G. Hewitt, The genetic legacy of the Quaternary ice ages, Nature, vol.15, issue.6789, pp.907-920, 2000.
DOI : 10.1038/ng0197-99

R. Bose, F. Munoz, B. Ramesh, and R. Pélissier, Past potential habitats shed light on the biogeography of endemic tree species of the Western Ghats biodiversity hotspot, South India, Journal of Biogeography, vol.13, issue.5, pp.899-910, 2016.
DOI : 10.1111/j.1461-0248.2010.01515.x

M. Arenas, N. Ray, M. Currat, and L. Excoffier, Consequences of Range Contractions and Range Shifts on Molecular Diversity, Molecular Biology and Evolution, vol.174, issue.1, pp.207-225, 2012.
DOI : 10.1038/416389a

URL : https://academic.oup.com/mbe/article-pdf/29/1/207/13648182/msr187.pdf

G. Hewitt, Some genetic consequences of ice ages, and their role in divergence and speciation, Biological Journal of the Linnean Society, vol.11, issue.3, pp.247-76, 1996.
DOI : 10.1006/mpev.1993.1028

L. Knowles, B. Carstens, K. Marcia, and L. , Coupling Genetic and Ecological-Niche Models to Examine How Past Population Distributions Contribute to Divergence, Current Biology, vol.17, issue.11, pp.940-946, 2007.
DOI : 10.1016/j.cub.2007.04.033

URL : https://doi.org/10.1016/j.cub.2007.04.033

A. Yang, C. Dick, X. Yao, and H. Huang, Impacts of biogeographic history and marginal population genetics on species range limits: a case study of Liriodendron chinense, Scientific Reports, vol.27, issue.1, pp.25632-25642, 2016.
DOI : 10.1046/j.1365-2699.2000.00382.x

J. Avise, Phylogeography: the history and formation of species, 2010.

H. Kim, A. Ratan, G. Perry, A. Montenegro, W. Miller et al., Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history, Nature Communications, vol.441, issue.1, p.25471224, 2014.
DOI : 10.1038/nature04789

URL : http://www.nature.com/articles/ncomms6692.pdf

P. Morat, T. Jaffre, F. Tronchet, J. Munzinger, Y. Pillon et al., Le r??f??rentiel taxonomique Florical et les caract??ristiques de la flore vasculaire indig??ne de la Nouvelle-Cal??donie, Adansonia, vol.34, issue.2, pp.179-221, 2012.
DOI : 10.5252/a2012n2a1

J. Leebens-mack, L. Raubeson, L. Cui, J. Kuehl, M. Fourcade et al., Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way Out of the Felsenstein Zone, Molecular Biology and Evolution, vol.22, issue.10, pp.1948-63, 2005.
DOI : 10.1080/10635150290102339

B. Bremer, K. Bremer, M. Chase, M. Fay, J. Reveal et al., An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III, Botanical Journal of the Linnean Society, vol.161, issue.2, pp.105-126, 2009.

S. Kim, P. Soltis, K. Wall, and D. Soltis, Phylogeny and Domain Evolution in the APETALA2-like Gene Family, Molecular Biology and Evolution, vol.23, issue.1, pp.107-127, 2006.
DOI : 10.1046/j.1365-313X.2003.01963.x

URL : https://academic.oup.com/mbe/article-pdf/23/1/107/13433341/msj014.pdf

C. Finet, A. Berne-dedieu, C. Scutt, and F. Marletaz, Evolution of the ARF Gene Family in Land Plants: Old Domains, New Tricks, Molecular Biology and Evolution, vol.9, issue.1, pp.45-56, 2013.
DOI : 10.1101/gad.9.14.1740

V. Poncet, C. Scutt, R. Tournebize, M. Villegente, G. Cueff et al., The Amborella vacuolar processing enzyme family. Frontiers in plant science, pp.618-26347753, 2015.
DOI : 10.3389/fpls.2015.00618

URL : https://hal.archives-ouvertes.fr/hal-01563836

V. Poncet, M. Couderc, C. Tranchant-dubreuil, C. Gomez, P. Hamon et al., Microsatellite markers for Amborella (Amborellaceae), a monotypic genus endemic to New Caledonia, American Journal of Botany, vol.99, issue.10, pp.411-415, 2012.
DOI : 10.3732/ajb.1200131

