M. Aguilera, F. Díaz, J. , A. Ortega, J. Tarrús et al., Climate at the onset of western Mediterranean agriculture expansion: Evidence from stable isotopes of sub-fossil oak tree rings in Spain, Palaeogeography, Palaeoclimatology, Palaeoecology, vol.299, issue.3-4, pp.541-551, 2011.
DOI : 10.1016/j.palaeo.2010.11.026

S. Aitken, S. Yeaman, J. Holliday, T. Wang, and S. Curtis-mclane, Adaptation, migration or extirpation: climate change outcomes for tree populations, Evolutionary Applications, vol.273, issue.1, pp.95-111, 2008.
DOI : 10.1098/rspb.2006.3498
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1752-4571.2007.00013.x/pdf

M. Allentoft, M. Collins, and D. Harker, The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils, Proceedings of the Royal Society B: Biological Sciences, vol.52, issue.2, pp.4724-4733, 2012.
DOI : 10.1007/s00239-011-9474-z

B. Becker, An 11,000-Year German Oak and Pine Dendrochronology for Radiocarbon Calibration, Radiocarbon, vol.22, issue.01, pp.201-213, 2006.
DOI : 10.1007/978-1-4757-4249-7_4
URL : https://www.cambridge.org/core/services/aop-cambridge-core/content/view/4DDD82ECC7E4E5C73089C24F9A7CD51E/S0033822200013898a.pdf/div-class-title-an-11-000-year-german-oak-and-pine-dendrochronology-for-radiocarbon-calibration-div.pdf

B. Becker, B. Kromer, and P. Trimborn, A stable-isotope tree-ring timescale of the Late Glacial/Holocene boundary, Nature, vol.353, issue.6345, pp.353-647, 1991.
DOI : 10.1038/353647a0

A. Billamboz, Regional patterns of settlement and woodland developments: Dendroarchaeology in the Neolithic pile-dwellings on Lake Constance (Germany), The Holocene, vol.168, issue.10, pp.1-10, 2014.
DOI : 10.1007/978-3-642-77157-6

A. Billamboz and N. Martinelli, Dendrochronology and Bronze Age pile-dwellings on both sides of, 2015.

, the Alps: from chronology to dendrotypoloy highlithing settlement developments and woodland structural changes In: The end of the lake-dwellings in the Circum-Alpine region Oxbow books, pp.68-84

A. Briggs, U. Stenzel, and P. Johnson, Patterns of damage in genomic DNA sequences from a Neandertal, Proceedings of the National Academy of Sciences, vol.35, issue.17, pp.14616-14621, 2007.
DOI : 10.1093/nar/gkm588

U. Büntgen, W. Tegel, and K. Nicolussi, 2500 Years of European Climate Variability and Human Susceptibility, Science, vol.319, issue.5863, pp.578-582, 2011.
DOI : 10.1126/science.1152339

E. Cappellini, M. Gilbert, and F. Geuna, A multidisciplinary study of archaeological grape seeds, Naturwissenschaften, vol.52, issue.2, pp.205-217, 2010.
DOI : 10.1007/BF00211051

R. Cheddadi, G. Vendramin, and T. Litt, Imprints of glacial refugia in the modern genetic diversity of Pinus sylvestris, Global Ecology and Biogeography, vol.70, issue.3, pp.271-282, 2006.
DOI : 10.1016/j.quascirev.2004.06.002
URL : https://hal.archives-ouvertes.fr/halsde-00303681

M. Collins, ?. Nielsen, C. Marsh, and J. Hiller, The survival of organic matter in bone: a review, Archaeometry, vol.44, issue.3, pp.383-394, 2002.
DOI : 10.1111/1475-4754.t01-1-00071

C. Corinaldesi, F. Beolchini, and A. Dell-'anno, Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences, Molecular Ecology, vol.317, issue.17, pp.3939-3951, 2008.
DOI : 10.1007/978-1-4684-7956-0_1

K. ?ufar, B. Kromer, T. Tolar, and A. Velu??ek, Dating of 4th millennium BC pile-dwellings on Ljubljansko barje, Slovenia, Journal of Archaeological Science, vol.37, issue.8, pp.2031-2039, 2010.
DOI : 10.1016/j.jas.2010.03.008

M. Deguilloux, L. Bertel, and A. Celant, Genetic analysis of archaeological wood remains: first results and prospects, Journal of Archaeological Science, vol.33, issue.9, pp.1216-1227, 2006.
DOI : 10.1016/j.jas.2005.12.012

