C. Parmesan, Ecological and Evolutionary Responses to Recent Climate Change, Annual Review of Ecology, Evolution, and Systematics, vol.37, issue.1, pp.637-669, 2006.
DOI : 10.1146/annurev.ecolsys.37.091305.110100

K. Willis and S. Bhagwat, Biodiversity and Climate Change, Science, vol.326, issue.5954, pp.806-807, 2009.
DOI : 10.1126/science.1178838

H. Pereira, P. Leadley, V. Proenca, R. Alkemade, and J. Scharlemann, Scenarios for Global Biodiversity in the 21st Century, Science, vol.330, issue.6010, pp.1496-1501, 2010.
DOI : 10.1126/science.1196624

T. Dawson, S. Jackson, J. House, I. Prentice, and G. Mace, Beyond Predictions: Biodiversity Conservation in a Changing Climate, Science, vol.332, issue.6025, pp.53-58, 2011.
DOI : 10.1126/science.1200303

S. Mcmahon, S. Harrison, W. Armbruster, P. Bartlein, and C. Beale, Improving assessment and modelling of climate change impacts on global terrestrial biodiversity, Trends in Ecology & Evolution, vol.26, issue.5, pp.249-259, 2011.
DOI : 10.1016/j.tree.2011.02.012

C. Bellard, C. Bertelsmeier, P. Leadley, W. Thuiller, and F. Courchamp, Impacts of climate change on the future of biodiversity, Ecology Letters, vol.105, issue.4, pp.365-377, 2012.
DOI : 10.1111/j.1461-0248.2011.01736.x
URL : https://hal.archives-ouvertes.fr/hal-01359347

J. Avise, The history and purview of phylogeography: a personal reflection, Molecular Ecology, vol.7, issue.4, pp.371-379, 1998.
DOI : 10.1146/annurev.ecolsys.26.1.343

K. Pease, A. Freedman, J. Pollinger, J. Mccormack, and W. Buermann, ): the roles of ecological and historical factors in generating differentiation, Molecular Ecology, vol.163, issue.9, pp.1848-1862, 2009.
DOI : 10.1111/j.1365-294X.2009.04112.x

G. Beaty and J. Provan, Comparative phylogeography of two related plant species with overlapping ranges in Europe, and the potential effects of climate change on their intraspecific genetic diversity, BMC Evolutionary Biology, vol.24, issue.1, p.29, 2011.
DOI : 10.1016/j.tree.2009.06.007

M. Poelchau and J. Hamrick, Comparative phylogeography of three common Neotropical tree species, Journal of Biogeography, vol.37, issue.4, pp.618-631, 2013.
DOI : 10.1111/j.1365-2699.2011.02599.x

B. Faleh, A. Granjon, L. Tatard, C. Duplantier, J. Dobigny et al., Phylogeography of two cryptic species of African desert jerboas (Dipodidae: Jaculus), Biological Journal of the Linnean Society, vol.107, issue.1, pp.27-38, 2012.
DOI : 10.1111/j.1095-8312.2012.01920.x

V. Nicolas, J. Mboumba, E. Verheyen, C. Denys, and E. Lecompte, (Rodentia: Muridae) in tropical Africa, Journal of Biogeography, vol.10, issue.11, pp.2074-2089, 2008.
DOI : 10.1111/j.1365-2699.2008.01950.x
URL : https://hal.archives-ouvertes.fr/hal-00336791

J. Bryja, L. Granjon, G. Dobigny, H. Patzenhauerova, and A. Konecny, Plio-Pleistocene history of West African Sudanian savanna and the phylogeography of the Praomys daltoni complex (Rodentia): the environment/geography/genetic interplay, Molecular Ecology, vol.96, issue.21, pp.4783-4799, 2010.
DOI : 10.1111/j.1365-294X.2010.04847.x
URL : https://hal.archives-ouvertes.fr/hal-00553191

C. Brouat, D. Tatard, K. Bâ, J. Cosson, and G. Dobigny, ): a case study for Sahelian species in West Africa, Journal of Biogeography, vol.14, issue.12, pp.2237-2250, 2009.
DOI : 10.1111/j.1365-2699.2009.02184.x

G. Dobigny, J. Catalan, P. Gauthier, O. Brien, P. Brouat et al., Geographic patterns of inversion polymorphisms in a wild African rodent, Mastomys erythroleucus, Heredity, vol.52, issue.4, pp.378-386, 2010.
DOI : 10.1038/hdy.2009.119

