From Gene-Scale to Genome-Scale Phylogenetics: the Data Flood In, but the Challenges Remain -- Phylogenomic Analysis by Chromosome Sorting and Painting -- FISH for Mapping Single Copy Genes -- Construction of Radiation Hybrid Panels -- Survey Sequencing and Radiation Hybrid Mapping to Construct Comparative Maps -- Construction of High-Resolution Comparative Maps in Mammals Using BAC-End Sequences -- Amniote Phylogenomics: Testing Evolutionary Hypotheses with BAC Library Scanning and Targeted Clone Analysis of Large-Scale DNA Sequences from Reptiles -- Comparative Physical Mapping: Universal Overgo Hybridization Probe Design and BAC Library Hybridization -- Phylogenomic Resources at the UCSC Genome Browser -- Computational Tools for the Analysis of Rearrangements in Mammalian Genomes -- Computational Reconstruction of Ancestral DNA Sequences -- Sequencing and Phylogenomic Analysis of Whole Mitochondrial Genomes of Animals -- Retroposons: Genetic Footprints on the Evolutionary Paths of Life -- LINE-1 Elements: Analysis by Fluorescence In-Situ Hybridization and Nucleotide Sequences -- Identification of Cryptic Sex Chromosomes and Isolation of X- and Y-Borne Genes.

The past decade has seen the emergence of a new field of scientific inquiry at the intersection of phylogenetics and genomics: phylogenomics. In Phylogenomics, leading researchers contribute cutting-edge protocols and resources in order to describe many of the molecular methods and bioinformatics tools that have brought this field to fruition. Chapters cover topics such as the use of cytogenetic methods for characterizing the genomes of different species and BAC clone isolation, sequencing, and analysis. Written in the highly successful Methods in Molecular Biology™ series format, each subject is covered with a brief introduction, readily reproducible protocols, a list of the necessary materials and reagents, and tips for troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, Phylogenomics is a resource that will invigorate the comparative analysis of genomes across all branches of the tree of life.