Molecular Methods for Evolutionary Genetics

Chapter 1 Genome Size Determination Using Flow Cytometry of Propidium Iodide-Stained Nuclei

Chapter 2 Chromosome Analysis in Invertebrates and Vertebrates

Chapter 3 Genomic libraries: I. Construction and screening of fosmid genomic libraries.

Chapter 4 Genomic Libraries: II. Subcloning, Sequencing, and Assembling Large-Insert Genomic DNA Clones.

Chapter 5 Reduced Representation Methods for Subgenomic Enrichment and Next-Generation Sequencing

Chapter 6 Accessing the Transcriptome: How to Normalize mRNA Pools

Chapter 7 Transcriptome Sequencing Goals, Assembly, and Assessment

Chapter 8 Rapid retrieval of DNA target sequences by primer extension capture.

Chapter 9 SNP Discovery and Genotyping for Evolutionary Genetics Using RAD Sequencing.

Chapter 10 DNA Microarray-Based Mutation Discovery and Genotyping

Chapter 11 Genotyping with Sequenom

Chapter 12 Isolating Microsatellite Loci: Looking Back, Looking Ahead

Chapter 13 Design of Custom Oligonucleotide Microarrays for Single Species or Interspecies Hybrids Using Array Oligo Selector

Chapter 14 Identification of Homologous Gene Sequences by PCR with Degenerate Primers

Chapter 15 Characterizing cDNA Ends by Circular RACE

Chapter 16 Identification of DNA Sequences that Flank a Known Region by Inverse PCR

Chapter 17 Quantification of Transcript Levels with Quantitative RT-PCR

Chapter 18 Using Pyrosequencing to Measure Allele-Specific mRNA Abundance and Infer the Effects of Cis- and Trans-regulatory Differences

Chapter 19 Whole-Mount In Situ Hybridization of Sectioned Tissues of Species Hybrids to Detect Cis -regulatory Changes in Gene Expression Pattern

Chapter 20 Identifying Fluorescently Labeled Single Molecules in Image Stacks Using Machine Learning

Chapter 21 Experimental Approaches to Evaluate the Contributions of Candidate Cis- regulatory Mutations to Phenotypic Evolution

Chapter 22 Experimental Approaches to Evaluate the Contributions of Candidate Protein-Coding Mutations to Phenotypic Evolution

Chapter 23 Making Reporter Gene Constructs to Analyze Cis -regulatory Elements

Chapter 24 PCR-Directed In Vivo Plasmid Construction Using Homologous Recombination in Baker’s Yeast

Chapter 25 Production of Fosmid Genomic Libraries Optimized for Liquid Culture Recombineering and Cross-Species Transgenesis

Chapter 26 Recombination-Mediated Genetic Engineering of Large Genomic DNA Transgenes

Chapter 27 Overlap Extension PCR: An Efficient Method for Transgene Construction

Chapter 28 Gene Knockdown Analysis by Double-Stranded RNA Injection