M. Deguilloux, M. Pemonge, and R. Petit, Novel perspectives in wood certification and forensics: dry wood as a source of DNA, Proceedings of the Royal Society of London. Series B, pp.1039-1046, 2002.
DOI : 10.1098/rspb.2002.1982
URL : https://hal.archives-ouvertes.fr/halshs-00457891

S. Franks, J. Weber, and S. Aitken, Evolutionary and plastic responses to climate change in terrestrial plant populations, Evolutionary Applications, vol.273, issue.1, pp.123-139, 2014.
DOI : 10.1098/rspb.2006.3498

N. Frascaria, L. Maggia, M. Michaud, and J. Bousquet, L gene sequence from chestnut indicates a slow rate of evolution in the Fagaceae, Genome, vol.36, issue.4, p.36, 1993.
DOI : 10.1139/g93-089

M. Friedrich, B. Kromer, M. Spurk, J. Hofmann, F. Kaiser et al., Paleo-environment and radiocarbon calibration as derived from Lateglacial/Early Holocene tree-ring chronologies -an intercomparison of Quercus robur, Quaternary International, pp.61-88, 1999.

M. Friedrich, S. Remmele, and B. Kromer, The 12,460-Year Hohenheim Oak and Pine Tree-Ring Chronology from Central Europe???A Unique Annual Record for Radiocarbon Calibration and Paleoenvironment Reconstructions, Radiocarbon, vol.20, issue.50, pp.1111-1122, 2004.
DOI : 10.1179/096576696800688178

C. Gamba, K. Hanghøj, and C. Gaunitz, Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing, Molecular Ecology Resources, vol.105, issue.2, pp.459-469, 2016.
DOI : 10.1002/(SICI)1096-8644(199804)105:4<539::AID-AJPA10>3.0.CO;2-1

C. Giguet-covex, J. Pansu, and F. Arnaud, Long livestock farming history and human landscape shaping revealed by lake sediment DNA, Nature Communications, vol.51, issue.1, 2014.
DOI : 10.1111/j.1365-294X.2011.05424.x
URL : https://hal.archives-ouvertes.fr/halsde-00944038

J. Gómez-zeledón, W. Grasse, F. Runge, A. Land, and O. Spring, TaqMan qPCR pushes boundaries for the analysis of millennial wood, Journal of Archaeological Science, vol.79, pp.53-61, 2017.
DOI : 10.1016/j.jas.2017.01.010

E. Guichoux, L. Lagache, S. Wagner, P. Léger, and R. Petit, Two highly validated multiplexes (12- plex and 8-plex) for species delimitation and parentage analysis in oaks, 2011.

, Molecular Ecology Resources, vol.11, pp.578-585

E. Guichoux and R. Petit, Déclaration d'invention (n° DI-RV-13-00566) auprès de l'INPI : Méthode de traçabilité géographique des bois de chêne, 2014.

C. Harwood and J. Gibson, Anaerobic and aerobic metabolism of diverse aromatic compounds by the photosynthetic bacterium Rhodopseudomonas palustris, Applied and Environmental Microbiology, vol.54, pp.712-717, 1988.

H. Jónsson, A. Ginolhac, M. Schubert, P. Johnson, and L. Orlando, mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters, Bioinformatics, vol.108, issue.13, pp.1682-1684, 2013.
DOI : 10.1073/pnas.1105107108

T. Jørgensen, J. Haile, and P. Möller, A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability, Molecular Ecology, vol.59, issue.7, 1989.
DOI : 10.1126/science.1141758

S. Kato, K. Chino, and N. Kamimura, Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil, Scientific Reports, vol.39, issue.1, p.14295, 2015.
DOI : 10.1111/j.1558-5646.1985.tb00420.x

L. Kistler, O. Smith, and R. Ware, Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments, 2015.
DOI : 10.1101/032060

L. Kistler, R. Ware, O. Smith, M. Collins, and R. Allaby, A new model for ancient DNA decay based on paleogenomic meta-analysis, Nucleic Acids Research, vol.5, issue.11, pp.6310-6320, 2017.
DOI : 10.1126/science.1146971

A. König, B. Ziegenhagen, and B. Van-dam, Chloroplast DNA variation of oaks in western Central Europe and genetic consequences of human influences, Forest Ecology and Management, vol.156, issue.1-3, pp.147-166, 2002.
DOI : 10.1016/S0378-1127(01)00640-5

A. Kremer, J. Kleinschmit, and J. Cottrell, Is there a correlation between chloroplastic and nuclear divergence, or what are the roles of history and selection on genetic diversity in European oaks? Forest Ecology and Management, pp.75-87, 2002.

