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Author: Joseph Felsenstein
Publisher: Sinauer Associates Incorporated
ISBN: 9780878931774
Category : Science
Languages : en
Pages : 664
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Book Description
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.
Author: Joseph Felsenstein
Publisher: Sinauer Associates Incorporated
ISBN: 9780878931774
Category : Science
Languages : en
Pages : 664
Get Book Here
Book Description
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.
Author: Joseph Felsenstein
Publisher:
ISBN: 9781605355009
Category :
Languages : en
Pages : 580
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Book Description
Author: Anthony William Fairbank Edwards
Publisher: Cambridge University Press
ISBN: 1107111722
Category : Mathematics
Languages : en
Pages : 553
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Book Description
Seminal papers by A. W. F. Edwards, published together for the first time with commentaries from leading experts to contextualise his contribution.
Author: Emmanuel Paradis
Publisher: Springer Science & Business Media
ISBN: 0387351000
Category : Science
Languages : en
Pages : 221
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Book Description
This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. 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. 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.
Author: Rasmus Grønfeldt Winther
Publisher: Cambridge University Press
ISBN: 1108613985
Category : Science
Languages : en
Pages : 553
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Book Description
A. W. F. Edwards is one of the most influential mathematical geneticists in the history of the discipline. One of the last students of R. A. Fisher, Edwards pioneered the statistical analysis of phylogeny in collaboration with L. L. Cavalli-Sforza, and helped establish Fisher's concept of likelihood as a standard of statistical and scientific inference. In this book, edited by philosopher of science Rasmus Grønfeldt Winther, Edwards's key papers are assembled alongside commentaries by leading scientists, discussing Edwards's influence on their own research and on thinking in their field overall. In an extensive interview with Winther, Edwards offers his thoughts on his contributions, their legacy, and the context in which they emerged. This book is a resource both for anyone interested in the history and philosophy of genetics, statistics, and science, and for scientists seeking to develop new algorithmic and statistical methods for understanding the genetic relationships between and among species both extant and extinct.
Author: Olaf R.P. Bininda-Emonds
Publisher: Springer Science & Business Media
ISBN: 1402023308
Category : Science
Languages : en
Pages : 547
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Book Description
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.
Author: David A. Baum
Publisher: Roberts
ISBN: 9781936221165
Category : Science
Languages : en
Pages : 0
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Book Description
Baum and Smith, both professors evolutionary biology and researchers in the field of systematics, present this highly accessible introduction to phylogenetics and its importance in modern biology. Ever since Darwin, the evolutionary histories of organisms have been portrayed in the form of branching trees or “phylogenies.” However, the broad significance of the phylogenetic trees has come to be appreciated only quite recently. Phylogenetics has myriad applications in biology, from discovering the features present in ancestral organisms, to finding the sources of invasive species and infectious diseases, to identifying our closest living (and extinct) hominid relatives. Taking a conceptual approach, Tree Thinking introduces readers to the interpretation of phylogenetic trees, how these trees can be reconstructed, and how they can be used to answer biological questions. Examples and vivid metaphors are incorporated throughout, and each chapter concludes with a set of problems, valuable for both students and teachers. Tree Thinking is must-have textbook for any student seeking a solid foundation in this fundamental area of evolutionary biology.
Author: Emília P. Martins
Publisher: Oxford University Press, USA
ISBN: 0195092104
Category : Animal behavior
Languages : en
Pages : 429
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Book Description
In the last ten years, the "comparative method" has been revolutionized by modern statistical ways of incorporating phylogenies into the design and analysis of comparative studies. The results of this revolution are particularly important in the study of animal behavior, which has relied on interspecific comparisons to infer universal trends and evolutionary patterns. The chapters of this edited volume consider the impact of modern phylogenetic comparative methods on the study of animal behavior and discuss the main issues that need to be considered in design and analysis of a comparative study, considers possible differences between the evolution of behavior and the evolution of morphology, and reviews how phylogenetic comparative studies have been used in certain areas of behavioral research.
Author: Rutger Aldo Vos
Publisher:
ISBN:
Category : Animals
Languages : en
Pages : 0
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Book Description
Phylogenetic trees are graph-like structures whose topology describes the inferred pattern of relationships among a set of biological entities, such as species or DNA sequences. Inference of these phylogenies typically involves evaluating large numbers of possible solutions and choosing the optimal topology, or set of topologies, from among all evaluated solutions. Such analyses are computationally intensive, especially when the pattern of relationships among a large number of entities is being sought. This thesis introduces two novel algorithms for the inference of large trees; one is applicable to the likelihood framework, the other to the Bayesian framework. Both approaches rely on the notion of a multi-modal tree 'landscape' through which inferential algorithms traverse. Using sampling techniques, the landscape can be perturbed sequentially, such that local optima can be evaded. The algorithms find good solutions in reasonable time, as demonstrated using real and simulated data sets. An example of large phylogeny inference is presented in the form of a novel estimate of Primate phylogeny- the largest estimate for this Order to date. The phylogeny is based on previously published smaller phylogenies, and hence serves as a summary of the present state of Primate phylogeny. In addition to this 'supertree's' topology, composite estimates of divergence are provided also. These estimates are based on multiple, clock-like genes combined using a novel approach presented here. Handling sets of trees and sequences poses practical problems in terms of conversion of data and the interoperation between computer programs. The thesis therefore concludes with a chapter discussing suitable data structures and programming patterns for phylogenetics. The appendix discusses an implementation of some of these concepts in an object-oriented application programming interface.
Author: Pablo A. Goloboff
Publisher: CRC Press
ISBN: 1000550036
Category : Science
Languages : en
Pages : 299
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Book Description
Taxonomists specializing in different groups once based phylogenetic analysis only on morphological data; molecular data was used more rarely. Although molecular systematics is routine today, the use of morphological data continues to be important, especially for phylogenetic placement of many taxa known only from fossils and rare or difficult to collect species. In addition, morphological analyses help identify potential biases in molecular analyses. And finally, scenarios with respect to morphology continue to motivate biologists: the beauty of a cheetah or a baobab does not lie in their DNA sequence, but instead on what they are and do! This book is an up-to-date revision of methods and principles of phylogenetic analysis of morphological data. It is also a general guide for using the computer program TNT in the analysis of such data. The book covers the main aspects of phylogenetic analysis and general methods to compare classifications derived from molecules and morphology. The basic aspects of molecular analysis are covered only as needed to highlight the differences with methods and assumptions for analysis of morphological datasets.
