J. Avise, Phylogeography: the history and formation of species, 2000.

N. Barton and G. Hewitt, Analysis of Hybrid Zones, Annual Review of Ecology and Systematics, vol.16, issue.1, pp.113-148, 1985.
DOI : 10.1146/annurev.es.16.110185.000553

G. Hewitt, Genetic consequences of climatic oscillations in the Quaternary, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.359, issue.1442, pp.183-195, 2004.
DOI : 10.1098/rstb.2003.1388

G. Hewitt, The genetic legacy of the Quaternary ice ages, Nature, vol.405, issue.6789, pp.907-913, 2000.
DOI : 10.1038/35016000

P. Taberlet, L. Fumagalli, A. Wust-saucy, and J. Cosson, Comparative phylogeography and postglacial colonization routes in Europe, Molecular Ecology, vol.7, issue.4, pp.453-464, 1998.
DOI : 10.1146/annurev.ecolsys.19.1.513
URL : https://hal.archives-ouvertes.fr/halsde-00280580

U. Joger, U. Fritz, D. Guicking, S. Kalyabina-hauf, Z. Nagy et al., Phylogeography of western Palaearctic reptiles ??? Spatial and temporal speciation patterns, Zoologischer Anzeiger - A Journal of Comparative Zoology, vol.246, issue.4, pp.293-313, 2007.
DOI : 10.1016/j.jcz.2007.09.002

A. Gómez and D. Lunt, Refugia within Refugia: Patterns of Phylogeographic Concordance in the Iberian Peninsula, Phylogeography of Southern European Refugia, pp.155-188
DOI : 10.1007/1-4020-4904-8_5

Y. Surget-groba, B. Heulin, C. Guillaume, R. Thorpe, L. Kupriyanova et al., Intraspecific Phylogeography of Lacerta vivipara and the Evolution of Viviparity, Molecular Phylogenetics and Evolution, vol.18, issue.3, pp.449-459, 2001.
DOI : 10.1006/mpev.2000.0896

B. Heulin, Y. Surget-groba, A. Guiller, C. Guillaume, and J. Deunff, Comparisons of mitochondrial DNA (mtDNA) sequences (16S rRNA gene) between oviparous and viviparous strains of Lacerta vivipara: a preliminary study, Molecular Ecology, vol.26, issue.10, pp.1627-1631, 1999.
DOI : 10.1146/annurev.bi.46.070177.003041

C. Guillaume, B. Heulin, M. Arrayago, A. Bea, and F. Braña, Refuge areas and suture zones in the Pyrenean and Cantabrian regions: geographic variation of the female MPI sex-linked alleles among oviparous populations of the lizard Lacerta (Zootoca) vivipara, Ecography, vol.2, issue.1, pp.3-10, 2000.
DOI : 10.1111/j.1600-0587.2000.tb00255.x

S. Edwards and P. Beerli, PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES, Evolution, vol.92, issue.6, pp.1839-1854, 2000.
DOI : 10.1017/S001667239700270X

R. Zink and G. Barrowclough, Mitochondrial DNA under siege in avian phylogeography, Molecular Ecology, vol.40, issue.9, pp.2107-2121, 2008.
DOI : 10.1111/j.1365-294X.2008.03737.x

W. Moore, Inferring Phylogenies from mtDNA Variation: Mitochondrial-Gene Trees Versus Nuclear-Gene Trees, Evolution, vol.49, issue.4, pp.718-726, 1995.
DOI : 10.2307/2410325

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

B. Milá, D. Toews, T. Smith, and R. Wayne, A cryptic contact zone between divergent mitochondrial DNA lineages in southwestern North America supports past introgressive hybridization in the yellow-rumped warbler complex (Aves: Dendroica coronata), Biological Journal of the Linnean Society, vol.103, issue.3, pp.696-706, 2011.
DOI : 10.1111/j.1095-8312.2011.01661.x

J. Mcguire, C. Linkem, M. Koo, D. Hutchison, A. Lappin et al., MITOCHONDRIAL INTROGRESSION AND INCOMPLETE LINEAGE SORTING THROUGH SPACE AND TIME: PHYLOGENETICS OF CROTAPHYTID LIZARDS, Evolution, vol.59, issue.12, pp.2879-2897, 2007.
DOI : 10.1111/j.1095-8312.1985.tb02048.x

D. Funk and K. Omland, Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA, Annual Review of Ecology, Evolution, and Systematics, vol.34, issue.1, pp.397-423, 2003.
DOI : 10.1146/annurev.ecolsys.34.011802.132421

