Inferring Phylogenies

Yet no book has summarized this work until now. Inferring Phylogenies explains clearly the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes.


Author: Joseph Felsenstein

Publisher: Sinauer Associates Incorporated

ISBN: 0878931775

Category: Science

Page: 664

View: 734

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.

The Phylogenetic Handbook

Numerical methods for inferring evolutionary trees. Quarterly Review of Biology, 57, 3794404. Felsenstein, I. (1984). Distance methods for inferring phylogenies: a justification. Evolution, 38, 16*24. Felsenstein, I. (1985).


Author: Philippe Lemey

Publisher: Cambridge University Press

ISBN: 9780521877107

Category: Science

Page: 723

View: 184

A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

The Text of Galatians and Its History

Therefore , it must be kept in mind that the result of a cladistic analysis of the data by any computer program does not necessarily represent the actual 125 126 127 128 129 121 122 123 124 Felsenstein , Inferring Phylogenies , 24–25 .


Author: Stephen C. Carlson

Publisher: Mohr Siebeck

ISBN: 3161533232

Category: Religion

Page: 322

View: 290

Based on the author's doctoral dissertation. This volume investigates the text of Paul's Epistle to the Galatians and its history, how it changed over time. This wok performs a stemmatic analysis of 92 witnesses to the text of Galatians, using cladistic methods developed by computational biologists, to construct an unoriented stemma of the textual tradition. The stemma is then oriented based on the internal evidence of textual variants.

Analysis of Phylogenetics and Evolution with R

Inferring Phylogenies. Sinauer Associates, Sunderland, MA. [40] Felsenstein J. & Churchill G. A. 1996. A Hidden Markov model approach to variation among sites in rate of evolution. Molecular Biology and Evolution 13: 93–104.


Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 9780387351001

Category: Science

Page: 211

View: 884

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.

Estimating Species Trees

Inferring Phylogenies. Sunderland, MA: Sinauer Associates. Hey, J. 1994. Bridging phylogenetics and population genetics with gene tree models. In B. Shierwater, B. Streit, G. Wagner, and R. DeSalle, eds. Molecular Ecology and Evolution: ...


Author: L. Lacey Knowles

Publisher: John Wiley and Sons

ISBN: 9781118126028

Category: Science

Page: 232

View: 856

Recent computational and modeling advances have produced methods for estimating species trees directly, avoiding the problems and limitations of the traditional phylogenetic paradigm where an estimated gene tree is equated with the history of species divergence. The overarching goal of the volume is to increase the visibility and use of these new methods by the entire phylogenetic community by specifically addressing several challenges: (i) firm understanding of the theoretical underpinnings of the methodology, (ii) empirical examples demonstrating the utility of the methodology as well as its limitations, and (iii) attention to technical aspects involved in the actual software implementation of the methodology. As such, this volume will not only be poised to become the quintessential guide to training the next generation of researchers, but it will also be instrumental in ushering in a new phylogenetic paradigm for the 21st century.

Phylogenetic Ecology

Conversely, for those mapping trait evolution and biogeographic history onto phylogenetic trees to infer the assembly of biotas, typical phylogenetic ecology phylogenies generated from easily implemented informatics tools are not good ...


Author: Nathan G. Swenson


ISBN: 9780226671505

Category: Science

Page: 240

View: 212

Over the past decade, ecologists have increasingly embraced phylogenetics, the study of evolutionary relationships among species. As a result, they have come to discover the field's power to illuminate present ecological patterns and processes. Ecologists are now investigating whether phylogenetic diversity is a better measure of ecosystem health than more traditional metrics like species diversity, whether it can predict the future structure and function of communities and ecosystems, and whether conservationists might prioritize it when formulating conservation plans. In Phylogenetic Ecology, Nathan G. Swenson synthesizes this nascent field's major conceptual, methodological, and empirical developments to provide students and practicing ecologists with a foundational overview. Along the way, he highlights those realms of phylogenetic ecology that will likely increase in relevance--such as the burgeoning subfield of phylogenomics--and shows how ecologists might lean on these new perspectives to inform their research programs.

Phylogenetic Inference of the Tibeto Burman Languages Or on the Usefulness of Lexicostatistics and megalo comparison for the Subgrouping of Tibeto Burman

Biologists have developed a number of different algorithms designed to infer phylogenies (see Felsenstein 2004 for a general review). These algorithms are particularly useful as they allow the researcher to calculate huge amounts of ...



Publisher: Stanford University

ISBN: STANFORD:wv919xj7158



View: 160

It has been argued that lexicostatistical methods cannot be fruitfully applied to the Tibeto-Burman (or the larger Sino-Tibetan) language family. This dissertation first develops a statistical method for determining linguistic cognates (or sound correspondences) between arbitrarily many languages. This method is then applied to a subset of the Sino-Tibetan languages to infer the correspondences and further develops a method for lexicostatistical analysis for subgrouping those languages. The output of these methods agrees very well with that determined by the traditional comparative method. Furthermore, this method yields both greater resolution of the subgroupings, and provides statistical inference of the confidence in the various groupings.

Microbial Phylogeny and Evolution

N. Galtier and M. Guoy, “Inferring Phylogenies from DNA Sequences of Unequal Base Compositions,” Proc. Natl. Acad. Sci. USA 92 (1995): 11317–11321. N. Galtier, N. Tourasse, and M. Gouy, “A Nonhyperthermophilic Common Ancestor to Extant ...


Author: Jan Sapp

Publisher: Oxford University Press

ISBN: 9780190290726

Category: Science

Page: 352

View: 356

The birth of bacterial genomics since the mid-1990s brought withit several conceptual modifications and wholly new controversies. Working beyond the scope of the neo-Darwinian evolutionary synthesis, a group of leading microbial evolutionists addresses the following and related issues, often with markedly varied viewpoints: · Did the eukaryotic nucleus, cytoskeleton and cilia also orginate from symbiosis? · Do the current scenarios about he origin of mitochondria and plastids require revision? · What is the extent of lateral gene transfer (between "species") among bacteria? · Does the rDNA phylogenetic tree still stand in the age of genomics? · Is the course of the first 3 billion years of evolution even knowable?

Handbook of Computational Molecular Biology

It also means that methods designed for inferring phylogenies need to be robust to missing taxa. ... that is used for reconstructing the phylogeny truly represents interspecific variation rather than ancestral variation that has been ...


Author: Srinivas Aluru

Publisher: CRC Press

ISBN: 9781420036275

Category: Computers

Page: 1104

View: 614

The enormous complexity of biological systems at the molecular level must be answered with powerful computational methods. Computational biology is a young field, but has seen rapid growth and advancement over the past few decades. Surveying the progress made in this multidisciplinary field, the Handbook of Computational Molecular Biology of

Understanding Bioinformatics

Saitou N & Nei M ( 1987 ) The neighbor - joining method : a new method for reconstructing phylogenetic trees . Mol . Biol . Evol . 4 , 406–425 . ... Felsenstein J ( 2004 ) Inferring Phylogenies , chapter 20 . Sunderland , MA : Sinauer .


Author: Marketa J. Zvelebil

Publisher: Garland Science

ISBN: 0815340249

Category: Medical

Page: 772

View: 166

Suitable for advanced undergraduates & postgraduates, this book provides a definitive guide to bioinformatics. It takes a conceptual approach & guides the reader from first principles through to an understanding of the computational techniques & the key algorithms.