Data production and analysis in population genomics: methods and protocols / ed. by F.Pompanon, A.Bonin. - New York: Humana Press, 2012. - xi, 337 p.: ill. - (Methods in molecular biology; 888) (Springer protocols). - Incl. bibl. ref. - Ind.: p.331-337. - ISBN 978-1-61779-869-6  Место хранения:   021 | Институт цитологии и генетики CO РАН | Новосибирск | Библиотека

Оглавление / Contents

Preface ......................................................... v Contributors ................................................... ix Part I Sampling and Experimental design 1 Sampling in Landscape Genomics ............................... 3 Stéphanie Mattel, Cécile H. Albert, and Nigel G. Yoccoz 2 OligoTag: A Program for Designing Sets of Tags for Next-Generation Sequencing of Multiplexed Samples ........... 13 Eric Coissac 3 SNP Discovery in Non-model Organisms Using 454 Next Generation Sequencing .................................. 33 Christopher W. Wheat 4 In Silico Fingerprinting (ISIF): A User-Friendly In Silico AFLP Program ................................................ 55 Margot Paris and Laurence Despres Part II Producing Data 5 Diversity Arrays Technology: A Generic Genome Profiling Technology on Open Platforms ................................ 67 Andrzej Kilian, Peter Wenzl, Eric Huttner, Jason Carling, Ling Xia, Hélène Blots, 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 ....................................... 91 Margot Paris, Claire-Lise Meyer, Christelle Blassiau, Eric Coissac, Pierre Taberlet, and Laurence Desprès 7 Roche Genome Sequencer FLX Based High-Throughput Sequencing of Ancient DNA .................................. 109 David E. Alquezar-Planas and Sarah L. Fordyce 8 Preparation of Normalized cDNA Libraries for 454 Titanium Transcriptome Sequencing .......................... 119 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 ................... 135 Paul D. Etter and Eric Johnson Part III Analyzing Data 10 Automated Scoring of AFLPs Using RawGeno 2.0, a Free R CRAN Library ............................................... 155 Nils Arrigo, Rolf Holderegger, and Nadir Alvarez 11 Haplotype Inference ........................................ 177 Olivier Delaneau and Jean-François Zagury 12 Allele Identification in Assembled Genomic Sequence Datasets ................................................... 197 Katrina M. Dlugosch and Aurélie Bonin 13 Multiple Testing in Large-Scale Genetic Studies ............ 213 Matthieu Bouaziz, Marine Jeanmougin, and Mickaël Guedj 14 Population Genomic Analysis of Model and Nonmodel Organisms Using Sequenced RAD Tags ......................... 235 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 .. 261 Andrés Pérez-Figueroa, Silvia T. Rodríguez-Ramilo, and Armando Caballero 16 DetSel: An R-Package to Detect Marker Loci Responding to Selection .................................................. 277 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 ................................................... 295 Stephane 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 ....... 315 Carlos M. Herrera Index ......................................................... 331