Population genomics is a recently emerged discipline, which aims at understanding how evolutionary processes influence genetic variation across genomes. Today, in the era of cheaper next-generation sequencing, it is no longer as daunting to obtain whole genome data for any species of interest and population genomics is now conceivable in a wide range of fields, from medicine and pharmacology to ecology and evolutionary biology. However, because of the lack of reference genome and of enough a priori data on the polymorphism, population genomics analyses of populations will still involve higher constraints for researchers working on non-model organisms, as regards the choice of the genotyping/sequencing technique or that of the analysis methods. Therefore, Data Production and Analysis in Population Genomics purposely puts emphasis on protocols and methods that are applicable to species where genomic resources are still scarce. It is divided into three convenient sections, each one tackling one of the main challenges facing scientists setting up a population genomics study. The first section helps devising a sampling and/or experimental design suitable to address the biological question of interest. The second section addresses how to implement the best genotyping or sequencing method to obtain the required data given the time and cost constraints as well as the other genetic resources already available, Finally, the last section is about making the most of the (generally huge) dataset produced by using appropriate analysis methods in order to reach a biologically relevant conclusion. Written in the successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, advice on methodology and implementation, and notes on troubleshooting and avoiding known pitfalls.

 

Authoritative and easily accessible, Data Production and Analysis in Population Genomics serves a wide readership by providing guidelines to help choose and implement the best experimental or analytical strategy for a given purpose.

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