URL : http://www.amjbot.org/content/99/10/e411.full.pdf

S. Dellicour, C. Kastally, O. Hardy, and P. Mardulyn, Comparing Phylogeographic Hypotheses by Simulating DNA Sequences under a Spatially Explicit Model of Coalescence, Molecular Biology and Evolution, vol.29, issue.5, pp.3359-72, 2014.
DOI : 10.1093/molbev/msr212

URL : https://academic.oup.com/mbe/article-pdf/31/12/3359/13172473/msu277.pdf

N. Ray, M. Currat, M. Foll, and L. Excoffier, SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination, Bioinformatics, vol.26, issue.23, pp.2993-2997, 2010.
DOI : 10.1186/1471-2105-11-116

URL : https://academic.oup.com/bioinformatics/article-pdf/26/23/2993/590610/btq579.pdf

R. Rasteiro, P. Bouttier, V. Sousa, and L. Chikhi, Investigating sex-biased migration during the Neolithic transition in Europe, using an explicit spatial simulation framework, Proceedings of the Royal Society B: Biological Sciences, vol.2, issue.12, pp.2409-2425, 1737.
DOI : 10.1371/journal.pbio.0020421

URL : http://rspb.royalsocietypublishing.org/content/royprsb/279/1737/2409.full.pdf

P. Endress and A. Igersheim, (Amborellaceae), International Journal of Plant Sciences, vol.161, issue.S6, pp.237-285, 2000.
DOI : 10.1086/317571

L. Thien, T. Sage, T. Jaffré, P. Bernhardt, V. Pontieri et al., The Population Structure and Floral Biology of Amborella Trichopoda (Amborellaceae), Annals of the Missouri Botanical Garden, vol.90, issue.3, pp.466-90, 2003.
DOI : 10.2307/3298537

. Amborella-genome and . Project, The Amborella Genome and the Evolution of Flowering Plants, Science, vol.20, issue.24, 2013.
DOI : 10.1016/j.cub.2010.11.035

N. Anger, B. Fogliani, C. Scutt, and G. Gateble, Dioecy in Amborella trichopoda: evidence for genetically based sex determination and its consequences for inferences of the breeding system in early angiosperms, Ann Bot, p.28110266, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01601162

E. Frichot, F. Mathieu, T. Trouillon, G. Bouchard, and O. François, Fast and Efficient Estimation of Individual Ancestry Coefficients, Genetics, vol.196, issue.4, pp.973-83, 2014.
DOI : 10.1534/genetics.113.160572

URL : https://hal.archives-ouvertes.fr/hal-01119670

D. Alexander, J. Novembre, and K. Lange, Fast model-based estimation of ancestry in unrelated individuals, Genome Research, vol.19, issue.9, pp.1655-64, 2009.
DOI : 10.1101/gr.094052.109

URL : http://genome.cshlp.org/content/19/9/1655.full.pdf

L. Skotte, T. Korneliussen, and A. Albrechtsen, Estimating Individual Admixture Proportions from Next Generation Sequencing Data, Genetics, vol.195, issue.3, pp.693-702, 2013.
DOI : 10.1534/genetics.113.154138

URL : http://www.genetics.org/content/genetics/195/3/693.full.pdf

T. Korneliussen, A. Albrechtsen, and R. Nielsen, ANGSD: Analysis of Next Generation Sequencing Data, BMC Bioinformatics, vol.449, issue.7164, pp.1-13, 2014.
DOI : 10.1038/nature06258

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-014-0356-4?site=bmcbioinformatics.biomedcentral.com

L. Excoffier and M. Foll, fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios, Bioinformatics, vol.11, issue.9, p.21398675, 2011.
DOI : 10.1186/1471-2105-11-116

URL : https://academic.oup.com/bioinformatics/article-pdf/27/9/1332/16902887/btr124.pdf

L. Excoffier, I. Dupanloup, E. Huerta-sánchez, V. Sousa, and M. Foll, Robust demographic inference from genomic and SNP data):e1003905. https, PLoS Genet, vol.9, issue.10, p.24204310, 2013.
DOI : 10.1371/journal.pgen.1003905

URL : http://doi.org/10.1371/journal.pgen.1003905

K. Csilléry, O. François, and M. Blum, abc: an R package for approximate Bayesian computation (ABC) Methods in Ecology and Evolution, pp.475-484, 2012.