V. Nicolas, L. Granjon, J. Duplantier, C. Cruaud, and G. Dobigny, Phylogeography of spiny mice (genus Acomys, Rodentia: Muridae) from the south-western margin of the Sahara with taxonomic implications, Biological Journal of the Linnean Society, vol.98, issue.1, 2009.
DOI : 10.1111/j.1095-8312.2009.01273.x

K. Mouline, L. Granjon, M. Galan, C. Tatard, and D. Abdoullaye, Phylogeography of a Sahelian rodent species Mastomys huberti: a Plio-Pleistocene story of emergence and colonization of humid habitats, Molecular Ecology, vol.397, issue.4, pp.1036-1053, 2008.
DOI : 10.1111/j.1365-294X.2007.03610.x

J. Mboumba, P. Deleporte, M. Colyn, and N. V. , Phylogeography of Mus (Nannomys) minutoides (Rodentia, Muridae) in West Central African savannahs: singular vicariance in neighbouring populations, Journal of Zoological Systematics and Evolutionary Research, vol.10, issue.(6), pp.77-85, 2011.
DOI : 10.1111/j.1439-0469.2010.00579.x
URL : https://hal.archives-ouvertes.fr/hal-00592143

V. Nicolas, J. Bryja, B. Akpatou, A. Konecny, and E. Lecompte, ) in West Africa: different reactions to past forest fragmentation, Molecular Ecology, vol.9, issue.16), pp.5118-5134, 2008.
DOI : 10.1111/j.1365-294X.2008.03974.x

V. Nicolas, A. Missoup, C. Denys, K. Peterhans, J. Katuala et al., The roles of rivers and Pleistocene refugia in shaping genetic diversity in Praomys misonnei in tropical Africa, Journal of Biogeography, vol.9, issue.1, pp.191-207, 2011.
DOI : 10.1111/j.1365-2699.2010.02399.x
URL : https://hal.archives-ouvertes.fr/hal-00558396

V. Nicolas, A. Missoup, M. Colyn, C. Cruaud, and C. Denys, West-Central African Pleistocene lowland forest evolution revealed by the phylogeography of Misonne's soft-furred mouse, African Zool, vol.47, pp.100-112, 2012.

G. Musser and M. Carleton, Arvicanthis Mammals of the World: a taxonomic and geographic reference, pp.1285-1292, 2005.

L. Granjon and J. Duplantier, Les rongeurs de l'Afrique sahélosoudanienne, Editions IRD, Publications Scientifiques du MNHN, 2009.

L. Granjon, J. Duplantier, J. Catalan, and J. Britton-davidian, Karyotypic data on rodents from Senegal, Israel J Zool, vol.38, pp.263-276, 1992.

J. Ducroz, Contribution des approches cytogénétique et moléculaire a ` l'e ´tude systématique et e ´volutive des genres de rongeurs Murinae de la division « Arvicanthis, Muséum National d'Histoire Naturelle, 1998.

J. Ducroz, L. Granjon, P. Chevret, J. Duplantier, and M. Lombard, Characterization of two distinct species of Arvicanthis (Rodentia, Muridae) in West Africa: cytogenetic, molecular and reproductive evidence, J Zool, vol.214, pp.709-723, 1997.

J. Ducroz, V. Volobouev, and L. Granjon, A Molecular Perspective on the Systematics and Evolution of the GenusArvicanthis(Rodentia, Muridae): Inferences from Complete CytochromebGene Sequences, Molecular Phylogenetics and Evolution, vol.10, issue.1, pp.104-117, 1998.
DOI : 10.1006/mpev.1997.0477

V. Volobouev, J. Ducroz, V. Aniskin, J. Britton-davidian, and R. Castiglia, Chromosomal characterization of <i>Arvicanthis</i> species (Rodentia, Murinae) from western and central Africa: implications for taxonomy, Cytogenetic and Genome Research, vol.96, issue.1-4, pp.250-260, 2002.
DOI : 10.1159/000063041

R. Castiglia, M. Corti, P. Tesha, A. Scanzani, and C. Fadda, Cytogenetics of the genus Arvicanthis (Rodentia, Murinae): 3. Comparative cytogenetics of A. neumanni and A. nairobae from Tanzania, Genetica, vol.118, issue.1, pp.33-39, 2003.
DOI : 10.1023/A:1022903112274

