Book excerpt: Few aspects of American military history have been as vigorously debated as Harry Truman's decision to use atomic bombs against Japan. In this carefully crafted volume, Michael Kort describes the wartime circumstances and thinking that form the context for the decision to use these weapons, surveys the major debates related to that decision, and provides a comprehensive collection of key primary source documents that illuminate the behavior of the United States and Japan during the closing days of World War II. Kort opens with a summary of the debate over Hiroshima as it has evolved since 1945. He then provides a historical overview of thye events in question, beginning with the decision and program to build the atomic bomb. Detailing the sequence of events leading to Japan's surrender, he revisits the decisive battles of the Pacific War and the motivations of American and Japanese leaders. Finally, Kort examines ten key issues in the discussion of Hiroshima and guides readers to relevant primary source documents, scholarly books, and articles.

Download or read book Phylogenetic Supertrees written by Olaf R.P. Bininda-Emonds and published by Springer Science & Business Media. This book was released on 2004-05-31 with total page 547 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first book on "phylogenetic supertrees", a recent, but controversial development for inferring evolutionary trees. Rather than analyze the combined primary character data directly, supertree construction proceeds by combining the tree topologies derived from those data. This difference in strategy has allowed for the exciting possibility of larger, more complete phylogenies than are otherwise currently possible, with the potential to revolutionize evolutionarily-based research. This book provides a comprehensive look at supertrees, ranging from the methods used to build supertrees to the significance of supertrees to bioinformatic and biological research. Reviews of many the major supertree methods are provided and four new techniques, including a Bayesian implementation of supertrees, are described for the first time. The far-reaching impact of supertrees on biological research is highlighted both in general terms and through specific examples from diverse clades such as flowering plants, even-toed ungulates, and primates. The book also critically examines the many outstanding challenges and problem areas for this relatively new field, showing the way for supertree construction in the age of genomics. Interdisciplinary contributions from the majority of the leading authorities on supertree construction in all areas of the bioinformatic community (biology, computer sciences, and mathematics) will ensure that this book is a valuable reference with wide appeal to anyone interested in phylogenetic inference.

Download or read book The Age of Mammals in Europe Asia and North America written by Henry Fairfield Osborn and published by . This book was released on 1910 with total page 680 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The Monkey s Voyage written by Alan de Queiroz and published by Basic Books. This book was released on 2014-01-07 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: Throughout the world, closely related species are found on landmasses separated by wide stretches of ocean. What explains these far-flung distributions? Why are such species found where they are across the Earth? Since the discovery of plate tectonics, scientists have conjectured that plants and animals were scattered over the globe by riding pieces of ancient supercontinents as they broke up. In the past decade, however, that theory has foundered, as the genomic revolution has made reams of new data available. And the data has revealed an extraordinary, stranger-than-fiction story that has sparked a scientific upheaval. In The Monkey's Voyage, biologist Alan de Queiroz describes the radical new view of how fragmented distributions came into being: frogs and mammals rode on rafts and icebergs, tiny spiders drifted on storm winds, and plant seeds were carried in the plumage of sea-going birds to create the map of life we see today. In other words, these organisms were not simply constrained by continental fate; they were the makers of their own geographic destiny. And as de Queiroz shows, the effects of oceanic dispersal have been crucial in generating the diversity of life on Earth, from monkeys and guinea pigs in South America to beech trees and kiwi birds in New Zealand. By toppling the idea that the slow process of continental drift is the main force behind the odd distributions of organisms, this theory highlights the dynamic and unpredictable nature of the history of life. In the tradition of John McPhee's Basin and Range, The Monkey's Voyage is a beautifully told narrative that strikingly reveals the importance of contingency in history and the nature of scientific discovery.

