Part I. Sampling and Experimental Design
1. Sampling in Landscape Genomics
Stéphanie Manel, Cécile H. Albert, and Nigel G. Yoccoz
2. oligoTag: A Program for Designing Sets of Tags for Next-Generation Sequencing of Multiplexed Samples
Eric Coissac
3. SNP Discovery in Non-Model Organisms Using 454 Next Generation Sequencing
Christopher W. Wheat
4. ISIF (In Silico Fingerprinting): A User-Friendly in silico AFLP Program
Margot Paris and Laurence Després
Part II. Producing Data
5. Diversity Arrays Technology (DArT) - A Generic Genome Profiling Technology on Open Platforms
Andrzej Kilian, Peter Wenzl, Eric Huttner, Jason Carling, Ling Xia, Hélène Blois, Vanessa Caig, Katarzyna Heller-Uszynska, Damian Jaccoud, Colleen Hopper, Malgorzata Aschenbrenner-Kilian, Margaret Evers, Kaiman Peng, Cyril Cayla, Puthick Hok, and Grzegorz Uszynski
6. Two Methods to Easily Obtain Nucleotide Sequences from AFLP Loci of Interest
Margot Paris, Claire-Lise Meyer, Christelle Blassiau, Eric Coissac, Pierre Taberlet, and Laurence Després
7. Roche Genome Sequencer FLX Based High-Throughput Sequencing of Ancient DNA
David E. Alquezar Planas and Sarah L. Fordyce
8. Preparation of Normalized cDNA Libraries for 454 Titanium Transcriptome Sequencing
Zhao Lai, Yi Zou, Nolan C. Kane, Jeong-Hyeon Choi, Xinguo Wang, and Loren H. Rieseberg
9. RAD Paired-End Sequencing for Local de novo Assembly and SNP Discovery in Non-Model Organisms
Paul D. Etter and Eric Johnson
Part III. Analyzing Data
10. Automated Scoring of AFLPs Using RawGeno v 2.0, A Free R CRAN Library
Nils Arrigo, Rolf Holderegger, and Nadir Alvarez
11. Haplotype Inference
Olivier Delaneau and Jean-Francois Zagury
12. Allele Identification in Assembled Genomic Sequence Datasets
Katrina M. Dlugosch and Aurélie Bonin
13. Multiple-Testing in Large-Scale Genetic Studies
Matthieu Bouaziz, Marine Jeanmougin, and Mickaël Guedj
14. Population Genomic Analysis of Model and Non-Model Species Using Sequenced RAD Tags
Paul A. Hohenlohe, Julian Catchen, and William A. Cresko
15. Analysis and Management of Gene and Allelic Diversity in Subdivided Populations Using the Software Program METAPOP
Andrés Pérez-Figueroa, Silvia T. Rodríguez-Ramilo, and Armando Caballero
16. DETSEL: An R-Package to Detect Marker Loci Responding to Selection
Renaud Vitalis
17. Use of Qualitative Environmental and Phenotypic Variables in the Context of Allele Distribution Models: Detecting Signatures of Selection in the Genome of Lake Victoria Cichilds
Stéphane Joost, Michael Kalbermatten, Etienne Bezault, and Ole Seehausen
18. Genomic Scan as a Tool for Assessing the Genetic Component of Phenotypic Variance in Wild Populations
Carlos M. Herrera
