J. J. Hublin, Suggested guidelines for invasive sampling of hominid remains, Journal of Human Evolution, vol.55, issue.4, pp.756-757, 2008.
DOI : 10.1016/j.jhevol.2008.04.010

URL : https://hal.archives-ouvertes.fr/hal-00358058

G. D. Richards, R. S. Jabbour, C. F. Horton, C. L. Ibarra, and A. A. Macdowell, Color changes in modern and fossil teeth induced by synchrotron microtomography, American Journal of Physical Anthropology, vol.161, issue.Suppl 50, pp.172-180, 2012.
DOI : 10.1667/RR3114.1

P. Tafforeau and T. M. Smith, Nondestructive imaging of hominoid dental microstructure using phase contrast X-ray synchrotron microtomography, Journal of Human Evolution, vol.54, issue.2, pp.272-278, 2008.
DOI : 10.1016/j.jhevol.2007.09.018

URL : https://hal.archives-ouvertes.fr/hal-00263984

A. J. Grosovsky, J. G. De-boer, P. J. De-jong, E. A. Drobetsky, and B. W. Glickman, Base substitutions, frameshifts, and small deletions constitute ionizing radiation-induced point mutations in mammalian cells., Proceedings of the National Academy of Sciences, vol.85, issue.1, pp.185-188, 1988.
DOI : 10.1073/pnas.85.1.185

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC279508/pdf

R. Teoule, Radiation-induced DNA Damage and Its Repair, International Journal of Radiation Biology and Related Studies in Physics, Chemistry and Medicine, vol.42, issue.4, pp.573-589, 1987.
DOI : 10.2307/3575737

L. Cabec, A. Tang, N. Tafforeau, and P. , Accessing Developmental Information of Fossil Hominin Teeth Using New Synchrotron Microtomography-Based Visualization Techniques of Dental Surfaces and Interfaces, PLOS ONE, vol.36, issue.4, p.123019, 2015.
DOI : 10.1371/journal.pone.0123019.s022

T. M. Smith, Dental Ontogeny in Pliocene and Early Pleistocene Hominins, PLOS ONE, vol.52, issue.Suppl., p.118118, 2015.
DOI : 10.1371/journal.pone.0118118.s001

URL : http://doi.org/10.1371/journal.pone.0118118

T. M. Smith, Dental evidence for ontogenetic differences between modern humans and Neanderthals, Proceedings of the National Academy of Sciences, vol.46, issue.3, pp.20923-20928, 2010.
DOI : 10.1177/0013164486463005

URL : https://hal.archives-ouvertes.fr/hal-00591877

H. L. Liber, P. M. Leong, V. H. Terry, and J. B. Little, X-rays mutate human lymphoblast cells at genetic loci that should respond only to point mutagens, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, vol.163, issue.1, pp.91-97, 1986.
DOI : 10.1016/0027-5107(86)90062-X

H. J. Muller, ARTIFICIAL TRANSMUTATION OF THE GENE, Science, vol.66, issue.1699, pp.84-87, 1927.
DOI : 10.1126/science.66.1699.84

S. Wolff, Radiation Genetics, Annual Review of Genetics, vol.1, issue.1, pp.221-224, 1967.
DOI : 10.1146/annurev.ge.01.120167.001253

S. C. Bushong, Radiologic Science for Technologists: Physics, Biology and Protection, 2001.

K. M. Jefferies, &. R. Adler, and . Carlton, In Introduction to Radiography and Patient Care, 1999.

R. Roots and S. Okada, Estimation of Life Times and Diffusion Distances of Radicals Involved in X-Ray-Induced DNA Strand Breaks or Killing of Mammalian Cells, Radiation Research, vol.64, issue.2, pp.306-320, 1975.
DOI : 10.2307/3574267

S. Clancy, DNA damage & repair: mechanisms for maintaining DNA integrity, Nature Education, vol.1, 2008.

T. Lindahl, Instability and decay of the primary structure of DNA, Nature, vol.362, issue.6422, pp.709-715, 1993.
DOI : 10.1038/362709a0

D. Mitchell, E. Willerslev, and A. Hansen, Damage and repair of ancient DNA, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, vol.571, issue.1-2, pp.265-276, 2005.
DOI : 10.1016/j.mrfmmm.2004.06.060

J. Wanek and F. J. Ruhli, Risk to fragmented DNA in dry, wet, and frozen states from computed tomography: a comparative theoretical study, Radiation and Environmental Biophysics, vol.46, issue.3, 2016.
DOI : 10.1269/jrr.46.333

A. Götherstrom, C. Fischer, and K. Linden, X-raying ancient bone: a destructive method in connection with DNA analysis, Laborativ Arkeologi, vol.8, pp.26-28, 1995.

B. M. Grieshaber, D. L. Osborne, A. F. Doubleday, and F. A. Kaestle, A pilot study into the effects of X-ray and computed tomography exposure on the amplification of DNA from bone, Journal of Archaeological Science, vol.35, issue.3, pp.681-687, 2008.
DOI : 10.1016/j.jas.2007.06.001

U. M. Paredes, Micro-CT X-rays do not fragment DNA in preserved bird skins, Journal of Zoological Systematics and Evolutionary Research, vol.1, issue.3, pp.247-250, 2012.
DOI : 10.1146/annurev.ge.01.120167.001253

M. O. Bradley and K. W. Kohn, X-ray induced DNA double strand break production and repair in mammalian cells as measured by neutral filter elution, Nucleic Acids Research, vol.7, issue.3, pp.793-804, 1979.
DOI : 10.1093/nar/7.3.793

T. Maricic, M. Whitten, and S. Paabo, Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products, PLoS ONE, vol.12, issue.11, p.14004, 2010.
DOI : 10.1371/journal.pone.0014004.s001

M. E. Allentoft, 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. E. Deagle, J. P. Eveson, and S. N. Jarman, 32969 | DOI: 10.1038/srep32969 25 Quantification of damage in DNA recovered from highly degraded samples?a case study on DNA in faeces, Scientific RepoRts | Frontiers in zoology, vol.6, issue.11, pp.10-1186, 2006.

