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1 Octobre 22 Octobre PALÉOGENOMICS Eva Maria GEIGL geigl.eva paris diderot.fr Institut Jacques Monod 15 rue Hélène Brion Paris Direction scientifique : Giovanna Chimini Contact : Dominique Donzella tél :

2 French network of palaeogenetics RTP paléogénétique de l Homme et de son environnement (CNRS INEE) RTP Paleogenetique.htm Ecole thématique Paléogénomique Workshop Palaeogenomics October 17 to 21, 2011 Cargèse, Corsica

3 Program Monday 17/10/2011: Introduction into the field of palaeogenomics 8:30 Welcome address, General Introduction, Practical Aspects Archaeological and sampling methods 9:00 Bruno Maureille: Archaeological context: Excavation of Pleistocene (hominin) remains 9:30 Didier Binder: Archaeological context: Excavation of Holocene remains 10:00 Coffee break Archaeogenetics 10:30 Jean Marc Elalouf: Integrating stratigraphy, DNA and radiocarbon analysis 11:00 Eva Maria Geigl: adna analysis and molecular taphonomy from the field to the laboratory: pitfalls and solutions 11:30 Christine Keyser: Strategies developed by our lab for the analysis of degraded DNA molecules 12:00 Thierry Grange: Introduction into NGS techniques 12:45 Lunch Population Genetics and Phylogenetics 14:30 Evelyne Heyer: The fate of haplotypes through time 15:00 Ludovic Orlando: Serial coalescent: basics, methods and power 15:30 Olivier Gascuel: Introduction into Phylogenetics 16:15 Coffee break Introduction into Bioinformatics 16:45 Eric Rivals: Analysis of genomic data from high throughput sequencing: concepts and basic methods 17:30 Martin Kircher: Using bioinformatics tools from a command line interface. 18:15 Thierry Grange: Using bioinformatics tools from a graphical interface (Galaxy), use of Galaxy for workflow management 19:00 Aurelien Ginolhac: Paleogenomic workflows at CGG

4 Tuesday 18/10/2011: Palaeogenomic: data production and interpretation The power of palaeogenomics 8:30 Hendrik Poinar (keynote address): From Palaeogenetics to Paleogenomics 9:15 Johannes Krause : Palaeogenomics of human evolution 9:45 Morten Rasmussen: Ancient human genomes and history of peopling 10:15 Patrick Hollender: The Ion Torrent Personal Genome Machine 10:30 Coffee break Palaeogenomics: libraries and capture 11:00 Jean Marc Elalouf: Recovery of ancient DNA suitable for metagenomic Illumina sequencing 11:30 E. Andrew Bennett: Various priming strategies: empcr versus tradi PCR 12:00 Hendrik Poinar/Régis Debruyne: Fractionation of ancient DNA extracts when to go short? Enrichment using in solution floating bait. The values of qpcr 12:30 Ludovic Orlando: 3rd generation sequencing of ancient DNA templates: what is different from 2nd generation? 13:00 Lunch 14:15 Morten Rasmussen: Ancient DNA capture strategies 14:45 Johannes Krause: Targeted Enrichment strategies applied to ancient hominin DNA and historic human pathogens 15:45 17:15 Hands on session Bash group I 17:15 18:45 Hands on session Bash group II Coffee break during the Hands on session for the people not involved 18:45 20:00 Short presentations of participants: María C. Ávila Arcos: Application and comparison of large scale solution based DNA captureenrichment methods on ancient DNA Gregory Maes: Marine Conservation Paleogenomics: A novel tool to disentangle historical natural and anthropogenic selective forces triggering genetic adaption in the endangered European eel Pontus Skoglund : Analysis of population structure and demographic history using ancient genomic data Laura Epp : Environmental metabarcoding of permafrost samples to track ancient Arctic ecosystem changes Eline Lorenzen: Species specific responses of Late Quaternary megafauna to climate and humans Cristina Gamba: Modeling the Neolithic impact in North Eastern Iberia: an ancient DNA Perspective Romy Müller: An adna study on tuberculosis in Roman Britain Pascal Barbry: Presentation of «France Génomique», a network of French sequencing platforms

