Data production and analysis in population genomics : methods and protocols / edited by Francois Pompanon and Aurelie Bonin. — New York : Humana Press, c2012. – (58.17/M592/v.888)

Contents

    CONTENTS
    
    Preface v
    Contributors ix
    PART I SAMPLING AND EXPERIMENTAL DESIGN
    1 Sampling in Landscape Genomics 3
    2 OligoTag: A Program for Designing Sets of Tags for Next-Generation Sequencing of Multiplexed Samples
    3 SNP Discovery in Non-model Organisms Using 454 Next Generation Sequencing
    4 In Silico Fingerprinting (ISIF): A User-Friendly In Silico AFLP Program
    PART II PRODUCINC; DATA
    5 Diversity Arrays Technology: A Generic Genome Profiling Technology on Open Platforms
    6 Two Methods to Easily Obtain Nucleotide Sequences from AFLP Loci of Interest 91
    7 Roche Genome Sequencer FLX Based High-Throughput Sequencing of Ancient DNA 109
    8 Preparation of Normalized cDNA Libraries for 454 Titanium Transcriptome Sequencing 119
    9 RAD Paired-End Sequencing for Local de Novo Assembly and SNP Discovery in Non-model Organisms 135
    PART III ANALYZING DATA
    10 Automated Scoring of AFLPs Using RawGeno v 2.0， a Free RCRAN Library 155
    11 Haplotype Inference 177
    12 Allele Identification in Assembled Genomic Sequence Datasets 197
    13 Multiple Testing in Large-Scale Genetic Studies 213
    14 Population Genomic Analysis of Model and Nonmodel Organisms Using Sequenced RAD Tags 235
    15 Analysis and Management of Gene and Allelic Diversity in Subdivided Populations Using the Software Program METAPOP 261
    16 DETSEL: An R-Package to Detect Marker Loci Responding to Selection 277
    17 Use of Qualitative Environmental and Phenotypic Variables in the Context of Allele Distribution Models: Detecting Signatures of Selection in the Genome of Lake Victoria Cichilds 295
    18 Genomic Scan as a Tool for Assessing the Genetic Component of Phenotypic Variance in Wild Populations 315
    Index 331