Download or read book Bayesian Evolutionary Analysis with BEAST written by Alexei J. Drummond and published by Cambridge University Press. This book was released on 2015-08-06 with total page 263 pages. Available in PDF, EPUB and Kindle. Book excerpt: What are the models used in phylogenetic analysis and what exactly is involved in Bayesian evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you choose and apply these models, which parameterisations and priors make sense, and how can you diagnose Bayesian MCMC when things go wrong? These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. This practical guide: • Addresses the theoretical aspects of the field • Advises on how to prepare and perform phylogenetic analysis • Helps with interpreting analyses and visualisation of phylogenies • Describes the software architecture • Helps developing BEAST 2.2 extensions to allow these models to be extended further. With an accompanying website providing example files and tutorials (http://beast2.org/), this one-stop reference to applying the latest phylogenetic models in BEAST 2 will provide essential guidance for all users – from those using phylogenetic tools, to computational biologists and Bayesian statisticians.

Download or read book Evolving Genes and Proteins written by Vernon Bryson and published by . This book was released on 1965 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Details new perspectives of structural and functional features of proteins and nucleic acids in biochemistry.

Download or read book Computational Molecular Evolution written by Ziheng Yang and published by Oxford University Press, USA. This book was released on 2006-10-05 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book The Biology of Chameleons written by Krystal A. Tolley and published by Univ of California Press. This book was released on 2013-11-16 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: They change color depending on their mood. They possess uniquely adapted hands and feet distinct from other tetrapods. They feature independently movable eyes. This comprehensive volume delves into these fascinating details and thorough research about one of the most charismatic families of reptilesÑChameleonidae. Written for professional herpetologists, scholars, researchers, and students, this book takes readers on a voyage across time to discover everything that is known about chameleon biology: anatomy, physiology, adaptations, ecology, behavior, biogeography, phylogeny, classification, and conservation. A description of the natural history of chameleons is given, along with the fossil record and typical characteristics of each genus. The state of chameleons in the modern world is also depicted, complete with new information on the most serious threats to these remarkable reptiles.

Download or read book Early Flowers and Angiosperm Evolution written by Else Marie Friis and published by Cambridge University Press. This book was released on 2011-08-18 with total page 597 pages. Available in PDF, EPUB and Kindle. Book excerpt: The recent discovery of diverse fossil flowers and floral organs in Cretaceous strata has revealed astonishing details about the structural and systematic diversity of early angiosperms. Exploring the rich fossil record that has accumulated over the last three decades, this is a unique study of the evolutionary history of flowering plants from their earliest phases in obscurity to their dominance in modern vegetation. The discussion provides comprehensive biological and geological background information, before moving on to summarise the fossil record in detail. Including previously unpublished results based on research into Early and Late Cretaceous fossil floras from Europe and North America, the authors draw on direct palaeontological evidence of the pattern of angiosperm evolution through time. Synthesising palaeobotanical data with information from living plants, this unique book explores the latest research in the field, highlighting connections with phylogenetic systematics, structure and the biology of extant angiosperms.

Download or read book Bayesian Phylogenetics written by Ming-Hui Chen and published by CRC Press. This book was released on 2014-05-27 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of current trends in Bayesian phylogenetic research. Encouraging interdisciplinary research, this book introduces state-of-the-art phylogenetics to the Bayesian statistical community and, likewise, presents state-of-the-art Bayesian statistics to the phylogenetics community. The book emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. It also discusses new approaches to improve mixing in Bayesian phylogenetic analyses in which the tree topology varies. In addition, the book covers divergence time estimation, biologically realistic models, and the burgeoning interface between phylogenetics and population genetics.

