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, p.199, 2008.
DOI : 10.1186/1471-2148-8-199

URL : https://hal.archives-ouvertes.fr/hal-00336780

V. Nicolas, E. Verheyen, W. Verheyen, J. Hulselmans, and M. Dillen, Systematics of African lowland rainforest Praomys (Rodentia, Muridae) based on molecular and craniometrical data, Zoological Journal of the Linnean Society, vol.145, issue.4, pp.539-553, 2005.
DOI : 10.1111/j.1096-3642.2005.00196.x

E. Lecompte, C. Denys, and L. Granjon, Confrontation of morphological and molecular data: The Praomys group (Rodentia, Murinae) as a case of adaptive convergences and morphological stasis, Molecular Phylogenetics and Evolution, vol.37, issue.3, pp.899-919, 2005.
DOI : 10.1016/j.ympev.2005.06.018

E. Van-der-straeten, E. Lecompte, and C. Denys, Praomys petteri: une nouvelle espèce de Muridae africains (Mammalia, Rodentia), Bonn Zool Beitr, vol.50, pp.329-345, 2003.

V. Nicolas, S. Quérouil, E. Verheyen, W. Verheyen, and J. Mboumba, Mitochondrial phylogeny of African wood mice, genus Hylomyscus (Rodentia, Muridae): Implications for their taxonomy and biogeography, Molecular Phylogenetics and Evolution, vol.38, issue.3, pp.779-793, 2006.
DOI : 10.1016/j.ympev.2005.11.024

URL : https://hal.archives-ouvertes.fr/hal-00022913

V. Nicolas, W. Wendelen, P. Barrière, A. Dudu, and M. Colyn, (Rodentia: Muridae), and Description of a New Species, Journal of Mammalogy, vol.89, issue.1, pp.222-231, 2008.
DOI : 10.1644/06-MAMM-A-286.1

URL : https://hal.archives-ouvertes.fr/hal-00312645

V. Nicolas, A. Olayemi, W. Wendelen, and M. Colyn, Mitochondrial DNA and morphometrical identification of a new species of Hylomyscus (Rodentia: Muridae) from West Africa, Zootaxa, vol.2579, pp.30-44, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00553077

E. Van-der-straeten, Notes on the Praomys of Angola with the description of a new species (Mammalia: Rodentia: Muridae), pp.121-131, 2008.

E. Van-der-straeten, K. Peterhans, and J. , , a new species of Muridae (Mammalia) from central Africa, South African Journal of Zoology, vol.34, issue.2, pp.80-90, 1999.
DOI : 10.1080/02541858.1999.11448492

E. Van-der-straeten and A. Dudu, Systematics and distribution of Praomys from the Masako Forest Reserve (Zaire) with the description of a new species, Vertebrates in the tropics, pp.73-83, 1990.

E. Van-der-straeten and F. Dieterlen, Praomys misonnei, an new species of muridae from eastern Za?¨reZa?¨re, pp.1-11, 1987.

G. Dobigny, E. Lecompte, C. Tatard, P. Gauthier, and K. Ba, (Muridae, Murinae) using combined cytogenetic and molecular data, Journal of Zoology, vol.9, issue.(Suppl. 1), pp.368-374, 2008.
DOI : 10.1111/j.1469-7998.2008.00500.x

URL : https://hal.archives-ouvertes.fr/hal-00351317

E. Lecompte, C. Brouat, J. Duplantier, M. Galan, and L. Granjon, Molecular identification of four cryptic species of Mastomys (Rodentia, Murinae), Biochemical Systematics and Ecology, vol.33, issue.7, pp.681-689, 2005.
DOI : 10.1016/j.bse.2004.12.015

E. Lecompte, L. Granjon, J. Peterhans, and C. Denys, Cytochrome??b-based phylogeny of the Praomys group (Rodentia, Murinae): a new African radiation?, Comptes Rendus Biologies, vol.325, issue.7, pp.827-840, 2002.
DOI : 10.1016/S1631-0691(02)01488-9

V. Nicolas, B. Akpatou, W. Wendelen, K. Peterhans, J. Olayemi et al., Molecular and morphometric variation in two sibling species of the genus Praomys (Rodentia: Muridae): implications for biogeography, Zoological Journal of the Linnean Society, vol.160, issue.2, pp.397-419, 2010.
DOI : 10.1111/j.1096-3642.2009.00602.x

URL : https://hal.archives-ouvertes.fr/hal-00553224

D. Coulibaly-n-'golo, B. Allali, S. Kouassi, E. Fichet-calvet, and B. Becker-ziaja, Novel Arenavirus Sequences in Hylomyscus sp. and Mus (Nannomys) setulosus from C??te d'Ivoire: Implications for Evolution of Arenaviruses in Africa, PLoS ONE, vol.106, issue.6, p.20893, 2011.
DOI : 10.1371/journal.pone.0020893.s002

URL : https://hal.archives-ouvertes.fr/pasteur-00643284

A. Olayemi and A. Akinpelu, Diversity and distribution of murid rodent populations between forest and derived savanna sites within south western Nigeria, Biodiversity and Conservation, vol.73, issue.1, pp.10531-10539, 1007.
DOI : 10.1007/s10531-008-9389-1

O. 'brien, C. Mcshea, W. Guimondou, S. Barrière, P. Carleton et al., Petits mammifères terrestres (Soricidés et Muridés) du Complexe d'Aires Protégées de Gamba, Gabon: composition taxinomique et comparaison de méthodes d'e ´chantillonnage, Bull Biol Soc Wash, vol.12, pp.137-148, 2006.