G. Lang, Quartäre Vegetationsgeschichte Europas: Methoden und Ergebnisse, 1994.

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.
DOI : 10.1093/bioinformatics/btp352

B. Lendvay, M. Hartmann, and S. Brodbeck, Improved recovery of ancient DNA from subfossil wood - application to the world's oldest Late Glacial pine forest, New Phytologist, vol.9, issue.4, 2017.
DOI : 10.1371/journal.pone.0086827

T. Leroy, C. Roux, and L. Villate, Extensive recent secondary contacts between four European white oak species, New Phytologist, vol.20, issue.2, pp.865-878, 2017.
DOI : 10.1016/0160-9327(96)10019-3
URL : https://hal.archives-ouvertes.fr/hal-01608621

S. Liepelt, R. Cheddadi, and J. De-beaulieu, Postglacial range expansion and its genetic imprints in Abies alba (Mill.) ??? A synthesis from palaeobotanic and genetic data, Review of Palaeobotany and Palynology, vol.153, issue.1-2, pp.139-149, 2009.
DOI : 10.1016/j.revpalbo.2008.07.007
URL : https://hal.archives-ouvertes.fr/halsde-00476316

S. Liepelt, C. Sperisen, and M. Deguilloux, Authenticated DNA from Ancient Wood Remains, Annals of Botany, vol.7, issue.5, pp.1107-1111, 2006.
DOI : 10.1006/mpev.1996.0398
URL : https://hal.archives-ouvertes.fr/halshs-00458931

H. Li, B. Handsaker, and A. Wysoker, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.9, issue.11, pp.2078-2079, 2009.
DOI : 10.1146/annurev.genom.9.081307.164359
URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2078/531810/btp352.pdf

G. Louvel, D. Sarkissian, C. Hanghøj, K. Orlando, and L. , metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data, Molecular Ecology Resources, vol.5, issue.6, pp.1415-1427, 2016.
DOI : 10.1038/srep16498

A. Lowe, R. Munro, S. Samuel, and J. Cottrell, The utility and limitations of chloroplast DNA analysis for identifying native British oak stands and for guiding replanting strategy, Forestry, vol.77, issue.4, pp.335-347, 2004.
DOI : 10.1093/forestry/77.4.335

K. Macdicken, Introduction to the Changes in Global Forest Resources from 1990 to 2015, Forest Ecology and Management, vol.352, pp.1-2, 2015.
DOI : 10.1016/j.foreco.2015.06.018

D. Magri, Patterns of post-glacial spread and the extent of glacial refugia of European beech (Fagus sylvatica), Journal of Biogeography, vol.100, issue.3, pp.450-463, 2008.
DOI : 10.1016/j.quascirev.2005.03.017

N. Martinelli, Dendrotypology in Italy: The case studies of the pile-dwelling villages Lucone D (Brescia) and Sabbione (Varese) In: Dendro: Chronologie, Typologie, Oekologie, Festschrift für André Billamboz zum 65, Geburtstag, pp.117-124, 2013.

M. Meyer and M. Kircher, Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing, Cold Spring Harbor Protocols, vol.2010, issue.6, p.5448, 2010.
DOI : 10.1101/pdb.prot5448

G. Muir, C. Fleming, and C. Schltterer, Species status of hybridizing oaks, Nature, vol.405, issue.6790, pp.405-1016, 2000.
DOI : 10.1038/hdy.1997.67

N. Nayling, S. Manning, and B. Kromer, Dating the submerged forests: dendrochronology and radiocarbonwiggle-match dating, CBA Research Reports, vol.149, p.90, 2007.

C. Nielsen-marsh, C. Smith, and M. Jans, Bone diagenesis in the European Holocene II: taphonomic and environmental considerations, Journal of Archaeological Science, vol.34, issue.9, pp.1523-1531, 2007.
DOI : 10.1016/j.jas.2006.11.012

L. Orlando, M. Gilbert, and E. Willerslev, Reconstructing ancient genomes and epigenomes, Nature Reviews Genetics, vol.4, issue.7, pp.395-408, 2015.
DOI : 10.1371/journal.pgen.1002947

F. Palla, G. Barresi, D. Carlo, and E. , Identification of bacterial taxa in archaeological waterlogged wood. Conservation Science in Cultural Heritage, pp.247-254, 2014.

