The past decade has seen the emergence of a new field of scientific inquiry at the intersection of phylogenetics and genomics: phylogenomics. 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.

The past decade has seen the emergence of a new field of scientific inquiry at the intersection of phylogenetics and genomics: phylogenomics. This volume is a collection of protocols and resources compiled by leading researchers in the field. It describes many of the molecular methods and bioinformatics tools that have brought this field to fruition in recent years. It contains step-by-step instructions that ensure successful results, and provides tricks of the trade and notes on troubleshooting and avoiding known pitfalls.

Contents Preface v Contributors ix 1. From gene-scale to genome-scale phylogenetics; the data flood in but the challenges remain, Antonis Rokas and Stylianos Chatzimanolis 2. Phylogenomic analysis by chromosome sorting and painting, Roscoe Stanyon and Gary Stone 3. FISH for mapping single copy genes, Terje Raudsepp and Bhanu P. Chowdhary 4. Construction of radiation hybrid panels, John E. Page and William J. Murphy 5. Survey sequencing and radiation hybrid mapping to construct comparative maps, Christophe Hitte, Ewen F. Kirkness, Elaine A. Ostrander and Francis Galibert. 6. Construction of high-resolution comparative maps in mammals using BAC-end sequences, Denis M. Larkin and Harris A. Lewin 7. Amniote phylogenomics: testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large scale sequences from reptiles, Andrew M. Shedlock, Daniel Janes and Scott V. Edwards 8. Comparative physical mapping: universal overgo hybridization probe design and BAC library hybridization. James W. Thomas 9. Phylogenomic resources at the UCSC Genome browser, Kate Rosenbloom, James Taylor, Stephen Schaeffer, Jim Kent, David Haussler and Webb Miller 10. Computational tools for the analysis of rearrangments in mammalian genomes, Glenn Tesler and Guillaume Bourque 11. Computational reconstruction of ancestral DNA sequences, Mathieu Blanchette, Abdoulaye Baniré Diallo, Eric D. Green, Webb Miller and David Haussler. 12. Sequencing and phylogenomic analysis of whole mitochondrial genomes of animals, Rafael Zardoya and Mónica Suárez. 13. Retroposons: Genetic Footprints on the Evolutionary Paths of Life. Norihiro Okada and Nishihara Hidenori. 14. LINE-1 elements: analysis by fluorescence in situ hybridization(FISH) and nucleotide sequences, Paul D. Waters, Gauthier Dobigny, Peter J. Waddell and Terence J. Robinson. 15. Identification of cryptic sex chromosomes and isolation of X and Y borne genes, Paul D. Waters, Jennifer A. Marshall Graves, Katherine Thompson, Natasha Sankovic, and Tariq Ezaz.