PALÉOGENOMICS - Institut d'études scientifiques de Cargèse (IESC)
PALÉOGENOMICS - Institut d'études scientifiques de Cargèse (IESC)
PALÉOGENOMICS - Institut d'études scientifiques de Cargèse (IESC)
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2011<br />
17 Octobre<br />
22 Octobre<br />
<strong>PALÉOGENOMICS</strong><br />
Eva‐Maria GEIGL<br />
geigl.eva‐maria@ijm.univ‐paris‐di<strong>de</strong>rot.fr<br />
<strong>Institut</strong> Jacques Monod<br />
15 rue Hélène Brion<br />
75013 Paris<br />
01 57 27 81 82<br />
Direction scientifique :<br />
Giovanna Chimini<br />
Contact :<br />
Dominique Donzella<br />
tél : 04 95 26 80 40<br />
www.iesc.univ-corse.fr
French network of palaeogenetics<br />
RTP “paléogénétique <strong>de</strong> l’Homme et <strong>de</strong> son environnement”<br />
(CNRS‐INEE)<br />
http://www.cnrs.fr/inee/recherche/actionsincitatives‐RTP‐Paleogenetique.htm<br />
Ecole thématique “Paléogénomique”<br />
Workshop “Palaeogenomics”<br />
https://sites.google.com/site/palaeogenomicssummerschool2011/<br />
October 17 to 21, 2011<br />
<strong>Cargèse</strong>, Corsica
Program<br />
Monday 17/10/2011: Introduction into the field of palaeogenomics<br />
8:30 Welcome address, General Introduction, Practical Aspects<br />
Archaeological and sampling methods<br />
9:00 Bruno Maureille: Archaeological context: Excavation of Pleistocene (hominin) remains<br />
9:30 Didier Bin<strong>de</strong>r: Archaeological context: Excavation of Holocene remains<br />
10:00 Coffee break<br />
Archaeogenetics<br />
10:30 Jean‐Marc Elalouf: Integrating stratigraphy, DNA and radiocarbon analysis<br />
11:00 Eva‐Maria Geigl: aDNA analysis and molecular taphonomy‐ from the field to the laboratory:<br />
pitfalls and solutions<br />
11:30 Christine Keyser: Strategies <strong>de</strong>veloped by our lab for the analysis of <strong>de</strong>gra<strong>de</strong>d DNA molecules<br />
12:00 Thierry Grange: Introduction into NGS techniques<br />
12:45 Lunch<br />
Population Genetics and Phylogenetics<br />
14:30 Evelyne Heyer: The fate of haplotypes through time<br />
15:00 Ludovic Orlando: Serial coalescent: basics, methods and power<br />
15:30 Olivier Gascuel: Introduction into Phylogenetics<br />
16:15 Coffee break<br />
Introduction into Bioinformatics<br />
16:45 Eric Rivals: Analysis of genomic data from high throughput sequencing: concepts and basic<br />
methods<br />
17:30 Martin Kircher: Using bioinformatics tools from a command line interface.<br />
18:15 Thierry Grange: Using bioinformatics tools from a graphical interface (Galaxy), use of Galaxy<br />
for workflow management<br />
19:00 Aurelien Ginolhac: Paleogenomic workflows at CGG
Tuesday 18/10/2011: Palaeogenomic: data production and interpretation<br />
The power of palaeogenomics<br />
8:30 Hendrik Poinar (keynote address): From Palaeogenetics to Paleogenomics<br />
9:15 Johannes Krause : Palaeogenomics of human evolution<br />
9:45 Morten Rasmussen: Ancient human genomes and history of peopling<br />
10:15 Patrick Hollen<strong>de</strong>r: The Ion Torrent Personal Genome Machine<br />
10:30 Coffee break<br />
Palaeogenomics: libraries and capture<br />
11:00 Jean‐Marc Elalouf: Recovery of ancient DNA suitable for metagenomic Illumina sequencing<br />
11:30 E. Andrew Bennett: Various priming strategies: emPCR versus tradi PCR<br />
12:00 Hendrik Poinar/Régis Debruyne: Fractionation of ancient DNA extracts‐ when to go short?<br />
Enrichment using in solution floating bait. The values of qPCR<br />
12:30 Ludovic Orlando: 3rd generation sequencing of ancient DNA templates: what is different from<br />
2nd generation?<br />
13:00 Lunch<br />
14:15 Morten Rasmussen: Ancient DNA capture strategies<br />