Download or read book Introduction to Paleobiology and the Fossil Record written by Michael J. Benton and published by John Wiley & Sons. This book was released on 2013-04-25 with total page 1001 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a comprehensive overview of the science of the history of life. Paleobiologists bring many analytical tools to bear in interpreting the fossil record and the book introduces the latest techniques, from multivariate investigations of biogeography and biostratigraphy to engineering analysis of dinosaur skulls, and from homeobox genes to cladistics. All the well-known fossil groups are included, including microfossils and invertebrates, but an important feature is the thorough coverage of plants, vertebrates and trace fossils together with discussion of the origins of both life and the metazoans. All key related subjects are introduced, such as systematics, ecology, evolution and development, stratigraphy and their roles in understanding where life came from and how it evolved and diversified. Unique features of the book are the numerous case studies from current research that lead students to the primary literature, analytical and mathematical explanations and tools, together with associated problem sets and practical schedules for instructors and students. “..any serious student of geology who does not pick this book off the shelf will be putting themselves at a huge disadvantage. The material may be complex, but the text is extremely accessible and well organized, and the book ought to be essential reading for palaeontologists at undergraduate, postgraduate and more advanced levels—both in Britain as well as in North America.” Falcon-Lang, H., Proc. Geol. Assoc. 2010 “...this is an excellent introduction to palaeontology in general. It is well structured, accessibly written and pleasantly informative .....I would recommend this as a standard reference text to all my students without hesitation.” David Norman Geol Mag 2010 Companion website This book includes a companion website at: www.blackwellpublishing.com/paleobiology The website includes: · An ongoing database of additional Practical’s prepared by the authors · Figures from the text for downloading · Useful links for each chapter · Updates from the authors

Download or read book Homology Genes and Evolutionary Innovation written by Günter P. Wagner and published by Princeton University Press. This book was released on 2018-07-10 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: A major synthesis of homology, written by a top researcher in the field Homology—a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird’s wing—is one of the most fundamental yet challenging concepts in evolutionary biology. This groundbreaking book provides the first mechanistically based theory of what homology is and how it arises in evolution. Günter Wagner, one of the preeminent researchers in the field, argues that homology, or character identity, can be explained through the historical continuity of character identity networks—that is, the gene regulatory networks that enable differential gene expression. He shows how character identity is independent of the form and function of the character itself because the same network can activate different effector genes and thus control the development of different shapes, sizes, and qualities of the character. Demonstrating how this theoretical model can provide a foundation for understanding the evolutionary origin of novel characters, Wagner applies it to the origin and evolution of specific systems, such as cell types; skin, hair, and feathers; limbs and digits; and flowers. The first major synthesis of homology to be published in decades, Homology, Genes, and Evolutionary Innovation reveals how a mechanistically based theory can serve as a unifying concept for any branch of science concerned with the structure and development of organisms, and how it can help explain major transitions in evolution and broad patterns of biological diversity.

Download or read book Fossil Fungi written by Thomas N Taylor and published by Academic Press. This book was released on 2014-08-14 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fungi are ubiquitous in the world and responsible for driving the evolution and governing the sustainability of ecosystems now and in the past. Fossil Fungi is the first encyclopedic book devoted exclusively to fossil fungi and their activities through geologic time. The book begins with the historical context of research on fossil fungi (paleomycology), followed by how fungi are formed and studied as fossils, and their age. The next six chapters focus on the major lineages of fungi, arranging them in phylogenetic order and placing the fossils within a systematic framework. For each fossil the age and provenance are provided. Each chapter provides a detailed introduction to the living members of the group and a discussion of the fossils that are believed to belong in this group. The extensive bibliography (~ 2700 entries) includes papers on both extant and fossil fungi. Additional chapters include lichens, fungal spores, and the interactions of fungi with plants, animals, and the geosphere. The final chapter includes a discussion of fossil bacteria and other organisms that are fungal-like in appearance, and known from the fossil record. The book includes more than 475 illustrations, almost all in color, of fossil fungi, line drawings, and portraits of people, as well as a glossary of more than 700 mycological and paleontological terms that will be useful to both biologists and geoscientists. - First book devoted to the whole spectrum of the fossil record of fungi, ranging from Proterozoic fossils to the role of fungi in rock weathering - Detailed discussion of how fossil fungi are preserved and studied - Extensive bibliography with more than 2000 entries - Where possible, fungal fossils are placed in a modern systematic context - Each chapter within the systematic treatment of fungal lineages introduced with an easy-to-understand presentation of the main characters that define extant members - Extensive glossary of more than 700 entries that define both biological, geological, and mycological terminology