R. Castiglia, A. Bekele, R. Makundi, N. Oguge, and M. Corti, Chromosomal diversity in the genus Arvicanthis (Rodentia, Muridae) from East Africa: a taxonomic and phylogenetic evaluation, Journal of Zoological Systematics and Evolutionary Research, vol.9, issue.3, pp.223-235, 2006.
DOI : 10.1159/000063054

A. Rahman, A. Ducroz, J. Mitchell, A. Lamb, J. Contrafatto et al., Phylogeny and historical demography of economically important rodents of the genus Arvicanthis (Mammalia, Muridae) from the Nile Valley: of mice and men, Biol J Linnean Soc, vol.93, pp.641-655, 2008.

G. Dobigny, C. Tatard, M. Kane, P. Gauthier, and C. Brouat, A cytotaxonomic and DNA-based survey of rodents from Northern Cameroon and Western Chad, Mammalian Biology - Zeitschrift f??r S??ugetierkunde, vol.76, issue.4, pp.417-427, 2011.
DOI : 10.1016/j.mambio.2010.10.002

E. Githure, J. Schnur, L. , L. Blancq, S. Hendricks et al., as new hosts of Leishmania major, Annals of Tropical Medicine & Parasitology, vol.8, issue.5, pp.501-507, 1986.
DOI : 10.1016/0035-9203(85)90259-7

J. Trape, B. Godeluck, G. Diatta, C. Rogier, and F. Legros, The spread of tick-borne borreliosis in West Africa and its relationship to sub-Saharan drought, Ann J Trop Med Hyg, vol.54, pp.289-293, 1996.

Z. Sebek, W. Sixl, F. Reinthaler, M. Valova, and W. Schneeweiss, Results of serological examination for leptospirosis of domestic and wild animals in the Upper Nile province (Sudan), J Hyg Epid Microbiol Immunol, vol.33, pp.337-345, 1989.

J. Julvez, A. Michault, and C. Kerdelhue, Etude sérologique des rickettsioses a ` Niamey, Niger. Méd Trop, vol.57, pp.153-156, 1997.

J. Duplantier and M. Sene, Rodents as definitive hosts of Schistosoma, with special reference to S. mansoni transmission, Micromammals and Macroparasites, pp.527-543, 2006.
DOI : 10.1007/978-4-431-36025-4_24

A. Mercier, M. Garba, H. Bonnabau, M. Kane, and J. Rossi, Toxoplasmosis seroprevalence in urban rodents: a survey in Niamey, Niger, Mem??rias do Instituto Oswaldo Cruz, vol.108, issue.4, pp.399-407, 2013.
DOI : 10.1590/S0074-0276108042013002
URL : https://hal.archives-ouvertes.fr/hal-01219025

J. Ducroz, V. Volobouev, and L. Granjon, An assessment of systematics of Arvicanthine rodents using mitochondrial DNA sequences: evolutionary and biogeographical implications, Journal of Mammalian Evolution, vol.8, issue.3, pp.173-206, 2001.
DOI : 10.1023/A:1012277012303

E. Lecompte, K. Aplin, C. Denys, F. Catzeflis, and M. Chades, Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily, BMC Evolutionary Biology, vol.8, issue.1, pp.199-219, 2008.
DOI : 10.1186/1471-2148-8-199
URL : https://hal.archives-ouvertes.fr/hal-00336780

R. Sikes and W. Gannon, Guidelines of the American Society of Mammalogists for the use of wild mammals in research, Journal of Mammalogy, vol.92, issue.1, pp.235-253, 2011.
DOI : 10.1644/10-MAMM-F-355.1

E. Lecompte, L. Granjon, and C. Denys, The phylogeny of the Praomys complex (Rodentia: Muridae) and its phylogeographic implications, Journal of Zoological Systematics and Evolutionary Research, vol.315, issue.1, pp.8-25, 2002.
DOI : 10.1126/science.276.5320.1855

T. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucl Acids Symp Ser, vol.41, pp.95-98, 1999.