A. Monadjem and J. Fahr, A rapid survey of bats from north Lorma, Gola and Grebo forests, Liberia, with notes on other small mammal groups (shrew and rodents). RAP, pp.20-25, 2005.

V. Sluydts, S. Davis, S. Mercelis, and H. Leirs, Comparison of multimammate mouse (Mastomys natalensis) demography in monoculture and mosaic agricultural habitat: Implications for pest management, Crop Protection, vol.28, issue.8, pp.647-654, 2009.
DOI : 10.1016/j.cropro.2009.03.018

N. Stenseth, H. Leirs, S. Mercelis, and P. Mwanjabe, Comparing strategies for controlling an African pest rodent: an empirically based theoretical study, Journal of Applied Ecology, vol.40, issue.Supplement, pp.1020-1031, 2001.
DOI : 10.1046/j.1365-2664.2001.00656.x

R. Makundi, A. Massawe, L. Mulungu, A. Katakweba, and T. Mbise, Potential mammalian reservoirs in a bubonic plague outbreak focus in Mbulu District, northern Tanzania, Mammalia, vol.72, pp.253-257, 2007.

J. Holt, S. Davis, and H. Leirs, A model of Leptospirosis infection in an African rodent to determine risk to humans: Seasonal fluctuations and the impact of rodent control, Acta Tropica, vol.99, issue.2-3, pp.218-225, 2006.
DOI : 10.1016/j.actatropica.2006.08.003

E. Lecompte, E. Fichet-calvet, S. Daffis, K. Koulemou, and O. Sylla, s and Lassa Fever, West Africa, Emerging Infectious Diseases, vol.12, issue.12, pp.1971-1974, 2006.
DOI : 10.3201/eid1212.060812

O. Ogbu, E. Ajuluchukwu, and C. Uneke, Lassa fever in West African subregion: an overview, J Vector Borne Dis, vol.44, pp.1-11, 2007.

L. Durnez, M. Eddyani, G. Mgode, A. Katakweba, and C. Katholi, First Detection of Mycobacteria in African Rodents and Insectivores, Using Stratified Pool Screening, Applied and Environmental Microbiology, vol.74, issue.3, pp.768-773, 2008.
DOI : 10.1128/AEM.01193-07

L. Durnez, P. Suykerbuyk, V. Nicolas, P. Barrière, and E. Verheyen, Terrestrial Small Mammals as Reservoirs of Mycobacterium ulcerans in Benin, Applied and Environmental Microbiology, vol.76, issue.13, pp.4574-4577, 2010.
DOI : 10.1128/AEM.00199-10

P. Barrière, V. Nicolas, K. Oduro, and L. , Rapid Survey of the Small Mammals of Ajenjua Bepo and Mamang River Forest Reserves, Ghana, Rapid Biological Assessment of the Ajenjua Bepo and Mamang River Forest Reserves: Conservation International, pp.54-57, 2008.

J. Duplantier, Les rongeurs myomorphes forestiers du nord-est du Gabon: structure du peuplement, démographie, domaines vitaux, Rev Ecol Terre Vie, vol.44, pp.329-346, 1989.

V. Nicolas and M. Colyn, Seasonal variations in population and community structure of small rodents in a tropical forest of Gabon, Canadian Journal of Zoology, vol.81, issue.6, pp.1034-1046, 2003.
DOI : 10.1139/z03-092

URL : https://hal.archives-ouvertes.fr/hal-01346038

T. Caro, Species richness and abundance of small mammals inside and outside an African national park, Biological Conservation, vol.98, issue.3, pp.251-257, 2001.
DOI : 10.1016/S0006-3207(00)00105-1

E. Fichet-calvet, S. Koulémou, L. Koivogui, B. Soropogui, and O. Sylla, Spatial distribution of commensal rodents in regions with high and low Lassa fever prevalence in Guinea, Belg J Zool, vol.135, pp.63-67, 2005.

E. Fichet-calvet, E. Lecompte, F. Veyrunes, P. Barrière, and V. Nicolas, Diversity and dynamics in a community of small mammals in coastal guinea, West Africa, Belg J Zool, vol.139, pp.93-102, 2009.