5 Wednesday 19/10/2011: Bioinformatics of palaeogenomics data 8:30 Sarah Palmer: Archaeogenomic analysis of ancient cotton and comparative genome analysis of retroelements in modern and ancient cotton 9:00 Régis Debruyne: Quality of mammoth mitogenomes from different high throughput DNA sources 9:30 Eric Rivals: Analysis of genomic data from high throughput sequencing: algorithms and limitations 10:15 Coffee break 10:45 Martin Kircher Primary data processing: QC of NGS data, Base calling, quality score calibration and filtering Processing ancient DNA data: Paired end read merging of short insert libraries, library complexity/artifacts, endogenous DNA and contamination 11:30 Ludovic Orlando: Evaluating different mapping strategies for 2nd gen and 3rd gen seq data" 12:00 Céline Bon: Quantitative inventory of mammalian species DNA in coprolites using read mapping and de novo assembly 12:30 Lunch 14:00 20:00 Hands on sessions Rivals/Grange/Poncet: Galaxy Read quality analysis and read mapping algorithms Orlando/Ginolhac/Kircher: Ancient DNA NGS data: quality controls made easy Practical course following the presentation using GA/Helicos data

6 Thursday 20/10/2011: Comparative Genomics, Genome evolution, selection 8:30 Olivier Gascuel : Reconstructing ancestral sequences 9:30 Laurent Duret: Detecting positive selection within genomes: the problem of biased gene conversion 10:30 Coffee break 11:00 Lluis Quintana Murci: Detecting natural selection in the human genome: a matter of time and space 11:45 Olivier Gascuel: Model based phylogenetic inference 12:15 Pierre Pontarotti: Reconstruction of ancestral genomes focusing on the appearance of new genes and pseudogenisation 13:00 Lunch 14:30 Martin Kircher: Human derived positions and ancient genomes: Identification of genome differences and revisiting the concepts of SNPs/mutations post 1000 Genomes 15:15 Michael Blum: "Interrogating models of human origins with resequencing data" 16:00 Laurent Duret: The evolution of recombination hotspots in the human genome: insights from paleogenomic data 16:30 Coffee break 17:00 20:00 Hands on session phylogeny parallel sessions or not? Olivier Gascuel: Model based phylogenetic inference and Reconstructing ancestral sequences Michael Blum: R tutorial on approximate Bayesian computation for population genetics

7 Friday 21/10/2011: Environmental and dirt DNA, metagenomics and bacterial genomics 8:30 Denis Le Paslier: Contribution of the new sequencing technologies to metagenomics 9:15 Pascal Simonet: Metagenomics of the soil in the framework of the French national «Metasoil» and the international «Terragenome» project for deep sequencing of the metagenome of a reference soil «10:00 Morten Rasmussen: Palaeogenomics to reconstruct palaeoenvironments. Dirt DNA approaches: methods and related biases 10:45 Coffee break 11:15 Hendrik Poinar: Metagenomic analysis from sedimentary remains 12:00 Sarah Palmer: Microflora and the depositional environment 12:45 Céline Bon: Comparative analysis of the amount of animal and environmental DNA in cave hyena and wolf coprolites 13:15 Lunch 14:30 Hands on session metagenomics Joseph Nesme: Introduction to data analysis of metagenomic soil sequences Sarah Palmer: NGS metagenomic analysis using BLASTn and MEGAN Rescue period for the other hands on sessions

8 Lecturer s affiliations: Bennett, E. Andrew Institut Jacques Monod, Paris, France Binder, Didier CEPAM UMR6130, University Nice Sophia Antipolis, France Blum, Michael TIMC laboratory, Medical School, La Tronche, France Bon, Céline CEA Saclay, France Debruyne, Régis Muséum National d Histoire Naturelle, Paris, France Duret, Laurent University of Lyon, France Elalouf, Jean Marc CEA Saclay, France Gascuel, Olivier LIRMM CNRS, University of Montpellier, France Geigl, Eva Maria Institut Jacques Monod, Paris, France Ginolhac, Aurélien University of Copenhagen, Denmark Grange, Thierry Institut Jacques Monod, Paris, France Heyer, Evelyne Muséum National d Histoire Naturelle, Paris, France Keyser, Christine Institut de Médecine Légale, Laboratoire AMIS, UMR 5288, Strasbourg, France Kircher, Martin Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany Krause, Johannes Eberhard Ludwig University, Tübingen, Germany Le Paslier, Denis CEA, Gensocope, Evry, France Maureille, Bruno University of Bordeaux I, UMR5199 PACEA, France Nesme, Joseph Ecole Centrale, CNRS, Ecully, France Orlando, Ludovic University of Copenhagen, Denmark Palmer, Sarah University of Warwick, Great Britain Poinar Hendrik McMaster University, Hamilton, Ontario, Canada Poncet, Romain Institut Jacques Monod, Paris, France Pontarotti, Pierre University of Marseille, CNRS, France Prestat, Emmanuel Ecole Centrale, CNRS, Ecully, France Quintana Murci, Lluis Institut Pasteur, Paris, France Rasmussen, Morten University of Copenhagen, Denmark Rivals, Eric LIRMM CNRS, University of Montpellier, France Simonet, Pascal Ecole Centrale, CNRS, Ecully, France