E. Bazin, S. Glémin, and N. Galtier, Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals, Science, vol.312, issue.5773, pp.570-572, 2006.
DOI : 10.1126/science.1122033
URL : https://hal.archives-ouvertes.fr/halsde-00339540

D. Dowling, U. Friberg, and J. Lindell, Evolutionary implications of non-neutral mitochondrial genetic variation, Trends in Ecology & Evolution, vol.23, issue.10, pp.546-554, 2008.
DOI : 10.1016/j.tree.2008.05.011

J. Ballard and M. Whitlock, The incomplete natural history of mitochondria, Molecular Ecology, vol.22, issue.4, pp.729-744, 2004.
DOI : 10.1073/pnas.94.26.14900

L. Knowles, Statistical Phylogeography, Annual Review of Ecology, Evolution, and Systematics, vol.40, issue.1, pp.593-612, 2009.
DOI : 10.1146/annurev.ecolsys.38.091206.095702

M. Slatkin and R. Hudson, Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations, Genetics, vol.129, pp.555-562, 1991.

J. Pritchard and W. Wen, Documentation for Structure Software: Version 2 Available at: http://pritch, 2004.

B. Heulin, Y. Surget-groba, B. Sinervo, D. Miles, and A. Guiller, Dynamics of haplogroup frequencies and survival rates in a contact zone of two mtDNA lineages of the lizard Lacerta vivipara, Ecography, vol.2, issue.3, pp.436-447, 2011.
DOI : 10.1111/j.1600-0587.2010.06540.x
URL : https://hal.archives-ouvertes.fr/hal-00625507

S. Cooper, K. Ibrahim, and G. Hewitt, Postglacial expansion and genome subdivision in the European grasshopper Chorthippus parallelus, Molecular Ecology, vol.20, issue.1, pp.49-60, 1995.
DOI : 10.1038/hdy.1994.191

A. Helbig, M. Salomon, S. Bensch, and I. Seibold, Male-biased gene flow across an avian hybrid zone: evidence from mitochondrial and microsatellite DNA, Journal of Evolutionary Biology, vol.11, issue.2, pp.277-287, 2001.
DOI : 10.1046/j.1420-9101.2001.00273.x

H. Gonçalves, I. Martínez-solano, N. Ferrand, and M. García-parís, Conflicting phylogenetic signal of nuclear vs mitochondrial DNA markers in midwife toads (Anura, Discoglossidae, Alytes): Deep coalescence or ancestral hybridization?, Molecular Phylogenetics and Evolution, vol.44, issue.1, pp.494-500, 2007.
DOI : 10.1016/j.ympev.2007.03.001

G. Yannic, P. Basset, and J. Hausser, A new perspective on the evolutionary history of western European Sorex araneus group revealed by paternal and maternal molecular markers, Molecular Phylogenetics and Evolution, vol.47, issue.1, pp.237-250, 2008.
DOI : 10.1016/j.ympev.2008.01.029

F. Santucci, B. Emerson, and G. Hewitt, Mitochondrial DNA phylogeography of European hedgehogs, Molecular Ecology, vol.7, issue.9, pp.1163-1172, 1998.
DOI : 10.1046/j.1365-294x.1998.00436.x

P. Taberlet and J. Bouvet, Mitochondrial DNA Polymorphism, Phylogeography, and Conservation Genetics of the Brown Bear Ursus arctos in Europe, Proceedings of the Royal Society B: Biological Sciences, vol.255, issue.1344, pp.195-200, 1994.
DOI : 10.1098/rspb.1994.0028
URL : https://hal.archives-ouvertes.fr/halsde-00281059

V. Pérez-mellado, Lacerta vivipara Jaquin, 1797, Fauna Ibérica, pp.232-242, 1997.

P. Crochet, O. Chaline, Y. Surget-groba, C. Debain, and M. Cheylan, Speciation in mountains: phylogeography and phylogeny of the rock lizards genus Iberolacerta (Reptilia: Lacertidae), Molecular Phylogenetics and Evolution, vol.30, issue.3, pp.860-866, 2004.
DOI : 10.1016/j.ympev.2003.07.016

V. Mouret, A. Guillaumet, M. Cheylan, G. Pottier, A. Ferchaud et al., The legacy of ice ages in mountain species: post-glacial colonization of mountain tops rather than current range fragmentation determines mitochondrial genetic diversity in an endemic Pyrenean rock lizard, Journal of Biogeography, vol.17, issue.9, pp.1717-1731, 2011.
DOI : 10.1111/j.1365-2699.2011.02514.x

