Part I. Characterizing the Genome

1. Genome Size Determination using Flow Cytometry of Propidium Iodide-stained Nuclei

Emily E. Hare and J. Spencer Johnston

2. Chromosome Analysis in Invertebrates and Vertebrates

David M. Rowell, Shu Ly Lim and Frank Grutzner

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

Mike A. Quail, Lucy Matthews, Sarah Sims, Christine Lloyd, Helen Beasley, and Simon W. Baxter

4. Genomic Libraries. II. Subcloning, Sequencing, and Assembling Large-insert Genomic DNA Clones

Mike A. Quail, Lucy Matthews, Sarah Sims, Christine Lloyd, Helen Beasley, and Simon W. Baxter

Part II. Targeting Regions of the Genome

5. Reduced Representation Methods for Sub-genomic Enrichment and Next-generation Sequencing

Jeffrey M. Good

6. Accessing the Transcriptome: How to Normalize mRNA Pools

Heiko Vogel and Christopher W. Wheat

7. Transcriptome Sequencing Goals, Assembly, and Assessment

Christopher W. Wheat and Heiko Vogel

8. Rapid Retrieval of DNA Target Sequences by Primer Extension Capture

Adrian W. Briggs

Part III. Measuring Genetic Diversity

9. SNP Discovery and Genotyping for Evolutionary Genetics using RAD Sequencing

Paul D. Etter, Susan Bassham, Paul A. Hohenlohe, Eric Johnson, and William A. Cresko

10. DNA Microarray-based Mutation Discovery and Genotyping

David Gresham

11. Genotyping with Sequenom

Martina Bradic, João Costa, and Ivo M. Chelo

12. Isolating Microsatellite Loci: Looking Back, Looking Ahead

José A. Andrés and Steven M. Bogdanowicz

13. Design of Custom Oligonucleotide Microarrays for Single Species or Interspecies Hybrids using Array Oligo Selector

Amy A. Caudy

Part IV. Obtaining Candidate Gene Sequences

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

Michael Lang and Virginie Orgogozo

15. Characterizing cDNA Ends by Circular RACE

Patrick T. McGrath

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

Anastasios Pavlopoulos

Part V. Analyzing Candidate Gene Transcripts

17. Quantification of Transcript Levels with Quantitative RT-PCR

Karen L. Carleton

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

Patricia J. Wittkopp

19. Whole Mount In situ Hybridization of Sectioned Tissues of Species Hybrids to Detect Cis-Regulatory Changes in Gene Expression Pattern

Ryo Futahashi

20. Identifying Fluorescently Labeled Single Molecules in Image Stacks using Machine Learning

Scott Rifkin

Part VI. Testing Candidate Genes and Candidate Mutations

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

Mark Rebeiz and Thomas M. Williams

22. Experimental Approaches to Evaluate the Contributions of Candidate Protein-coding Mutations to Phenotypic Evolution

Jay F. Storz and Anthony J. Zera

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

José Bessa and José Luis Gómez-Skarmeta

24. PCR-directed In vivo Plasmid Construction using Homologous Recombination in Baker's Yeast

Erik C. Andersen

25. Pr