14:45 Johannes Krause: Targeted Enrichment strategies applied to ancient hominin DNA and<br />
historic human pathogens<br />
15:45 – 17:15 Hands‐on session Bash group I<br />
17:15 – 18:45 Hands‐on session Bash group II<br />
Coffee break during the Hands‐on session for the people not involved<br />
18:45‐20:00 Short presentations of participants:<br />
• María C. Ávila‐Arcos: Application and comparison of large‐scale solution‐based DNA captureenrichment<br />
methods on ancient DNA<br />
• Gregory Maes: Marine Conservation Paleogenomics: A novel tool to disentangle historical<br />
natural and anthropogenic selective forces triggering genetic adaption in the endangered<br />
European eel<br />
• Pontus Skoglund : Analysis of population structure and <strong>de</strong>mographic history using ancient<br />
genomic data<br />
• Laura Epp : Environmental metabarcoding of permafrost samples to track ancient Arctic<br />
ecosystem changes<br />
• Eline Lorenzen: Species‐specific responses of Late Quaternary megafauna to climate and humans<br />
• Cristina Gamba: Mo<strong>de</strong>ling the Neolithic impact in North Eastern Iberia: an ancient DNA<br />
Perspective<br />
• Romy Müller: An aDNA study on tuberculosis in Roman Britain<br />
• Pascal Barbry: Presentation of « France Génomique », a network of French sequencing<br />
platforms
Wednesday 19/10/2011: Bioinformatics of palaeogenomics data<br />
8:30 Sarah Palmer: Archaeogenomic analysis of ancient cotton and comparative genome analysis of<br />
retroelements in mo<strong>de</strong>rn and ancient cotton<br />
9:00 Régis Debruyne: Quality of mammoth mitogenomes from different high‐throughput DNA<br />
sources<br />
9:30 Eric Rivals: Analysis of genomic data from high throughput sequencing: algorithms and<br />
limitations<br />
10:15 Coffee break<br />
10:45 Martin Kircher<br />
• Primary data processing: QC of NGS data, Base calling, quality score calibration and<br />
filtering<br />
• Processing ancient DNA data: Paired end read merging of short insert libraries, library<br />
complexity/artifacts, endogenous DNA and contamination<br />
11:30 Ludovic Orlando: “Evaluating different mapping strategies for 2nd gen and 3rd gen seq data"<br />
12:00 Céline Bon: Quantitative inventory of mammalian species DNA in coprolites using read<br />
mapping and <strong>de</strong> novo assembly<br />
12:30 Lunch<br />
14:00 – 20:00 Hands‐on sessions<br />
Rivals/Grange/Poncet: Galaxy Read quality analysis and read mapping algorithms<br />
Orlando/Ginolhac/Kircher: Ancient DNA NGS data: quality controls ma<strong>de</strong> easy ‐ Practical course<br />
following the presentation using GA/Helicos data
Thursday 20/10/2011: Comparative Genomics, Genome evolution, selection<br />
8:30 Olivier Gascuel : Reconstructing ancestral sequences<br />
9:30 Laurent Duret: Detecting positive selection within genomes: the problem of biased gene<br />
conversion<br />
10:30 Coffee break<br />
11:00 Lluis Quintana‐Murci: Detecting natural selection in the human genome: a matter of time and<br />
space<br />
11:45 Olivier Gascuel: Mo<strong>de</strong>l‐based phylogenetic inference<br />
12:15 Pierre Pontarotti: Reconstruction of ancestral genomes focusing on the appearance of new<br />
genes and pseudogenisation<br />
13:00 Lunch<br />
14:30 Martin Kircher: Human <strong>de</strong>rived positions and ancient genomes: I<strong>de</strong>ntification of genome<br />
differences and revisiting the concepts of SNPs/mutations post 1000 Genomes<br />
15:15 Michael Blum: "Interrogating mo<strong>de</strong>ls of human origins with resequencing data"<br />