O. Paulo, C. Dias, M. Bruford, W. Jordan, and R. Nichols, The persistence of Pliocene populations through the Pleistocene climatic cycles: evidence from the phylogeography of an Iberian lizard, Proceedings of the Royal Society B: Biological Sciences, vol.268, issue.1476, pp.1625-1630, 2001.
DOI : 10.1098/rspb.2001.1706

C. Pinho, D. Harris, and N. Ferrand, Contrasting patterns of population subdivision and historical demography in three western Mediterranean lizard species inferred from mitochondrial DNA variation, Molecular Ecology, vol.11, issue.6, pp.1191-1205, 2007.
DOI : 10.1111/j.1365-294X.2007.03230.x

J. Alexandrino, E. Froufe, J. Arntzen, and N. Ferrand, Genetic subdivision, glacial refugia and postglacial recolonization in the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela), Molecular Ecology, vol.153, issue.6, pp.771-781, 2000.
DOI : 10.1146/annurev.es.13.110182.001035

A. Miraldo, G. Hewitt, O. Paulo, and B. Emerson, Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones, BMC Evolutionary Biology, vol.42, issue.1, p.170, 2011.
DOI : 10.1111/j.1439-0469.2004.00257.x

P. Fitze, V. González-jimena, L. San-josé, S. Mauro, D. Aragón et al., Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae), BMC Evolutionary Biology, vol.11, issue.1, p.347, 2011.
DOI : 10.2307/2346830

I. Martínez-solano, H. Gonçalves, and J. Arntzen, Phylogenetic relationships and biogeography of midwife toads (Discoglossidae: Alytes), Journal of Biogeography, vol.31, issue.4, pp.603-618, 2004.
DOI : 10.1046/j.1365-2699.2003.01033.x

I. Martínez-solano, D. Teixeira, D. Buckley, and M. García-parís, Mitochondrial DNA phylogeography of Lissotriton boscai (Caudata, Salamandridae): evidence for old, multiple refugia in an Iberian endemic, Molecular Ecology, vol.98, issue.11, pp.3375-3388, 2006.
DOI : 10.1111/j.1365-294X.2006.03013.x

H. Gonçalves, I. Martínez-solano, R. Pereira, B. Carvalho, M. García-parís et al., High levels of population subdivision in a morphologically conserved Mediterranean toad (Alytes cisternasii) result from recent, multiple refugia: evidence from mtDNA, microsatellites and nuclear genealogies, Molecular Ecology, vol.12, issue.24, pp.5143-5160, 2009.
DOI : 10.1111/j.1365-294X.2009.04426.x

O. Arribas, Morphological variability of the Cantabro-Pyrenean populations of Zootoca vivipara (Jaquin, 1787) with description of a new subspecies, Herpetozoa, vol.21, pp.123-146, 2009.

D. Stuart-fox, R. Godinho, J. Goüy-de-bellocq, N. Irwin, J. Brito et al., Variation in Phenotype, Parasite Load and Male Competitive Ability across a Cryptic Hybrid Zone, PLoS ONE, vol.21, issue.5, p.5677, 2009.
DOI : 10.1371/journal.pone.0005677.t001

V. Nunes, A. Miraldo, M. Beaumont, R. Butlin, and O. Paulo, Association of Mc1r variants with ecologically relevant phenotypes in the European ocellated lizard, Lacerta lepida, Journal of Evolutionary Biology, vol.98, issue.10, pp.2289-2298, 2011.
DOI : 10.1111/j.1420-9101.2011.02359.x

W. Babik, J. Szymura, and J. Rafi?ski, Nuclear markers, mitochondrial DNA and male secondary sexual traits variation in a newt hybrid zone (Triturus vulgaris x T. montandoni), Molecular Ecology, vol.68, issue.7, pp.1913-1930, 2003.
DOI : 10.1073/pnas.111455498

R. Pereira, W. Monahan, and D. Wake, Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence, BMC Evolutionary Biology, vol.160, issue.949, p.194, 2011.
DOI : 10.2307/1938423

I. Buño, E. Torroja, C. López-fernández, R. Butlin, G. Hewitt et al., A hybrid zone between two subspecies of the grasshopper Chorthippus parallelus along the Pyrenees: the west end, Heredity, vol.73, pp.625-634, 1994.

