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Phylogenomics

  • Book
  • © 2008

Overview

Editors:
  1. William J. Murphy

    1. Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Mail Stop 4458, Texas A&M University, College Station, USA

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Part of the book series: Methods in Molecular Biology (MIMB, volume 422)

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Table of contents (15 protocols)

  1. Front Matter

    Pages i-x
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  2. From Gene-Scale to Genome-Scale Phylogenetics: the Data Flood In, but the Challenges Remain

    • Antonis Rokas, Stylianos Chatzimanolis
    Pages 1-12

  3. Phylogenomic Analysis by Chromosome Sorting and Painting

    • Roscoe Stanyon, Gary Stone
    Pages 13-29

  4. FISH for Mapping Single Copy Genes

    • Terje Raudsepp, Bhanu P. Chowdhary
    Pages 31-49

  5. Construction of Radiation Hybrid Panels

    • John E. Page, William J. Murphy
    Pages 51-64

  6. Survey Sequencing and Radiation Hybrid Mapping to Construct Comparative Maps

    • Christophe Hitte, Ewen F. Kirkness, Elaine A. Ostrander, Francis Galibert
    Pages 65-77

  7. Construction of High-Resolution Comparative Maps in Mammals Using BAC-End Sequences

    • Denis M. Larkin, Harris A. Lewin
    Pages 79-90

  8. Amniote Phylogenomics: Testing Evolutionary Hypotheses with BAC Library Scanning and Targeted Clone Analysis of Large-Scale DNA Sequences from Reptiles

    • Andrew M. Shedlock, Daniel E. Janes, Scott V. Edwards
    Pages 91-117

  9. Comparative Physical Mapping: Universal Overgo Hybridization Probe Design and BAC Library Hybridization

    • James W. Thomas
    Pages 119-132

  10. Phylogenomic Resources at the UCSC Genome Browser

    • Kate Rosenbloom, James Taylor, Stephen Schaeffer, Jim Kent, David Haussler, Webb Miller
    Pages 133-144

  11. Computational Tools for the Analysis of Rearrangements in Mammalian Genomes

    • Glenn Tesler, Guillaume Bourque
    Pages 145-170

  12. Computational Reconstruction of Ancestral DNA Sequences

    • Mathauieu Blanchette, Abdoulaye Baniré Diallo, Eric D. Green, Webb Miller, David Haussler
    Pages 171-184

  13. Sequencing and Phylogenomic Analysis of Whole Mitochondrial Genomes of Animals

    • Rafael Zardoya, Mónica Suárez
    Pages 185-200

  14. Retroposons: Genetic Footprints on the Evolutionary Paths of Life

    • Hidenori Nishihara, Norihiro Okada
    Pages 201-225

  15. LINE-1 Elements: Analysis by Fluorescence In-Situ Hybridization and Nucleotide Sequences

    • Paul D. Waters, Gauthier Dobigny, Peter J. Waddell, Terence J. Robinson
    Pages 227-237

  16. Identification of Cryptic Sex Chromosomes and Isolation of X- and Y-Borne Genes

    • Paul D. Waters, Jennifer A. Marshall Graves, Katherine Thompson, Natasha Sankovic, Tariq Ezaz
    Pages 239-251

  17. Back Matter

    Pages 253-259
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Keywords

About this book

The past decade has seen the emergence of a new field of scientific inquiry at the intersection of phylogenetics and genomics: phylogenomics. From one perspective, phylogenomics is defined as the use of large genomic data sets to aid in difficult phylogeny problems. Alternatively, phylogenomics may be described as the use of phylogeny and comparative analysis to infer processes of genome evolution. Regardless of how one defines the field, the two app- cations are intertwined. This volume is a collection of protocols and resources compiled by leading researchers in the field and describes many of the molecular methods and bioinformatics tools that have brought this field to fruition in recent years. Several chapters in this volume highlight the use of cytogenetic methods for characterizing the genomes of different species. Fluorescent in-situ hybridization (FISH) is a powerful tool for establishing chromosome homologies between divergent species. The broadest of these techniques is chromosome painting, which in recent years has been performed on members of nearly every order of eutherian mammals, and across marsupial and avian orders. FISH mapping of single copy clones (e. g. cDNAs, fosmids, and BACS) can provide ordered gene mapping from megabase-pair resolution on metaphase preparations down to exquisite kilobase-pair resolution detail with extended-fiber techniques. Other chapters highlight the construction and development of radiation-hybrid (RH) maps, now fueled by thousands of markers from either large scale BAC-end sequencing projects or survey-sequenced genomes.

Editors and Affiliations

  • Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Mail Stop 4458, Texas A&M University, College Station, USA

    William J. Murphy

Bibliographic Information

  • Book Title: Phylogenomics

  • Editors: William J. Murphy

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-581-7

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2008

  • Hardcover ISBN: 978-1-58829-764-8Published: 16 April 2008

  • Softcover ISBN: 978-1-61737-764-8Published: 19 November 2010

  • eBook ISBN: 978-1-59745-581-7Published: 16 July 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 259

  • Number of Illustrations: 52 b/w illustrations

  • Topics: Biochemistry, general, Human Genetics

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