Molecular Methods for Evolutionary Genetics by Virginie OrgogozoMolecular Methods for Evolutionary Genetics by Virginie Orgogozo

Molecular Methods for Evolutionary Genetics

EditorVirginie Orgogozo, Matthew V. Rockman

Hardcover | September 29, 2011

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We are entering a particularly fruitful period in evolutionary genetics, as rapid technological progress transforms the investigation of genetic variation within and between species. Molecular Methods for Evolutionary Genetics is a collection of advanced molecular biology protocols and general overviews intended to represent the essential methods currently bringing evolutionary genetics to fruition. Divided into six thematic sections, this volume covers methods for characterizing genomes, diverse approaches to enrich DNA for subsets of the genome prior to sequencing, and state-of-the-art protocols for sampling genetic variation for genetic mapping studies and population genetic studies (RAD sequencing, Sequenom, microarrays, etc.). The volume concludes by focusing on methods to study candidate genes, from obtaining their sequences and analyzing their transcripts to experimentally manipulating their activities in vivo. Written in the highly successful Methods in Molecular BiologyT series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Molecular Methods for Evolutionary Genetics serves as a rich resource to biologists interested in evolution, whether they be specialists or beginners in molecular biology.
Title:Molecular Methods for Evolutionary GeneticsFormat:HardcoverDimensions:519 pagesPublished:September 29, 2011Publisher:Humana PressLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:1617792276

ISBN - 13:9781617792274

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Table of Contents

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 Sequences14. 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 Transcripts17. 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. Production of Fosmid Genomic Libraries Optimized for Liquid Culture Recombineering and Cross-species Transgensis             Radoslaw Kamil Ejsmont, Maria Bogdanzaliewa, Kamil Andrzej Lipinski, and Pavel Tomancak 26. Recombination-mediated Genetic Engineering of Large Genomic DNA Transgenes             Radoslaw Kamil Ejsmont, Peter Ahlfeld, Andrei Pozniakovsky, A. Francis Steward, Pavel Tomancak, and Mihail Sarov 27. Overlap Extension PCR: An Efficient Method for Transgene Construction             Matthew D. Nelson and David H. A. Fitch 28. Gene Knockdown Analysis by Double-stranded RNA Injection             Benjamin N. Philip and Yoshinori Tomoyasu