M. Salomon and Y. Hemin, Song Variation in the Chiffchaffs (Phylloscopus collybita) of the Western Pyrenees - the Contact Zone between the collybita and brehmii Forms, Ethology, vol.18, issue.4, pp.265-282, 1992.
DOI : 10.1111/j.1439-0310.1992.tb00965.x

J. Haldane, Sex ratio and unisexual sterility in hybrid animals, Journal of Genetics, vol.v, issue.2, pp.101-109, 1922.
DOI : 10.1007/BF02983075

J. Arntzen and G. Wallis, Restricted Gene Flow in a Moving Hybrid Zone of the Newts Triturus cristatus and T. marmoratus in Western France, Evolution, vol.45, issue.4, pp.805-826, 1991.
DOI : 10.2307/2409691

G. Martinsen, T. Whitham, R. Turek, and P. Keim, HYBRID POPULATIONS SELECTIVELY FILTER GENE INTROGRESSION BETWEEN SPECIES, Evolution, vol.244, issue.7, pp.1325-1335, 2001.
DOI : 10.1126/science.254.5033.779-b

S. Rohwer, E. Bermingham, and C. Wood, PLUMAGE AND MITOCHONDRIAL DNA HAPLOTYPE VARIATION ACROSS A MOVING HYBRID ZONE, Evolution, vol.8, issue.2, pp.405-422, 2001.
DOI : 10.1146/annurev.ecolsys.23.1.141

K. Chan and S. Levin, LEAKY PREZYGOTIC ISOLATION AND POROUS GENOMES: RAPID INTROGRESSION OF MATERNALLY INHERITED DNA, Evolution, vol.81, issue.4, pp.720-729, 2005.
DOI : 10.1023/A:1010874117127

M. Krosby and S. Rohwer, A 2000 km genetic wake yields evidence for northern glacial refugia and hybrid zone movement in a pair of songbirds, Proceedings of the Royal Society B: Biological Sciences, vol.47, issue.1, pp.615-621, 2009.
DOI : 10.1006/anbe.1999.1144

F. Sequeira, J. Alexandrino, S. Rocha, W. Arntzen, and N. Ferrand, Genetic exchange across a hybrid zone within the Iberian endemic golden-striped salamander, Chioglossa lusitanica, Molecular Ecology, vol.54, issue.1, pp.245-254, 2005.
DOI : 10.1111/j.1365-294X.2004.02390.x

R. Godinho, E. Crespo, and N. Ferrand, The limits of mtDNA phylogeography: complex patterns of population history in a highly structured Iberian lizard are only revealed by the use of nuclear markers, Molecular Ecology, vol.12, issue.21, pp.4670-4683, 2008.
DOI : 10.1111/j.1365-294X.2008.03929.x

C. Pinho, A. Kaliontzopoulou, M. Carretero, D. Harris, and N. Ferrand, : evidence for limited natural hybridization and a bimodal hybrid zone, Journal of Zoological Systematics and Evolutionary Research, vol.14, issue.4, pp.368-377, 2009.
DOI : 10.1111/j.1439-0469.2009.00532.x

J. Mallet, Hybridization as an invasion of the genome, Trends in Ecology & Evolution, vol.20, issue.5, pp.229-237, 2005.
DOI : 10.1016/j.tree.2005.02.010

M. Smith and J. Patton, Variation in mitochondrial cytochrome b sequences in natural populations of South American akodontine rodents (Muridae: Sigmodontinae), Mol Biol Evol, vol.8, pp.85-103, 1991.

J. Macey, A. Larson, N. Ananjeva, Z. Fang, and T. Papenfuss, Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome, Molecular Biology and Evolution, vol.14, issue.1, pp.91-104, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025706

J. Rozas, J. Sanchez-delbarrio, and X. Messeguer, DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, vol.19, issue.18, pp.2496-2497, 2003.
DOI : 10.1093/bioinformatics/btg359

M. Clement, D. Posada, and K. Crandall, TCS: a computer program to estimate gene genealogies, Molecular Ecology, vol.11, issue.10, pp.1657-1659, 2000.
DOI : 10.1046/j.1365-294x.2000.01020.x

R. Lanfear, B. Calcott, S. Ho, and S. Guindon, PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses, Molecular Biology and Evolution, vol.29, issue.6, pp.1695-1701, 2012.
DOI : 10.1093/molbev/mss020
URL : https://hal.archives-ouvertes.fr/lirmm-00705211

J. Huelsenbeck, F. Ronquist, R. Nielsen, and J. Bollback, Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology, Science, vol.294, issue.5550, pp.2310-2314, 2001.
DOI : 10.1126/science.1065889

D. Rambaut and A. Drummond, MCMC Trace Analysis Package (version 1.4) Available at, 2007.

A. Drummond, M. Suchard, D. Xie, and A. Rambaut, Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Molecular Biology and Evolution, vol.29, issue.8, pp.1969-1973, 2012.
DOI : 10.1093/molbev/mss075

S. Carranza and E. Arnold, A review of the geckos of the genus Hemidactylus (Squamata: Gekkonidae) from Oman based on morphology, mitochondrial and nuclear data, with descriptions of eight new species, Zootaxa, vol.3378, pp.1-95, 2012.

