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.

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.

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.