J. Seddon, F. Santucci, N. Reeve, and G. Hewitt, DNA footprints of European hedgehogs, Erinaceus europaeus and E. concolor: Pleistocene refugia, postglacial expansion and colonization routes, Molecular Ecology, vol.128, issue.9, pp.2187-2198, 2001.
DOI : 10.1023/A:1021902125382

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

A. Drummond, S. Ho, M. Phillips, and A. Rambaut, Relaxed Phylogenetics and Dating with Confidence, PLoS Biology, vol.20, issue.5, p.88, 2006.
DOI : 10.1371/journal.pbio.0040088.sd001

J. Nylander, F. Ronquist, J. Huelsenbeck, and J. Nieves-aldrey, Bayesian Phylogenetic Analysis of Combined Data, Systematic Biology, vol.53, issue.1, pp.47-67, 2004.
DOI : 10.1080/10635150490264699

D. Posada, jModelTest: Phylogenetic Model Averaging, Molecular Biology and Evolution, vol.25, issue.7, pp.1253-1256, 2008.
DOI : 10.1093/molbev/msn083

J. Heled and A. Drummond, Bayesian Inference of Species Trees from Multilocus Data, Molecular Biology and Evolution, vol.27, issue.3, pp.570-580, 2010.
DOI : 10.1093/molbev/msp274

N. Lartillot and P. H. , Computing Bayes Factors Using Thermodynamic Integration, Systematic Biology, vol.55, issue.2, pp.195-207, 2006.
DOI : 10.1080/10635150500433722

G. Baele, W. Li, A. Drummond, M. Suchard, and P. Lemey, Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics, Molecular Biology and Evolution, vol.30, issue.2, pp.239-243, 2013.
DOI : 10.1093/molbev/mss243

A. Stamatakis, T. Ludwig, and H. Meier, RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees, Bioinformatics, vol.21, issue.4, pp.456-463, 2005.
DOI : 10.1093/bioinformatics/bti191

A. Winkler, Neogene paleobiogeography and East African paleoenvironments: contributions from the Tugen Hills rodents and lagomorphs, Journal of Human Evolution, vol.42, issue.1-2, pp.237-256, 2002.
DOI : 10.1006/jhev.2001.0501

S. Ho and M. Phillips, Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times, Systematic Biology, vol.58, issue.3, pp.367-380, 2009.
DOI : 10.1093/sysbio/syp035

D. Graur and W. Martin, Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision, Trends in Genetics, vol.20, issue.2, pp.80-86, 2004.
DOI : 10.1016/j.tig.2003.12.003

P. Erixon, B. Svennblad, T. Britton, and B. Oxelman, Reliability of Bayesian Posterior Probabilities and Bootstrap Frequencies in Phylogenetics, Systematic Biology, vol.52, issue.5, pp.665-673, 2003.
DOI : 10.1080/10635150390235485

R. Kass and A. Raftery, Bayes Factors, Journal of the American Statistical Association, vol.2, issue.430, pp.773-795, 1995.
DOI : 10.1080/01621459.1995.10476572

W. Maddison and D. Maddison, Mesquite: a modular system for evolutionary analysis, 2011.

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1452, 2009.
DOI : 10.1093/bioinformatics/btp187

P. Gaubert, C. Bloch, S. Benyacoub, A. Abdelhamid, and P. Pagani, Reviving the African Wolf Canis lupus lupaster in North and West Africa: A Mitochondrial Lineage Ranging More than 6,000 km Wide, PLoS ONE, vol.7, issue.8, p.42740, 2012.
DOI : 10.1371/journal.pone.0042740.t005

R. Hudson, D. Boos, and N. Kaplan, A statistical test for detecting geographic subdivision, Mol. Biol. Evol, vol.9, pp.138-151, 1992.

R. Hudson, A new statistic for detecting genetic differentiation, Genetics, vol.155, pp.2011-2014, 2000.

R. Morales-hojas, C. Vieira, and J. Vieira, Inferring the evolutionary history of Drosophila americana and Drosophila novamexicana using a multilocus approach and the influence of chromosomal rearrangements in single gene analyses, Molecular Ecology, vol.164, issue.12, pp.2910-2926, 2008.
DOI : 10.1073/pnas.0336368100

F. Tajima, Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.

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

H. Bandelt, P. Forster, and A. Röhl, Median-joining networks for inferring intraspecific phylogenies, Molecular Biology and Evolution, vol.16, issue.1, pp.37-48, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026036

S. Woolley, D. Posada, and K. Crandall, A Comparison of Phylogenetic Network Methods Using Computer Simulation, PLoS ONE, vol.132, issue.4, p.1913, 2008.
DOI : 10.1371/journal.pone.0001913.s001

V. Volobouev, V. Aniskin, E. Lecompte, and J. Ducroz, Patterns of karyotype evolution in complexes of sibling species within three genera of African murid rodents inferred from the comparison of cytogenetic and molecular data, Cytogenetic and Genome Research, vol.96, issue.1-4, pp.261-275, 2002.
DOI : 10.1159/000063049

M. Baskevich and L. Lavrenchenko, Review of karyological studies and the problems of systematics of Ethiopian Arvicanthis Lesson, 1842 (Rodentia: Muridae), Bönner Zool Monogr, vol.46, pp.209-215, 2000.