S. Carranza, A. Romano, E. Arnold, and G. Sotgiu, Biogeography and evolution of European cave salamanders, Hydromantes (Urodela: Plethodontidae), inferred from mtDNA sequences, Journal of Biogeography, vol.15, issue.4, pp.724-738, 2008.
DOI : 10.1111/j.1095-8312.2006.00585.x

S. Cox, S. Carranza, and R. Brown, Divergence times and colonization of the Canary Islands by Gallotia lizards, Molecular Phylogenetics and Evolution, vol.56, issue.2, pp.747-757, 2010.
DOI : 10.1016/j.ympev.2010.03.020

S. Carranza, E. Arnold, J. Mateo, and M. Geniez, Relationships and evolution of the North African geckos, Geckonia and Tarentola (Reptilia: Gekkonidae), based on mitochondrial and nuclear DNA sequences, Molecular Phylogenetics and Evolution, vol.23, issue.2, pp.244-256, 2002.
DOI : 10.1016/S1055-7903(02)00024-6

Y. Fu, Statistical neutrality of mutations against population growth, hitchhiking and background selection, Genetics, vol.147, pp.915-925, 1997.

A. Rogers and H. Harpending, Population growth makes waves in the distribution of pairwise genetic differences, Mol Biol Evol, vol.9, pp.552-569, 1992.

S. Schneider and L. Excoffier, Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA, Genetics, vol.152, pp.1079-1089, 1999.

L. Excoffier and H. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Molecular Ecology Resources, vol.127, issue.3
DOI : 10.1111/j.1755-0998.2010.02847.x

B. Milá, S. Carranza, O. Guillaume, and J. Clobert, (Amphibia: Salamandridae) revealed by genome-wide AFLP but not mtDNA, Molecular Ecology, vol.272, issue.1, pp.108-120, 2010.
DOI : 10.1111/j.1365-294X.2009.04441.x

P. Vos, R. Hogers, M. Bleeker, M. Reijans, T. Van-de-lee et al., AFLP: a new technique for DNA fingerprinting, Nucleic Acids Research, vol.23, issue.21, pp.4407-4414, 1995.
DOI : 10.1093/nar/23.21.4407

A. Bonin, E. Bellemain, B. Eidesen, P. Pompanon, F. Brochmann et al., How to track and assess genotyping errors in population genetics studies, Molecular Ecology, vol.111, issue.11, pp.3261-3273, 2004.
DOI : 10.1111/j.1365-294X.2004.02346.x
URL : https://hal.archives-ouvertes.fr/halsde-00278842

M. Foll and O. Gaggiotti, A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective, Genetics, vol.180, issue.2, pp.977-993, 2008.
DOI : 10.1534/genetics.108.092221
URL : https://hal.archives-ouvertes.fr/halsde-00377961

L. Zhivotovsky, Estimating population structure in diploids with multilocus dominant DNA markers, Molecular Ecology, vol.18, issue.6, pp.907-913, 1999.
DOI : 10.1017/S0953756297003791

M. Lynch and B. Milligan, Analysis of population genetic structure with RAPD markers, Molecular Ecology, vol.15, issue.2, pp.91-99, 1994.
DOI : 10.1111/j.1365-294X.1994.tb00109.x

X. Vekemans, T. Beauwens, and M. Lemaire, Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size, Molecular Ecology, vol.119, issue.10, pp.139-151, 2002.
DOI : 10.1007/s001220050778

R. Peakall and P. Smouse, genalex 6: genetic analysis in Excel. Population genetic software for teaching and research, Molecular Ecology Notes, vol.35, issue.1, pp.288-295, 2006.
DOI : 10.1046/j.1365-2540.1999.00518.x

L. Orloci, Multivariate analysis in vegetation research. The Hague: Dr W, Junk B, 1978.

J. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using multilocus genotype data, Genetics, vol.155, pp.945-959, 2000.

M. Hubisz, D. Falush, M. Stephens, and J. Pritchard, Inferring weak population structure with the assistance of sample group information, Molecular Ecology Resources, vol.101, issue.5
DOI : 10.1111/j.1755-0998.2009.02591.x

G. Evanno, S. Regnaut, and J. Goudet, Detecting the number of clusters of individuals using the software structure: a simulation study, Molecular Ecology, vol.16, issue.8, pp.2611-2620, 2005.
DOI : 10.1098/rspb.2001.1600

D. Earl, STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method, Conservation Genetics Resources, vol.10, issue.2, pp.359-361, 2012.
DOI : 10.1007/s12686-011-9548-7