16:00 Laurent Duret: The evolution of recombination hotspots in the human genome: insights from<br />
paleogenomic data<br />
16:30 Coffee break<br />
17:00‐20:00 Hands‐on session phylogeny – parallel sessions or not?<br />
Olivier Gascuel: Mo<strong>de</strong>l‐based phylogenetic inference and Reconstructing ancestral sequences<br />
Michael Blum: R tutorial on approximate Bayesian computation for population genetics
Friday 21/10/2011: Environmental and dirt DNA, metagenomics and bacterial<br />
genomics<br />
8:30 Denis Le Paslier: Contribution of the new sequencing technologies to metagenomics<br />
9:15 Pascal Simonet: Metagenomics of the soil in the framework of the French national<br />
« Metasoil » and the international « Terragenome » project for <strong>de</strong>ep sequencing of the metagenome<br />
of a reference soil «<br />
10:00 Morten Rasmussen: Palaeogenomics to reconstruct palaeoenvironments. Dirt DNA<br />
approaches: methods and related biases<br />
10:45 Coffee break<br />
11:15 Hendrik Poinar: Metagenomic analysis from sedimentary remains<br />
12:00 Sarah Palmer: Microflora and the <strong>de</strong>positional environment<br />
12:45 Céline Bon: Comparative analysis of the amount of animal and environmental DNA in cave<br />
hyena and wolf coprolites<br />
13:15 Lunch<br />
14:30 Hands‐on session metagenomics<br />
Joseph Nesme: Introduction to data analysis of metagenomic soil sequences<br />
Sarah Palmer: NGS metagenomic analysis using BLASTn and MEGAN<br />
Rescue period for the other hands‐on sessions
Lecturer’s affiliations:<br />
Bennett , E. Andrew <strong>Institut</strong> Jacques Monod, Paris, France<br />
Bin<strong>de</strong>r, Didier<br />
CEPAM UMR6130, University Nice Sophia Antipolis, France<br />
Blum , Michael<br />
TIMC laboratory, Medical School, La Tronche, France<br />
Bon, Céline<br />
CEA Saclay, France<br />
Debruyne, Régis<br />
Muséum National d’Histoire Naturelle, Paris, France<br />
Duret, Laurent<br />
University of Lyon, France<br />
Elalouf , Jean‐Marc<br />
CEA Saclay, France<br />
Gascuel, Olivier<br />
LIRMM‐CNRS, University of Montpellier, France<br />
Geigl, Eva‐Maria<br />
<strong>Institut</strong> Jacques Monod, Paris, France<br />
Ginolhac, Aurélien<br />
University of Copenhagen, Denmark<br />
Grange, Thierry<br />
<strong>Institut</strong> Jacques Monod, Paris, France<br />
Heyer , Evelyne<br />
Muséum National d’Histoire Naturelle, Paris, France<br />
Keyser, Christine <strong>Institut</strong> <strong>de</strong> Mé<strong>de</strong>cine Légale, Laboratoire AMIS, UMR 5288,<br />
Strasbourg, France<br />
Kircher, Martin<br />
Max‐Planck‐<strong>Institut</strong>e for Evolutionary Anthropology, Leipzig, Germany<br />
Krause, Johannes<br />
Eberhard‐Ludwig University, Tübingen, Germany<br />
Le Paslier, Denis<br />
CEA, Gensocope, Evry, France<br />
Maureille, Bruno<br />
University of Bor<strong>de</strong>aux I, UMR5199 PACEA, France<br />
Nesme, Joseph<br />
Ecole Centrale, CNRS, Ecully, France<br />
Orlando, Ludovic<br />
University of Copenhagen, Denmark<br />
Palmer, Sarah<br />
University of Warwick, Great Britain<br />
Poinar Hendrik<br />
McMaster University, Hamilton, Ontario, Canada<br />
Poncet, Romain<br />
<strong>Institut</strong> Jacques Monod, Paris, France<br />
Pontarotti, Pierre<br />
University of Marseille, CNRS, France<br />
Prestat, Emmanuel<br />
Ecole Centrale, CNRS, Ecully, France<br />
Quintana‐Murci, Lluis <strong>Institut</strong> Pasteur, Paris, France<br />
Rasmussen, Morten University of Copenhagen, Denmark<br />
Rivals, Eric<br />
LIRMM‐CNRS, University of Montpellier, France<br />
Simonet, Pascal<br />
Ecole Centrale, CNRS, Ecully, France
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