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Phylogenetic Trees Made Easy: A How-to Manual, Third Edition
Phylogenetic Trees Made Easy helps the reader get started in creating phylogenetic trees from protein or nucleic acid sequence data. Although aimed at molecular and cell biologists, who may not be familiar with phylogenetic or evolutionary theory, it also serves students who may be familiar with phylogenetic theory but are unfamiliar with the tools used to apply that theory. The reader is led, step by step, through identifying sequences that are homologous to a sequence of interest, downloading these sequences from databases, creating multiple alignments, and using several different methods to construct trees. Learn More boxes present background on the various concepts and methods, and a website provides files needed for working through the tutorials in the text as well as additional software that facilitates some of the methods discussed. Key Changes to the Third Edition: * Over 90% of the text and screenshots are new. * A new program, MEGA, that has dramatically simplified and sped up the most tedious parts of making trees searching for and downloading sequences, aligning those sequences, and getting them into suitable formats is introduced as the primary tool for constructing trees. * PHYML, another new program that has sped up the Maximum Likelihood method by more than 100-fold, making it a practical alternative to other methods, is introduced. * Chapter 9 is devoted to a detailed method for reconstructing very ancient ancestral sequences, and software to facilitate that method is made available on the website. * Chapter 10 speaks to detecting adaptive evolution. * The final chapter comprises detailed instructions for working with programs on Macintosh, Windows, and Unix platforms..
Price: $35.59
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Inferring Phylogenies
Phylogenies (evolutionary trees) are basic to thinking about and analyzing differences between species. Statistical, computational, and algorithmic work on them has been ongoing for four decades, with great advances in understanding. "Inferring Phylogenies" explains clearly the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes. It is an essential text and reference for anyone who wants to understand how phylogenies are reconstructed and how they are used. As 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. This work is intended for graduate level courses, assuming some knowledge of statistics, mathematics (calculus and fundamental matrix algebra), molecular sequences, and quantitative genetics..
Price: $60.00
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On the Origin of Phyla
Owing its inspiration and title to On the Origin of Phlya, James W. Valentine's ambitious book synthesizes and applies the vast treasury of theory and research collected in the century and a half since Darwin's time. By investigating the origins of life's diversity, Valentine unlocks the mystery of the origin of phyla. One of the twentieth century's most distinguished paleobiologists, Valentine here integrates data from molecular genetics, evolutionary developmental biology, embryology, comparative morphology, and paleontology into an analysis of interest to scholars from any of these fields. He begins by examining the sorts of evidence that can be gleaned from fossils, molecules, and morphology, then reviews and compares the basic morphology and development of animal phyla, emphasizing the important design elements found in the bodyplans of both living and extinct phyla. Finally, Valentine undertakes the monumental task of developing models to explain the origin and early diversification of animal phyla, as well as their later evolutionary patterns. Truly a magnum opus, On the Origin of Phyla will take its place as one of the classic scientific texts of the twentieth century, affecting the work of paleontologists, morphologists, and developmental, molecular, and evolutionary biologists for decades to come. "A magisterial compendium . . . . Valentine offers a judicious evaluation of an astonishing array of evidence."—Richard Fortey, New Scientist
"Truly a magnum opus, On the Origin of Phyla has already taken its place as one of the classic scientific texts of the twentieth century, affecting the work of paleontologists, morphologists, and developmental, molecular, and evolutionary biologists for decades to come."— Ethology, Ecology & Evolution
"Valentine is one of the Renaissance minds of our time. . . . Darwin wisely called his best-known work On the Origin of the Species; the origin of the phyla is an even stickier problem, and Valentine deserves credit for tackling it at such breadth . . . . A magnificient book."—Stefan Bengtson, Nature .
Price: $27.57
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Analysis of Phylogenetics and Evolution with R (Use R)
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. This book integrates 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. 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. .
Price: $41.77
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The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny
The Phylogenetic Handbook is a broad introduction to the theory and practice of nucleotide and amino acid phylogenetic analysis. As an unique feature of this book, each chapter contains an extensive practical section, in which step-by-step exercises on real data sets introduce the most widely used phylogeny software including CLUSTAL, PHYLIP, PAUP*, DAMBE, TREE-PUZZLE, TREECON, SplitsTree, TreeView, SimPlot, MEGA2, PAML and BOOTSCANNING. The book provides a strong background in basic topics: the use of sequence databases, alignment algorithms, tree-building methods, estimation of genetic distances, and testing models of evolution..
Price: $72.98
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The Evolution of Artiodactyls
Artiodactyls are diverse and successful hoofed mammals, represented by nearly two hundred living species of pigs, peccaries, hippos, camels, deer, sheep, cattle, giraffes, and other even-toed ungulates. In the recent years, a tremendous amount of research has been conducted on this important order. The Evolution of Artiodactyls synthesizes this research into a single, comprehensive volume. Here Donald R. Prothero, Scott E. Foss, and a team of distinguished international experts explore a variety of topics, including molecular phylogeny of terrestrial artiodactyls phylogenetic relationships of cetaceans to terrestrial artiodactyls, and the earliest artiodactyls -- Diacodexidae, Dichobunidae, Homacodontidae, Leptochoeridae, and Raoellidae. A landmark reference, The Evolution of Artiodactyls belongs in the library of every paleontologist, mammalogist, and evolutionary biologist. Contributors: Jean-Renaud Boisserie, Muséum National d'Histoire Naturelle; Edward Byrd Davis, University of Oregon; Stéphane Ducrocq, Université de Poitiers; Jörg Erfurt, Martin-Luther-Universität Halle-Wittenberg; Jonathan H. Geisler, Georgia Southern University; Colin P. Groves, Australian National University; John M. Harris, George C. Page Museum; James G. Honey, University of Colorado, Boulder; Christine M. Janis, Brown University; Fabrice Lihoreau, Université de N'Djaména; Matthew R. Liter, Occidental College; Liu Li-Ping, Institute of Vertebrate Paleontology and Paleoanthropology, China; Joshua A. Ludtke, San Diego State University; Jonathan D. Marcot, University of Colorado Museum; Grégoire Métais, Carnegie Museum of Natural History; Gertrud E. Rössner, Ludwig-Maximilians-Universität München; Nikos Solounias, American Museum of Natural History; James Bowie Stevens and Margaret Skeels Stevens, Lamar University; Jessica M. Theodor, University of Calgary; Mark D. Uhen, Cranbrook Institute of Science; Inessa Vislobokova, Russian Academy of Sciences .
