Includes bibliographical references and index.

Characterizing the genome. Genome size determination using flow cyto metry of propidium iodide-stained nuclei / Emily E. Hare and J. Spencer Johnston. Chromosome analysis in invertebrates and vertebrates / David M. Rowell, Shu Ly Lim, and Frank Grutzner. Genomic libraries : I. Cons tuction and screening of fosmid genomic libraries / Mike A. Quail ... [ et al.] Genomic libraries : II. Subcloning, sequencing, and assembling large-insert genomic DNA clones / Mike A. Quail ... [et al.] -- Targeti ng regions of the genome. Reduced representation methods for subgenomic enrichment and next-generation sequencing / Jeffrey M. Good. Accessing the transcriptome : how to normalize mRNA pools / Heiko Vogel and Chri stopher W. Wheat. Transcriptome sequencing goals, assembly, and assessm ent / Christopher W. Wheat and Heiko Vogel. Rapid retrieval of DNA targ et sequences by primer extension capture / Adrian W. Briggs -- Measurin g genetic diversity. SNP discovery and genotyping for evolutionary gene tics using RAD sequencing / Paul D. Etter ... [et al.] DNA microarray-b ased mutation discovery and genotyping / David Gresham. Genotyping with Sequenom / Martina Bradiâc, Joäao Costa, and Ivo M. Chelo. Isolating m icrosatellite loci : looking back, looking ahead / Josâe A. Andrâes and Steven M. Bogdanowicz. Design of custom oligonucleotide microarrays fo r single species or interspecies hybrids using array olico selector / A my A. Caudy -- Obtaining candidate gene sequences. Identification of ho mologous gene sequences by PCR with degenerate primers / Michael Lang a nd Virginie Orgogozo.

Characterizing cDNA ends by circular RACE / Patrick T. McGrath. Iden tification of DNA sequences that flank a known region by inverse PCR / Anastasios Pavlopoulos -- Analyzing candidate gene transcripts. Quantif ication of transcript levels with quantitative RT-PCR / Karen L. Carlet on. Using pyrosequencing to measure allele-specific mRNA abundance and infer the effects of cis- and trans-regulatory differences / Patricia J . Wittkopp. Whole-mount in situ hybridization of sectioned tissues of s pecies hybrids to detect cis-regulatory changes in gene expression patt ern / Ryo Futahashi. Identifying fluorescently labeled single molecules in image stacks using machine learning / Scott A. Rifkin -- Testing ca ndidate genes and candidate mutations. Experimental approaches to evalu ate the contributions of candidate cis-regulatory mutations to phenotyp ic evolution / Mark Rebeiz and Thomas M. Williams. Experimental approac hes to evaluate the contributions of candidate protein-coding mutations to pheotypic evolution / Jay F. Storz and Anthony J. Zera. Making repo rter gene constructs to analyze cis-regulatory elements / Josâe Bessa a nd Josâe Luis Gâomez-Skarmeta. PCR directed in vivo plasmid constructio n using homologous recombination in baker's yeast / Erik C. Andersen. P roduction of fosmid genomic libraries optimized for liquid culture reco mbineering and cross-species transgenesis / Radoslaw Kamil Ejsmont ... [et al.] Recombination-mediated genetic engineering of large genomic DN A transgenes / Radoslaw Kamil Ejsmont ... [et al.] Overlap extension PC R : an efficient method for transgene construction / Matthew D. Nelson and David H.A. Fitch. Gene knockdown analysis by double-stranded RNA in jection / Benjamin N. Philip and Yoshinori Tomoyasu.