Phylogenomics »

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.

Preface     v
Contributors     ix
From Gene-Scale to Genome-Scale Phylogenetics: The Data Flood in, but the Challenges Remain   Antonis Rokas   Stylianos Chatzimanolis     1
Phylogenomic Analysis by Chromosome Sorting and Painting   Roscoe Stanyon   Gary Stone     13
FISH for Mapping Single Copy Genes   Terje Raudsepp   Bhanu P. Chowdhary     31
Construction of Radiation Hybrid Panels   John E. Page   William J. Murphy     51
Survey Sequencing and Radiation Hybrid Mapping to Construct Comparative Maps   Christophe Hitte   Ewen F. Kirkness   Elaine A. Ostrander   Francis Galibert     65
Construction of High-Resolution Comparative Maps in Mammals using BAC-End Sequences   Denis M. Larkin   Harris A. Lewin     79
Amniote Phylogenomics: Testing Evolutionary Hypotheses with BAC Library Scanning and Targeted Clone Analysis of Large-Scale Sequences from Reptiles   Andrew M. Shedlock   Daniel E. Janes   Scott V. Edwards     91
Comparative Physical Mapping: Universal Overgo Hybridization Probe Design and BAC Library Hybridization   James W. Thomas     119
Phylogenomic Resources at the UCSC Genome Browser   Kate Rosenbloom   James Taylor   Stephen Schaeffer   Jim Kent   David Haussler   Webb Miller     133
Computational Tools for the Analysis of Rearrangements in Mammalian Genomes   Glenn Tesler   Guillaume Bourque     145
Computational Reconstruction of Ancestral DNA Sequences   Mathieu Blanchette   Abdoulaye Banire Diallo   Eric D. Green   Webb Miller   David Haussler     171
Sequencing and Phylogenomic Analysis of Whole Mitochondrial Genomes of Animals   Rafael Zardoya   Monica Suarez     185
Retroposons: Genetic Footprints on the Evolutionary Paths of Life   Hidenori Nishihara   Norihiro Okada     201
LINE-1 Elements: Analysis by FISH and Nucleotide Sequences   Paul D. Waters   Gauthier Dobigny   Peter J. Waddell   Terence J. Robinson     227
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     239
Index     253