Phylogenomics

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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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.

• BAC
• Bioinformatics
• DNA
• Evolution
• FISH
• Genomics
• Molecular methods
• Phylogenetics
• chromosome
• genes
• genetics
• genome
• hybridization
• molecular biology

• 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

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