[PDF] Inferring Large Phylogenies eBook

Author : Joseph Felsenstein
Publisher : Sinauer Associates Incorporated
Page : 664 pages
File Size : 11,73 MB
Release : 2004-01
Category : Science
ISBN : 9780878931774

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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 : Rutger Aldo Vos
Publisher :
Page : 582 pages
File Size : 11,44 MB
Release : 2006
Category : Animals
ISBN :

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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 : Masatoshi Nei
Publisher : Oxford University Press
Page : 444 pages
File Size : 12,50 MB
Release : 2000-07-27
Category : Science
ISBN : 0199881227

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During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.

Author : Calyampudi Radhakrishna Rao
Publisher : World Scientific
Page : 213 pages
File Size : 29,27 MB
Release : 1997
Category : Mathematics
ISBN : 9810231113

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Written by one of the top most statisticians with experience in diverse fields of applications of statistics, the book deals with the philosophical and methodological aspects of information technology, collection and analysis of data to provide insight into a problem, whether it is scientific research, policy making by government or decision making in our daily lives.The author dispels the doubts that chance is an expression of our ignorance which makes accurate prediction impossible and illustrates how our thinking has changed with quantification of uncertainty by showing that chance is no longer the obstructor but a way of expressing our knowledge. Indeed, chance can create and help in the investigation of truth. It is eloquently demonstrated with numerous examples of applications that statistics is the science, technology and art of extracting information from data and is based on a study of the laws of chance. It is highlighted how statistical ideas played a vital role in scientific and other investigations even before statistics was recognized as a separate discipline and how statistics is now evolving as a versatile, powerful and inevitable tool in diverse fields of human endeavor such as literature, legal matters, industry, archaeology and medicine.Use of statistics to the layman in improving the quality of life through wise decision making is emphasized.

Author : Rama S. Singh
Publisher : Cambridge University Press
Page : 492 pages
File Size : 26,8 MB
Release : 2004-01-15
Category : Science
ISBN : 1139449540

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This 2004 collection of essays deals with the foundation and historical development of population biology and its relationship to population genetics and population ecology on the one hand and to the rapidly growing fields of molecular quantitative genetics, genomics and bioinformatics on the other. Such an interdisciplinary treatment of population biology has never been attempted before. The volume is set in a historical context, but it has an up-to-date coverage of material in various related fields. The areas covered are the foundation of population biology, life history evolution and demography, density and frequency dependent selection, recent advances in quantitative genetics and bioinformatics, evolutionary case history of model organisms focusing on polymorphisms and selection, mating system evolution and evolution in the hybrid zones, and applied population biology including conservation, infectious diseases and human diversity. This is the third of three volumes published in honour of Richard Lewontin.

Author : Daniel H. Huson
Publisher : Cambridge University Press
Page : 376 pages
File Size : 41,81 MB
Release : 2010-12-02
Category : Science
ISBN : 9780521755962

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The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.

Author :
Publisher : Academic Press
Page : 342 pages
File Size : 18,86 MB
Release : 2017-11-17
Category : Science
ISBN : 0128132620

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Fungal Phylogenetics and Phylogenomics, Volume 100, the latest release in the Advances in Genetics series, presents users with new chapters that delve into such topics as the Advances of fungal phylogenomics and the impact on fungal systematics, Data crunching for fungal phylogenomics: insights into data collection and phylogenetic inference based on genome data for fungi, Genomic and epigenomic traits of emerging fungal pathogens, Advances in fungal gene cluster diversity and evolution, Phylogenomics of Fusarium oxysporum species complex, Phylogenomic analyses of pathogenic yeasts, and the Phylogenetics and phylogenomics of rust fungi. The series continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines, critically analyzing future directions. Critically analyzes future directions for the study of clinical genetics Written and edited by recognized leaders in the field Presents new medical breakthroughs that are occurring as a result of advances in our knowledge of genetics

Author : Steven L. Salzberg
Publisher : Springer Science & Business Media
Page : 440 pages
File Size : 12,14 MB
Release : 2009-08-28
Category : Science
ISBN : 3642042406

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These proceedings contain papers from the 2009 Workshop on Algorithms in Bioinformatics (WABI), held at the University of Pennsylvania in Philadelphia, Pennsylvania during September 12–13, 2009. WABI 2009 was the ninth annual conference in this series, which focuses on novel algorithms that address imp- tantproblemsingenomics,molecularbiology,andevolution.Theconference- phasizes research that describes computationally e?cient algorithms and data structures that have been implemented and tested in simulations and on real data. WABI is sponsored by the European Association for Theoretical C- puter Science (EATCS) and the International Society for Computational Bi- ogy (ISCB). WABI 2009 was supported by the Penn Genome Frontiers Institute and the Penn Center for Bioinformatics at the University of Pennsylvania. For the 2009 conference, 90 full papers were submitted for review by the Program Committee, and from this strong ?eld of submissions, 34 papers were chosen for presentation at the conference and publication in the proceedings. The ?nal programcovered a wide range of topics including gene interaction n- works, molecular phylogeny, RNA and protein structure, and genome evolution.

Author : Roderick D.M. Page
Publisher : John Wiley & Sons
Page : 352 pages
File Size : 44,66 MB
Release : 2009-07-14
Category : Science
ISBN : 1444313363

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The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.

Author :
Publisher :
Page : pages
File Size : 31,14 MB
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Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G.G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis.