Molecular Methods for Evolutionary Genetics

Editors:

ISBN: 978-1-61779-227-4 (Print) 978-1-61779-228-1 (Online)

Table of contents (28 protocols)

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  1. Front Matter

    Pages i-xvi

  2. Characterizing the Genome

    1. Front Matter

      Pages 1-1

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      Pages 3-12

      Genome Size Determination Using Flow Cytometry of Propidium Iodide-Stained Nuclei

    3. No Access

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      Pages 13-35

      Chromosome Analysis in Invertebrates and Vertebrates

    4. No Access

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      Pages 37-58

      Genomic Libraries: I. Construction and Screening of Fosmid Genomic Libraries

    5. No Access

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      Pages 59-81

      Genomic Libraries: II. Subcloning, Sequencing, and Assembling Large-Insert Genomic DNA Clones

  3. Targeting Regions of the Genome

    1. Front Matter

      Pages 83-83

    2. No Access

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      Pages 85-103

      Reduced Representation Methods for Subgenomic Enrichment and Next-Generation Sequencing

    3. No Access

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      Pages 105-128

      Accessing the Transcriptome: How to Normalize mRNA Pools

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      Pages 129-144

      Transcriptome Sequencing Goals, Assembly, and Assessment

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      Pages 145-154

      Rapid Retrieval of DNA Target Sequences by Primer Extension Capture

  4. Measuring Genetic Diversity

    1. Front Matter

      Pages 155-155

    2. No Access

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      Pages 157-178

      SNP Discovery and Genotyping for Evolutionary Genetics Using RAD Sequencing

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      Pages 179-191

      DNA Microarray-Based Mutation Discovery and Genotyping

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      Pages 193-210

      Genotyping with Sequenom

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      Pages 211-232

      Isolating Microsatellite Loci: Looking Back, Looking Ahead

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      Pages 233-241

      Design of Custom Oligonucleotide Microarrays for Single Species or Interspecies Hybrids Using Array Oligo Selector

  5. Obtaining Candidate Gene Sequences

    1. Front Matter

      Pages 243-243

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      Pages 245-256

      Identification of Homologous Gene Sequences by PCR with Degenerate Primers

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      Pages 257-265

      Characterizing cDNA Ends by Circular RACE

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      Pages 267-275

      Identification of DNA Sequences that Flank a Known Region by Inverse PCR

  6. Analyzing Candidate Gene Transcripts

    1. Front Matter

      Pages 277-277

    2. No Access

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      Pages 279-295

      Quantification of Transcript Levels with Quantitative RT-PCR

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      Pages 297-317

      Using Pyrosequencing to Measure Allele-Specific mRNA Abundance and Infer the Effects of Cis- and Trans-regulatory Differences

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      Pages 319-328

      Whole-Mount In Situ Hybridization of Sectioned Tissues of Species Hybrids to Detect Cis-regulatory Changes in Gene Expression Pattern

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      Pages 329-348

      Identifying Fluorescently Labeled Single Molecules in Image Stacks Using Machine Learning

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