Price: $73.35
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Evolutionary Pathways in Nature: A Phylogenetic Approach
Reconstructing phylogenetic trees from DNA sequences has become a popular exercise in many branches of biology, and here the well-known geneticist John Avise explains why. Molecular phylogenies provide a genealogical backdrop for interpreting the evolutionary histories of many other types of biological traits (anatomical, behavioral, ecological, physiological, biochemical and even geographical). Guiding readers on a natural history tour along dozens of evolutionary pathways, the author describes how creatures ranging from microbes to elephants came to possess their current phenotypes. Essential reading for college students, professional biologists and anyone interested in natural history and biodiversity, this book is packed with fascinating examples of evolutionary puzzles from across the animal kingdom; how the toucan got its enormous bill, how reptiles grow back lost limbs and why Arctic fish don't freeze..
Price: $44.76
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Phylogeny and Evolution of the Mollusca
Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable anatomical diversity and include the bivalves (scallops, oysters, and clams), gastropods (limpets, snails, and slugs), and cephalopods (squid, cuttlefish, and octopus). This study treats each major taxon and supplies general information as well as overviews of evolution and phylogeny using data from different sources--morphological, ultrastructural, molecular, developmental, and from the fossil record..
Price: $39.96
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Ontogeny and Phylogeny
"Ontogeny recapitulates phylogeny" was Haeckel's answer--the wrong one--to the most vexing question of nineteenth-century biology: what is the relationship between individual development (ontogeny) and the evolution of species and lineages (phylogeny)? In this, the first major book on the subject in fifty years, Stephen Gould documents the history of the idea of recapitulation from its first appearance among the pre-Socratics to its fall in the early twentieth century. Mr. Gould explores recapitulation as an idea that intrigued politicians and theologians as well as scientists. He shows that Haeckel's hypothesis--that human fetuses with gill slits are, literally, tiny fish, exact replicas of their water-breathing ancestors--had an influence that extended beyond biology into education, criminology, psychoanalysis (Freud and Jung were devout recapitulationists), and racism. The theory of recapitulation, Gould argues, finally collapsed not from the weight of contrary data, but because the rise of Mendelian genetics rendered it untenable. Turning to modern concepts, Gould demonstrates that, even though the whole subject of parallels between ontogeny and phylogeny fell into disrepute, it is still one of the great themes of evolutionary biology. Heterochrony--changes in developmental timing, producing parallels between ontogeny and phylogeny--is shown to be crucial to an understanding of gene regulation, the key to any rapprochement between molecular and evolutionary biology. Gould argues that the primary evolutionary value of heterochrony may lie in immediate ecological advantages for slow or rapid maturation, rather than in long-term changes of form, as all previous theories proclaimed. Neoteny--the opposite of recapitulation--is shown to be the most important determinant of human evolution. We have evolved by retaining the juvenile characters of our ancestors and have achieved both behavioral flexibility and our characteristic morphology thereby (large brains by prolonged retention of rapid fetal growth rates, for example). Gould concludes that there may be nothing new under the sun, but permutation of the old within complex systems can do wonders. As biologists, we deal directly with the kind of material complexity that confers an unbounded potential upon simple, continuous changes in underlying processes. This is the chief joy of our science." .
Price: $24.97
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Animal Evolution: Interrelationships of the Living Phyla
Animal Evolution is a complete analysis of the evolutionary interrelationships and myriad diversity of the animal kingdom. Using modern phylogenetic reasoning based on characters from an extensive review of morphology, including ultrastructure, and embryology, each phylum is analysed to ascertain its monophyly and hence its ancestral characters. These ancestral characters are then used to construct a complete phylogenetic tree of the extant animal phyla. This new edition of Animal Evolution brings the subject fully up to date including some new ideas and emphases, as well as new bibliographic data. It also includes new chapters on the use of computer programmes and on the use of the new molecular techniques to create phylogenies, both techniques that have grown in prevalence in the field since the first edition was published. Illustrated throughout with finely detailed line drawings and clear diagrams. From reviews of the first edition of Animal Evolution: 'A clear and engaging style exemplified by a series of superbly concise descriptions of the phyla.... These are complemented by excellent illustrations.... The volume belongs on every biologist's bookshelf.' Simon Conway- Morris, Nature 'Texts like these constitute the very cream of taxonomic literature.... It really is a joy to read... and in my opinion it constitutes a highly recommended book for all zoologists. I think it is also particularly suited for seminars on animal classification for both undergraduate and graduate students.' JC von Vaupel Klein, Crustaceana 'I highly recommend this book as a fascinating theory of animal relationships, and an excellent summary of the phylogenetically informative aspects of the biology of the whole animal kingdom.' Maximilian J Telford, Systematic Entomology.
Price: $76.06
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