J. Avise and T. Robinson, Hemiplasy: A New Term in the Lexicon of Phylogenetics, Systematic Biology, vol.57, issue.3, pp.503-508, 2008.
DOI : 10.1080/10635150802164587

L. Jacobs and W. Downs, The evolution of murine rodents in Asia Rodent and Lagomorph Families of Asian origin and diversification, National Science Museum Monograph, pp.149-156, 1994.

S. Steppan, R. Adkins, and J. Anderson, Phylogeny and Divergence-Date Estimates of Rapid Radiations in Muroid Rodents Based on Multiple Nuclear Genes, Systematic Biology, vol.53, issue.4, pp.533-553, 2004.
DOI : 10.1080/10635150490468701

R. Bobe and A. Behrensmeyer, The expansion of grass land ecosystem in Africa in relation to mammalian evolution and the origin of the genus Homo, Pal Pal Pal, vol.207, pp.309-320, 2004.

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

J. Haffer, Speciation in Amazonian Forest Birds, Science, vol.165, issue.3889, pp.131-137, 1969.
DOI : 10.1126/science.165.3889.131

D. Menocal and P. , Plio-Pleistocene African Climate, Science, vol.270, issue.5233, pp.53-59, 1995.
DOI : 10.1126/science.270.5233.53

D. Menocal and P. , African climate change and faunal evolution during the Pliocene???Pleistocene, Earth and Planetary Science Letters, vol.220, issue.1-2, pp.3-24, 2004.
DOI : 10.1016/S0012-821X(04)00003-2

M. Trauth, J. Larrasoana, and M. Mudelsee, Trends, rhythms and events in Plio-Pleistocene African climate, Quaternary Science Reviews, vol.28, issue.5-6, pp.399-411, 2009.
DOI : 10.1016/j.quascirev.2008.11.003

L. Dupont, Orbital scale vegetation change in Africa, Quaternary Science Reviews, vol.30, issue.25-26, pp.3589-3602, 2011.
DOI : 10.1016/j.quascirev.2011.09.019

S. Cowling, P. Cox, C. Jones, M. Maslin, and M. Peros, Simulated glacial and interglacial vegetation across Africa: implications for species phylogenies and trans-African migration of plants and animals, Global Change Biology, vol.72, issue.4, pp.827-840, 2008.
DOI : 10.1111/j.1365-2486.2007.01524.x

J. Maley, Les changements climatiques de la fin du Tertiaire en Afrique : leur conséquence sur l'apparition du Sahara et de sa végétation The Sahara and the Nile: quaternary environments and prehistoric occupation in Northern Africa, pp.63-86, 1980.

J. Maley, The impact of arid phases on the African rain forest through geological history African rain forest ecology and conservation: an interdisciplinary perspective, pp.68-87, 2001.

L. Houérou and H. , Outline of the biological history of the Sahara, J Arid Env, vol.22, pp.3-30, 1992.

C. Ségalen, J. Lee-thorp, and T. Cerling, Timing of C4 grass expansion across sub-Saharan Africa, Journal of Human Evolution, vol.53, issue.5, pp.449-459, 2007.
DOI : 10.1016/j.jhevol.2006.12.010

L. Granjon, A. Bekele, and J. Ducroz, Arvicanthis niloticus Mammals of Africa, Volume III: Rodents, Hares and Rabbits, pp.387-388, 2013.

