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Molecular Methods for Evolutionary Genetics

Editors: Virginie Orgogozo and Matt Rockman
book cover
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 Biology 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.

you can buy this book on amazon.com  or amazon.fr or  springer.com

Table of Contents

R= overview/review papers


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) R
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 Bradić, 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) R
22.    Experimental approaches to evaluate the contributions of candidate protein-coding mutations to phenotypic evolution (Jay F. Storz and Anthony J. Zera) R
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 Nelson and David Fitch)
28.    Gene knockdown analysis by double-stranded RNA injection (Benjamin N. Philip and Yoshinori Tomoyasu)