L. Parducci, T. Jørgensen, and M. Tollefsrud, Glacial Survival of Boreal Trees in Northern Scandinavia, Science, vol.10, issue.4, pp.1083-1086, 2012.
DOI : 10.1111/j.1502-3885.1981.tb00511.x

L. Parducci, Y. Suyama, M. Lascoux, and D. Bennett, Ancient DNA from pollen: a genetic record of population history in Scots pine, Molecular Ecology, vol.17, issue.7, pp.2873-2882, 2005.
DOI : 10.1016/S0277-3791(97)00006-1

N. Pedersen, Microscopic and spectroscopic characterisation of waterlogged archaeological softwood from anoxic environments. Thesis, 2015.

M. Pedersen, A. Ruter, and C. Schweger, Postglacial viability and colonization in North America???s ice-free corridor, Nature, vol.51, issue.7618, pp.45-49, 2016.
DOI : 10.1017/S0033822200033865

R. Petit, U. Csaikl, and S. Bordács, Corrigendum to ???Chloroplast DNA variation in European white oaks phylogeography and patterns of diversity based on data from over 2600 populations???, Forest Ecology and Management, vol.176, issue.1-3, pp.5-26, 2002.
DOI : 10.1016/S0378-1127(02)00558-3

R. Petit, B. Simon, and B. Sándor, Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence, Forest Ecology and Management, vol.156, issue.1-3, pp.49-74, 2002.
DOI : 10.1016/S0378-1127(01)00634-X

R. Pinhasi, D. Fernandes, and K. Sirak, Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone, PLOS ONE, vol.112, issue.6, p.129102, 2015.
DOI : 10.1371/journal.pone.0129102.s004

C. Plomion, J. Aury, and J. Amselem, Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies, Molecular Ecology Resources, vol.10, issue.1, pp.254-265, 2016.
DOI : 10.1186/1471-2164-10-347
URL : https://hal.archives-ouvertes.fr/hal-01579667

C. Plomion, G. Leprovost, and A. Stokes, Wood Formation in Trees, PLANT PHYSIOLOGY, vol.127, issue.4, pp.1513-1523, 2001.
DOI : 10.1104/pp.010816
URL : https://hal.archives-ouvertes.fr/hal-01204210

B. Pollmann, S. Jacomet, and A. Schlumbaum, Morphological and genetic studies of waterlogged Prunus species from the Roman vicus Tasgetium (Eschenz, Switzerland), Journal of Archaeological Science, vol.32, issue.10, pp.1471-1480, 2005.
DOI : 10.1016/j.jas.2005.04.002

M. Rasmussen, S. Anzick, and M. Waters, The genome of a Late Pleistocene human from a Clovis burial site in western Montana, Nature, vol.320, issue.7487, pp.225-229, 2014.
DOI : 10.1126/science.1156533

A. Schlumbaum, S. Van-glabeke, and I. Roldan-ruiz, Towards the onset of fruit tree growing north of the Alps: Ancient DNA from waterlogged apple (Malus sp.) seed fragments, Annals of Anatomy - Anatomischer Anzeiger, vol.194, issue.1, pp.157-162, 2012.
DOI : 10.1016/j.aanat.2011.03.004

S. Schmid, R. Genevest, and E. Gobet, HyRAD-X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA, Methods in Ecology and Evolution, 2017.
DOI : 10.1016/j.cois.2015.10.007

M. Schubert, L. Ermini, and C. Sarkissian, Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX, Nature Protocols, vol.486, issue.5, pp.1056-1082, 2014.
DOI : 10.1093/nar/gkp1137

M. Schubert, A. Ginolhac, and S. Lindgreen, Improving ancient DNA read mapping against modern reference genomes, BMC Genomics, vol.13, issue.1, p.178, 2012.
DOI : 10.1126/science.1178158
URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-13-178?site=bmcgenomics.biomedcentral.com

C. Schwarz, R. Debruyne, and M. Kuch, New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains, Nucleic Acids Research, vol.317, issue.10, pp.3215-3229, 2009.
DOI : 10.1126/science.1146971
URL : https://academic.oup.com/nar/article-pdf/37/10/3215/16752228/gkp159.pdf

F. Schweingruber, Microscopic Wood Anatomy, 1990.

N. Segata, J. Izard, and L. Waldron, , 2011.

, Genome Biology, vol.12, p.60

N. Segata, L. Waldron, and A. Ballarini, Metagenomic microbial community profiling using unique clade-specific marker genes, Nature Methods, vol.2008, issue.8, pp.811-814, 2012.
DOI : 10.1093/nar/gkn879

C. Smith, A. Chamberlain, M. Riley, C. Stringer, and M. Collins, The thermal history of human fossils and the likelihood of successful DNA amplification, Journal of Human Evolution, vol.45, issue.3, pp.203-217, 2003.
DOI : 10.1016/S0047-2484(03)00106-4