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

G. Dobigny, V. Aniskin, L. Granjon, R. Cornette, and V. Volobouev, Recent radiation in West African Taterillus (Rodentia, Gerbillinae): the concerted role of chromosome and climatic changes, Heredity, vol.17, issue.5, pp.358-368, 2005.
DOI : 10.1101/gr.1891104

K. Hima, M. Thiam, J. Catalan, P. Gauthier, and J. Duplantier, Extensive Robertsonian polymorphism in the African rodent Gerbillus nigeriae: geographic aspects and meiotic data, Journal of Zoology, vol.96, issue.53, pp.276-285, 2011.
DOI : 10.1111/j.1469-7998.2011.00803.x

L. Granjon and G. Dobigny, The importance of cytotaxonomy in understanding the biogeography of African rodents: Lake Chad murids as an example, Mammal Review, vol.69, issue.1, pp.77-91, 2003.
DOI : 10.1159/000056910

G. Dobigny, R. Cornette, S. Moulin, A. Sidiyène, and E. , The mammals of Adrar des Iforas, Mali, with special emphasis on small mammals: systematic and biogeographical implications, Proceedings of African Small Mammals Symposium. Editions IRD, pp.445-458, 2001.

G. Dobigny, A. Nomao, and J. Gautun, Rodents from Niger: implications for systematics, biodiversity and biogeography, Mammalia, vol.66, pp.495-523, 2002.

M. Colyn, A. Gautier-hion, and W. Verheyen, A Re-Appraisal of Palaeoenvironmental History in Central Africa: Evidence for a Major Fluvial Refuge in the Zaire Basin, Journal of Biogeography, vol.18, issue.4, pp.403-407, 1991.
DOI : 10.2307/2845482
URL : https://hal.archives-ouvertes.fr/hal-01369834

A. Tosi, species group, Zoological Journal of the Linnean Society, vol.154, issue.2, pp.408-418, 2008.
DOI : 10.1111/j.1096-3642.2008.00419.x
URL : https://hal.archives-ouvertes.fr/hal-00895675

D. Zinner, L. Groeneveld, C. Keller, and C. Roos, Mitochondrial phylogeography of baboons (Papio spp.) ??? Indication for introgressive hybridization?, BMC Evolutionary Biology, vol.9, issue.1, pp.83-97, 2009.
DOI : 10.1186/1471-2148-9-83

N. Rohland, J. Pollack, D. Nagel, C. Beauval, and J. Airvaux, The Population History of Extant and Extinct Hyenas, Molecular Biology and Evolution, vol.22, issue.12, pp.2435-2443, 2005.
DOI : 10.1093/molbev/msi244

C. Mardsen, R. Woodroffe, M. Milss, J. Mcnutt, and S. Creel, Spatial and temporal patterns of neutral and adaptive variation in the endangered African wild dog (Lycaon pictus), Mol Ecol, vol.21, pp.1379-1393, 2012.

V. Muwanika, S. Nyakaana, H. Siegismund, and P. Arctander, Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci, Heredity, vol.91, issue.4, pp.361-372, 2003.
DOI : 10.1038/sj.hdy.6800341

D. Brown, R. Brenneman, K. Koepfli, J. Pollinger, and B. Mila, Extensive population genetic structure in the giraffe, BMC Biology, vol.5, issue.1, pp.57-69, 2007.
DOI : 10.1186/1741-7007-5-57

N. Smitz, C. Berthouly, D. Cornélis, R. Heller, V. Hooft et al., Pan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence, PLoS ONE, vol.167, issue.11, pp.56235-56241, 2013.
DOI : 10.1371/journal.pone.0056235.t007

P. Arctander, C. Johansen, and M. Coutellec-vreto, Phylogeography of three closely related African bovids (tribe Alcelaphini), Molecular Biology and Evolution, vol.16, issue.12, pp.1724-1739, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026085

O. Flagstad, P. Syvertsen, N. Stenseth, and K. Jakobsen, Environmental change and rates of evolution: the phylogeographic pattern within the hartebeest complex as related to climatic variation, Proceedings of the Royal Society B: Biological Sciences, vol.268, issue.1468, pp.667-677, 2001.
DOI : 10.1098/rspb.2000.1416

L. Nersting and P. Arctander, Phylogeography and conservation of impala and greater kudu, Molecular Ecology, vol.11, issue.3, pp.711-719, 2001.
DOI : 10.1046/j.1365-294x.2001.01205.x

E. Lorenzen, B. Simonsen, P. Kat, P. Arctander, and H. Siegismund, Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression, Molecular Ecology, vol.28, issue.12, pp.3787-3799, 2006.
DOI : 10.1111/j.1365-294X.2006.03059.x

