Molecular Methods for Evolutionary Genetics

Genome Size Determination using Flow Cytometry of Propidium Iodide-stained Nuclei.- Chromosome Analysis in Invertebrates and Vertebrates.- Genomic Libraries. I. Construction and Screening of Fosmid Genomic Libraries.- Genomic Libraries. II. Subcloning, Sequencing, and Assembling Large-insert Genomic DNA Clones.- Reduced Representation Methods for Sub-genomic Enrichment and Next-generation Sequencing.- Accessing the Transcriptome: How to Normalize mRNA Pools.- Transcriptome Sequencing Goals, Assembly, and Assessment.- Rapid Retrieval of DNA Target Sequences by Primer Extension Capture.- SNP Discovery and Genotyping for Evolutionary Genetics using RAD Sequencing.- DNA Microarray-based Mutation Discovery and Genotyping.- Genotyping with Sequenom.- Isolating Microsatellite Loci: Looking Back, Looking Ahead.- Design of Custom Oligonucleotide Microarrays for Single Species or Interspecies Hybrids using Array Oligo Selector.- Identification of Homologous Gene Sequences by PCR with Degenerate Primers.- Characterizing cDNA Ends by Circular RACE.- Identification of DNA Sequences that Flank a Known Region by Inverse PCR.- Quantification of Transcript Levels with Quantitative RT-PCR.- Using Pyrosequencing to Measure Allele-specific mRNA Abundance and Infer the Effects of Cis- and Trans-regulatory Differences.- Whole Mount In situ Hybridization of Sectioned Tissues of Species Hybrids to Detect Cis-Regulatory Changes in Gene Expression Pattern.- Identifying Fluorescently Labeled Single Molecules in Image Stacks using Machine Learning.- Experimental Approaches to Evaluate the Contributions of Candidate Cis-regulatory Mutations to Phenotypic Evolution.- Experimental Approaches to Evaluate the Contributions of Candidate Protein-coding Mutations to Phenotypic Evolution.- Making Reporter Gene Constructs to Analyze Cis-regulatory Elements.- PCR-directed In vivo Plasmid Construction using Homologous Recombination in Baker’s Yeast.- Production of Fosmid Genomic Libraries Optimized for Liquid Culture Recombineering and Cross-species Transgensis.- Recombination-mediated Genetic Engineering of Large Genomic DNA Transgenes.- Overlap Extension PCR: An Efficient Method for Transgene Construction.- Gene Knockdown Analysis by Double-stranded RNA Injection