[PDF] Inferring Phylogenies eBook

Author : Joseph Felsenstein
Publisher : Sinauer Associates Incorporated
Page : 664 pages
File Size : 31,95 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 : Anthony William Fairbank Edwards
Publisher : Cambridge University Press
Page : 553 pages
File Size : 35,77 MB
Release : 2018-07-19
Category : Mathematics
ISBN : 1107111722

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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
Page : 221 pages
File Size : 47,72 MB
Release : 2006-11-25
Category : Science
ISBN : 0387351000

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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
Page : 553 pages
File Size : 14,56 MB
Release : 2018-07-19
Category : Science
ISBN : 1108613985

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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 : David A. Baum
Publisher : Roberts
Page : 0 pages
File Size : 12,90 MB
Release : 2012-08-10
Category : Science
ISBN : 9781936221165

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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 : Pablo A. Goloboff
Publisher : CRC Press
Page : 299 pages
File Size : 40,7 MB
Release : 2022-07-22
Category : Science
ISBN : 1000550036

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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.

Author : Laura Kubatko
Publisher : Princeton University Press
Page : 352 pages
File Size : 37,6 MB
Release : 2023-03-14
Category : Science
ISBN : 0691207607

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"Inferring evolutionary relationships among a collection of organisms -- that is, their relationship to each other on the tree of life -- remains a central focus of much of evolutionary biology as these relationships provide the background for key hypotheses. For example, support for different hypotheses about early animal evolution are contingent upon the phylogenetic relationships among the earliest animal lineages. Within the last 20 years, the field of phylogenetics has grown rapidly, both in the quantity of data available for inference and in the number of methods available for phylogenetic estimation. The authors' first book, "Estimating Species Trees: Practical and Theoretical Aspects", published in 2010, gave an overview of the state of phylogenetic practice for analyzing data at the time, but much has changed since then. The goal of this book is to serve as an updated reference on current methods within the field. The book is organized in three sections, the first of which provides an overview of the analytical and methodological developments of species tree inference. Section two focuses on empirical inference. Section three explores various applications of species trees in evolutionary biology. The combination of theoretical and empirical approaches is meant to provide readers with a level of knowledge of both the advances and limitations of species-tree inference that can help researchers in applying the methods, while also inspiring future advances among those researchers with an interest in methodological development"--

Author : Asheesh Shanker
Publisher : Springer
Page : 402 pages
File Size : 36,26 MB
Release : 2018-10-13
Category : Science
ISBN : 9811315620

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This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files.

Author : Rutger Aldo Vos
Publisher :
Page : 0 pages
File Size : 13,71 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.