E. Lorenzen, D. Neergaard, R. Arctander, P. Siegismund, and H. , ), Molecular Ecology, vol.15, issue.15, pp.3241-3252, 2007.
DOI : 10.1111/j.1365-294X.2007.03382.x

Y. Moodley and M. Bruford, Molecular Biogeography: Towards an Integrated Framework for Conserving Pan-African Biodiversity, PLoS ONE, vol.292, issue.5, pp.454-462, 2007.
DOI : 10.1371/journal.pone.0000454.s003

E. Lorenzen, C. Masembe, P. Arctander, and H. Siegismund, A long-standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope, Journal of Biogeography, vol.9, issue.3, pp.571-581, 2010.
DOI : 10.1111/j.1365-2699.2009.02207.x

D. Alpers, V. Vuuren, B. Arctander, P. Robinson, and T. , Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation, Molecular Ecology, vol.11, issue.7, pp.1771-1784, 2004.
DOI : 10.1111/j.1365-294X.2004.02204.x

C. Fontaine, P. Lovett, H. Sanou, J. Maley, and J. Bouvet, Genetic diversity of the shea tree (Vitellaria paradoxa C.F. Gaertn), detected by RAPD and chloroplast microsatellite markers, Heredity, vol.93, issue.6, pp.639-648, 2004.
DOI : 10.1038/sj.hdy.6800591

M. Kebede, D. Ehrich, P. Taberlet, S. Nemomissa, and C. Brochmann, ) in Ethiopian and Tropical East African mountains, Molecular Ecology, vol.137, issue.139, pp.1233-1243, 2007.
DOI : 10.1111/j.1365-294X.2007.03232.x

C. Gomez, S. Dussert, P. Hamon, S. Hamon, and A. De-kochko, Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities, BMC Evolutionary Biology, vol.9, issue.1, pp.167-175, 2009.
DOI : 10.1186/1471-2148-9-167

M. Sezonlin, S. Dupas, L. Rü, B. , L. Gall et al., Phylogeography and population genetics of the maize stalk borer Busseola fusca (Lepidoptera, Noctuidae) in sub-Saharan Africa, Molecular Ecology, vol.330, issue.Suppl., pp.407-420, 2006.
DOI : 10.1111/j.1365-294X.2005.02761.x
URL : https://hal.archives-ouvertes.fr/hal-00118851

A. Barlow, K. Baker, C. Hendry, L. Peppin, and T. Phelps, ) reveals multiple Pleistocene refugia in southern Africa, Molecular Ecology, vol.38, issue.10, pp.1134-1157, 2013.
DOI : 10.1111/mec.12157

C. Matthee and A. Flemming, Population fragmentation in the southern rock agama, Agama atra: more evidence for vicariance in Southern Africa, Molecular Ecology, vol.10, issue.3, pp.465-471, 2002.
DOI : 10.1038/35002501

R. Bowie, J. Fjeldsa, S. Hackett, J. Bates, and T. Crowe, Coalescent models reveal the relative roles of ancestral polymorphism, vicariance, and dispersal in shaping phylogeographical structure of an African montane forest robin, Molecular Phylogenetics and Evolution, vol.38, issue.1, pp.171-188, 2006.
DOI : 10.1016/j.ympev.2005.06.001

J. Miller, S. Hallager, S. Monfort, J. Newby, and K. Bishop, Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus), Conservation Genetics, vol.46, issue.2, pp.423-431, 2010.
DOI : 10.1007/s10592-010-0149-x

R. Barnett, N. Yamaguchi, I. Barnes, and A. Cooper, The origin, current diversity and future conservation of the modern lion (Panthera leo), Proceedings of the Royal Society B: Biological Sciences, vol.263, issue.1558, pp.2119-2125, 2006.
DOI : 10.1098/rspb.2004.2813

G. Hewitt, Speciation, hybrid zones and phylogeography - or seeing genes in space and time, Molecular Ecology, vol.14, issue.3, pp.537-549, 2001.
DOI : 10.1046/j.1365-294x.2001.01202.x

G. Hewitt, Biodiversity: A climate for colonization, Heredity, vol.92, issue.1, pp.1-2, 2004.
DOI : 10.1038/sj.hdy.6800365

B. Emerson and G. Hewitt, Phylogeography, Current Biology, vol.15, issue.10, pp.367-371, 2004.
DOI : 10.1016/j.cub.2005.05.016