O. Smith, G. Momber, and R. Bates, Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago, Science, vol.38, issue.6, pp.998-1001, 2015.
DOI : 10.1093/nar/gkp1163

N. Song, H. Cai, Z. Yan, and H. Jiang, Cellulose degradation by one mesophilic strain Caulobacter sp. FMC1 under both aerobic and anaerobic conditions, Bioresource Technology, vol.131, pp.281-287, 2013.
DOI : 10.1016/j.biortech.2013.01.003

A. Speirs, M. Connachie, G. Lowe, and A. , Chloroplast DNA from 16th century waterlogged oak in a marine environment: initial steps in sourcing the Mary Rose timbers, Terra Australis, p.30, 2009.

N. Tani, Y. Tsumura, and H. Sato, Nuclear gene sequences and DNA variation of Cryptomeria japonica samples from the postglacial period, Molecular Ecology, vol.21, issue.4, pp.859-868, 2003.
DOI : 10.1146/annurev.ecolsys.30.1.457

B. Taylor, Other Methoxy-Aromatic Compounds by Pseudomonas sp. Strain PN-1, Applied and Environmental Microbiology, vol.46, pp.1286-1292, 1983.

W. Tegel, R. Elburg, D. Hakelberg, H. Stäuble, and U. Büntgen, Early Neolithic Water Wells Reveal the World's Oldest Wood Architecture, PLoS ONE, vol.40, issue.12, p.51374, 2012.
DOI : 10.1371/journal.pone.0051374.s025

M. Tollefsrud, R. Kissling, and F. Gugerli, Genetic consequences of glacial survival and postglacial colonization in Norway spruce: combined analysis of mitochondrial DNA and fossil pollen, Molecular Ecology, vol.53, issue.18, pp.4119-4135, 2008.
DOI : 10.1111/j.1095-8312.1996.tb01434.x

D. Truong, E. Franzosa, and T. Tickle, MetaPhlAn2 for enhanced metagenomic taxonomic profiling, Nature Methods, vol.486, issue.10, pp.902-903, 2015.
DOI : 10.1126/science.1171700

Y. Tsuji, R. Vanholme, and Y. Tobimatsu, sp. strain SYK-6, Plant Biotechnology Journal, vol.107, issue.6, pp.821-832, 2015.
DOI : 10.1073/pnas.1012900107

S. Wagner, S. Liepelt, S. Gerber, and R. Petit, Within-Range Translocations and Their Consequences in European Larch, PLOS ONE, vol.156, issue.5, p.127516, 2015.
DOI : 10.1371/journal.pone.0127516.s013
URL : https://doi.org/10.1371/journal.pone.0127516

S. Wagner, T. Litt, M. Sánchez-goñi, and R. Petit, History of Larix decidua Mill. (European larch) since 130??ka, Quaternary Science Reviews, vol.124, pp.224-247, 2015.
DOI : 10.1016/j.quascirev.2015.07.002
URL : https://hal.archives-ouvertes.fr/tel-00880539

N. Wales, K. Andersen, E. Cappellini, M. Ávila-arcos, and M. Gilbert, Optimization of DNA Recovery and Amplification from Non-Carbonized Archaeobotanical Remains, PLoS ONE, vol.106, issue.2, p.86827, 2014.
DOI : 10.1371/journal.pone.0086827.s021
URL : https://doi.org/10.1371/journal.pone.0086827

N. Wales, R. Madrigal, J. Cappellini, and E. , The limits and potential of paleogenomic techniques for reconstructing grapevine domestication, Journal of Archaeological Science, vol.72, pp.57-70, 2016.
DOI : 10.1016/j.jas.2016.05.014

N. Wales, J. Romero-navarro, E. Cappellini, and M. Gilbert, Choosing the Best Plant for the Job: A Cost-Effective Assay to Prescreen Ancient Plant Remains Destined for Shotgun Sequencing, PLoS ONE, vol.7, issue.9, p.45644, 2012.
DOI : 10.1371/journal.pone.0045644.s001

C. Weiß, M. Dannemann, K. Prüfer, and H. Burbano, Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data, p.4, 2015.

C. Weiß, V. Schuenemann, and J. Devos, Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens, Open Science, vol.3, p.160239, 2016.

E. Willerslev, J. Davison, and M. Moora, Fifty thousand years of Arctic vegetation and megafaunal diet, Nature, vol.276, issue.7486, pp.47-51, 2014.
DOI : 10.1016/j.quaint.2011.11.004