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