Phylogenomics / edited by William J. Murphy. — Totowa, NJ : Humana Press, 2008. – (58.17/M592/v.422)

Contents

    Contents
    
    Preface v
    Contributors ix
    1 From Gene-Scale to Genome-Scale Phylogenetics: The Data Flood in， but the Challenges Remain 1
    2 Phylogenomic Analysis by Chromosome Sorting and Painting 13
    3 FISH for Mapping Single Copy Genes 31
    4 Construction of Radiation Hybrid Panels 51
    5 Survey Sequencing and Radiation Hybrid Mapping to Construct Comparative Maps 65
    6 Construction of High-Resolution Comparative Maps in Mammals using BAC-End Sequences 79
    7 Amniote Phylogenomics: Testing Evolutionary Hypotheses with BAC Library Scanning and Targeted Clone Analysis of Large-Scale Sequences from Reptiles 91
    8 Comparative Physical Mapping: Universal Overgo Hybridization Probe Design and BAC Library Hybridization 119
    9 Phylogenomic Resources at the UCSC Genome Browser 133
    10 Computational Tools for the Analysis of Rearrangements in Mammalian Genomes 145
    11 Computational Reconstruction of Ancestral DNA Sequences 171
    12 Sequencing and Phylogenomic Analysis of Whole Mitochondrial Genomes of Animals 185
    13 Retroposons: Genetic Footprints on the Evolutionary Paths of Life 201
    14 LINE-1 Elements: Analysis by FISH and Nucleotide Sequences 227
    15 Identification of Cryptic Sex Chromosomes and Isolation of X- and Y- Borne Genes 239
    Index 253