A. W. Briggs, 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

J. Krause, The complete mitochondrial DNA genome of an unknown hominin from southern Siberia, Nature, vol.431, issue.7290, pp.894-897, 2010.
DOI : 10.1016/j.aeae.2008.07.002

S. Sawyer, J. Krause, K. Guschanski, V. Savolainen, and S. Paabo, Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA, PLoS ONE, vol.25, issue.3, p.34131, 2012.
DOI : 10.1371/journal.pone.0034131.s002

M. Hoss, P. Jaruga, T. H. Zastawny, M. Dizdaroglu, and S. Paabo, DNA Damage and DNA Sequence Retrieval from Ancient Tissues, Nucleic Acids Research, vol.24, issue.7, pp.1304-1307, 1996.
DOI : 10.1093/nar/24.7.1304

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC145783/pdf

S. Pääbo, Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification., Proceedings of the National Academy of Sciences, vol.86, issue.6, pp.1939-1943, 1989.
DOI : 10.1073/pnas.86.6.1939

M. Stoneking and J. Krause, Learning about human population history from ancient and modern genomes, Nature Reviews Genetics, vol.23, issue.9, pp.603-614, 2011.
DOI : 10.1038/13779

R. F. Egerton, P. Li, and M. Malac, Radiation damage in the TEM and SEM, Micron, vol.35, issue.6, pp.399-409, 2004.
DOI : 10.1016/j.micron.2004.02.003

M. Folkard, K. M. Prise, B. Brocklehurst, and B. Michael, DNA damage induction in dry and hydrated DNA by synchrotron radiation, Journal of Physics B: Atomic, Molecular and Optical Physics, vol.32, issue.11, pp.2753-2761, 1999.
DOI : 10.1088/0953-4075/32/11/321

G. M. Mrevlishvili and D. Svintradze, DNA as a matrix of collagen fibrils, International Journal of Biological Macromolecules, vol.36, issue.5, pp.324-326, 2005.
DOI : 10.1016/j.ijbiomac.2005.07.006

M. Brundin, D. Figdor, G. Sundqvist, and U. Sjogren, DNA Binding to Hydroxyapatite: A Potential Mechanism for Preservation of Microbial DNA, Journal of Endodontics, vol.39, issue.2, pp.211-216, 2013.
DOI : 10.1016/j.joen.2012.09.013

P. F. Campos, DNA in ancient bone ??? Where is it located and how should we extract it?, Annals of Anatomy - Anatomischer Anzeiger, vol.194, issue.1, pp.7-16, 2012.
DOI : 10.1016/j.aanat.2011.07.003

C. Schwarz, New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains, Nucleic Acids Research, vol.37, issue.10, pp.3215-3229, 2009.
DOI : 10.1093/nar/gkp159

URL : http://doi.org/10.1093/nar/gkp159

N. Rohland and M. Hofreiter, Ancient DNA extraction from bones and teeth, Nature Protocols, vol.6, issue.7, pp.1756-1762, 2007.
DOI : 10.1038/nprot.2007.247

M. Meyer and M. Kircher, Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc, p.5448, 2010.
DOI : 10.1101/pdb.prot5448

M. Kircher, S. Sawyer, and M. Meyer, Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform, Nucleic Acids Research, vol.40, issue.1, p.3, 2012.
DOI : 10.1093/nar/gkr771

R. Development and C. Team, R: A Language and Environment for Statistical Computing. The R Foundation for Statistical Computing, 2011.

A. Untergasser, Primer3Plus, an enhanced web interface to Primer3, Nucleic Acids Research, vol.35, issue.Web Server, pp.71-74, 2007.
DOI : 10.1093/nar/gkm306

URL : http://doi.org/10.1093/nar/gkm306

M. Kircher, P. Heyn, and J. Kelso, Addressing challenges in the production and analysis of illumina sequencing data, BMC Genomics, vol.20, issue.9, p.382, 2011.
DOI : 10.1101/gr.107524.110

H. Li and R. Durbin, Fast and accurate long-read alignment with Burrows???Wheeler transform, Bioinformatics, vol.26, issue.5, pp.589-595, 2010.
DOI : 10.1093/bioinformatics/btp698

URL : https://academic.oup.com/bioinformatics/article-pdf/26/5/589/558724/btp698.pdf

J. Dabney, Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments, Proceedings of the National Academy of Sciences, vol.30, issue.4, pp.15758-15763, 2013.
DOI : 10.1093/molbev/mst010

A. Peltzer, EAGER: efficient ancient genome reconstruction, Genome Biology, vol.2008, issue.166, 2016.
DOI : 10.1101/gr.111120.110

URL : http://doi.org/10.1186/s13059-016-0918-z

H. Li, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2078/531810/btp352.pdf

H. Jonsson, A. Ginolhac, M. Schubert, P. L. Johnson, and L. Orlando, mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters, Bioinformatics, vol.29, issue.13, pp.1682-1684, 2013.
DOI : 10.1093/bioinformatics/btt193