S. Phillips, R. Anderson, and R. Schapire, Maximum entropy modeling of species geographic distributions, Ecological Modelling, vol.190, issue.3-4, pp.3-4231, 2006.
DOI : 10.1016/j.ecolmodel.2005.03.026

J. Stevenson, J. Dodson, and I. Prosser, A late Quaternary record of environmental change and human impact from New Caledonia, Palaeogeography, Palaeoclimatology, Palaeoecology, vol.168, issue.1-2, pp.97-123, 2001.
DOI : 10.1016/S0031-0182(00)00251-0

R. Hijmans, S. Cameron, J. Parra, P. Jones, and A. Jarvis, Very high resolution interpolated climate surfaces for global land areas, International Journal of Climatology, vol.18, issue.15, pp.1965-78, 2005.
DOI : 10.1002/joc.1276

URL : http://onlinelibrary.wiley.com/doi/10.1002/joc.1276/pdf

J. Hellstrom, M. Mcculloch, and J. Stone, A Detailed 31,000-Year Record of Climate and Vegetation Change, from the Isotope Geochemistry of Two New Zealand Speleothems, Quaternary Research, vol.44, issue.02, pp.167-78, 1991.
DOI : 10.1006/qres.1995.1073

J. Lehtonen and R. Lanfear, Generation time, life history and the substitution rate of neutral mutations, Biology Letters, vol.31, issue.7412, p.25428931, 2014.
DOI : 10.1038/nature11396

URL : http://rsbl.royalsocietypublishing.org/content/roybiolett/10/11/20140801.full.pdf

B. Fogliani, G. Gateble, M. Villegente, I. Fabre, N. Klein et al., The morphophysiological dormancy in Amborella trichopoda seeds is a pleisiomorphic trait in angiosperms, p.28087660, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01607792

S. Ossowski, K. Schneeberger, J. Lucas-lledó, N. Warthmann, R. Clark et al., The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana, Science, vol.179, issue.2, pp.92-96, 2010.
DOI : 10.1534/genetics.107.085282

K. Bennett and J. Provan, What do we mean by 'refugia'? Quaternary Science Reviews, pp.27-282449, 2008.

G. Hope and K. Pask, Tropical vegetational change in the late Pleistocene of New Caledonia, Palaeogeography, Palaeoclimatology, Palaeoecology, vol.142, issue.1-2, pp.1-21, 1998.
DOI : 10.1016/S0031-0182(97)00140-5

C. Lazareth, B. Rosell, M. Turcq, B. , L. Cornec et al., Mid-Holocene climate in New Caledonia (southwest Pacific): coral and PMIP models monthly resolved results, Quaternary Science Reviews, vol.69, pp.83-97, 2013.
DOI : 10.1016/j.quascirev.2013.02.024

URL : https://hal.archives-ouvertes.fr/hal-00873352

A. Wulff, P. Hollingsworth, A. Ahrends, T. Jaffré, J. Veillon et al., Conservation Priorities in a Biodiversity Hotspot: Analysis of Narrow Endemic Plant Species in New Caledonia, PLoS ONE, vol.52, issue.3, p.24058470, 2013.
DOI : 10.1371/journal.pone.0073371.s003

L. Excoffier, M. Foll, and R. Petit, Genetic Consequences of Range Expansions, Annual Review of Ecology, Evolution, and Systematics, vol.40, issue.1, pp.481-501, 2009.
DOI : 10.1146/annurev.ecolsys.39.110707.173414

J. Elith and J. Leathwick, Species Distribution Models: Ecological Explanation and Prediction Across Space and Time, Annual Review of Ecology, Evolution, and Systematics, vol.40, issue.1, pp.677-97, 2009.
DOI : 10.1146/annurev.ecolsys.110308.120159

F. Jay, S. Manel, N. Alvarez, E. Durand, W. Thuiller et al., Forecasting changes in population genetic structure of alpine plants in response to global warming, Molecular Ecology, vol.459, issue.10, pp.2354-68, 2012.
DOI : 10.1038/nature07988

URL : https://hal.archives-ouvertes.fr/hal-00775883

S. Dellicour, S. Fearnley, A. Lombal, S. Heidl, E. Dahlhoff et al., INFERRING THE PAST AND PRESENT CONNECTIVITY ACROSS THE RANGE OF A NORTH AMERICAN LEAF BEETLE: COMBINING ECOLOGICAL NICHE MODELING AND A GEOGRAPHICALLY EXPLICIT MODEL OF COALESCENCE, Evolution, vol.7, issue.8, pp.2371-85, 2014.
DOI : 10.1046/j.1365-294x.1998.00289.x