P. Hebert, A. Cywinska, and S. Ball, Biological identifications through DNA barcodes, Proceedings of the Royal Society B: Biological Sciences, vol.270, issue.1512, pp.313-321, 2003.
DOI : 10.1098/rspb.2002.2218

P. Hebert, E. Penton, J. Burns, D. Janzen, and W. Hallwachs, Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator, Proceedings of the National Academy of Sciences, vol.101, issue.41, pp.14812-14817, 2004.
DOI : 10.1073/pnas.0406166101

P. Hebert, M. Stoeckle, T. Zemlak, and C. Francis, Identification of Birds through DNA Barcodes, PLoS Biology, vol.104, issue.10, p.312, 2004.
DOI : 10.1371/journal.pbio.0020312.sg001

D. Barrett and P. Hebert, Identifying spiders through DNA barcodes, Canadian Journal of Zoology, vol.83, issue.3, pp.481-491, 2005.
DOI : 10.1139/z05-024

A. Cywinska, F. Hunter, and P. Hebert, Identifying Canadian mosquito species through DNA barcodes, Medical and Veterinary Entomology, vol.6, issue.4, pp.413-424, 2006.
DOI : 10.1016/S0035-9203(03)00019-1

R. Ward, T. Zemlak, B. Innes, P. Last, and P. Hebert, DNA barcoding Australia's fish species, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.11, issue.6897, pp.1847-1857, 2005.
DOI : 10.1093/molbev/msg133

E. Clare, B. Lim, M. Engstrom, J. Eger, and P. Hebert, DNA barcoding of Neotropical bats: species identification and discovery within Guyana, Molecular Ecology Notes, vol.16, issue.2, pp.184-190, 2006.
DOI : 10.1111/j.1471-8286.2006.01657.x

J. Robins, M. Hingston, E. Matisoo-smith, and H. Ross, Identifying Rattus species using mitochondrial DNA, Molecular Ecology Notes, vol.54, issue.5, pp.717-729, 2007.
DOI : 10.1007/BF00283833

M. Pages, Y. Chaval, V. Herbreteau, S. Waengsothorn, and J. Cosson, Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries, BMC Evolutionary Biology, vol.10, issue.1, p.184, 2010.
DOI : 10.1186/1471-2148-10-184

URL : https://hal.archives-ouvertes.fr/hal-00521287

C. Francis, A. Borisenko, N. Ivanova, J. Eger, and B. Lim, The Role of DNA Barcodes in Understanding and Conservation of Mammal Diversity in Southeast Asia, PLoS ONE, vol.24, issue.9, p.12575, 2010.
DOI : 10.1371/journal.pone.0012575.g010

E. Clare, B. Lim, M. Fenton, and P. Hebert, Neotropical Bats: Estimating Species Diversity with DNA Barcodes, PLoS ONE, vol.85, issue.7, p.22648, 2011.
DOI : 10.1371/journal.pone.0022648.s003

URL : http://doi.org/10.1371/journal.pone.0022648

L. Frezal and R. Leblois, Four years of DNA barcoding: Current advances and prospects, Infection, Genetics and Evolution, vol.8, issue.5, pp.727-736, 2008.
DOI : 10.1016/j.meegid.2008.05.005

URL : https://hal.archives-ouvertes.fr/mnhn-00392451

R. Bradley and A. Baker, SEQUENCES AND MAMMALS, Journal of Mammalogy, vol.82, issue.4, pp.960-973, 2001.
DOI : 10.1644/1545-1542(2001)082<0960:ATOTGS>2.0.CO;2

S. Tobe, A. Kitchener, and A. Linacre, Reconstructing Mammalian Phylogenies: A Detailed Comparison of the Cytochrome b and Cytochrome Oxidase Subunit I Mitochondrial Genes, PLoS ONE, vol.5, issue.11, p.14156, 2010.
DOI : 10.1371/journal.pone.0014156.s020

C. Fadda, M. Corti, and E. Verheyen, Molecular phylogeny of Myomys/Stenocephalemys complex and its relationships with related African genera, Biochemical Systematics and Ecology, vol.29, issue.6, pp.585-596, 2001.
DOI : 10.1016/S0305-1978(00)00087-9

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

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

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

C. Brouat, C. 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

K. Dasmahapatra and J. Mallet, Taxonomy: DNA barcodes: recent successes and future prospects, Heredity, vol.95, issue.4, pp.254-255, 2006.
DOI : 10.1038/sj.hdy.6800858

F. Austerlitz, O. David, B. Schaeffer, K. Bleakley, and M. Olteanu, DNA barcode analysis: a comparison of phylogenetic and statistical classification methods, BMC Bioinformatics, vol.10, issue.Suppl 14, p.10, 2009.
DOI : 10.1186/1471-2105-10-S14-S10

URL : https://hal.archives-ouvertes.fr/inserm-00663565

P. Goldstein and R. Desalle, Integrating DNA barcode data and taxonomic practice: Determination, discovery, and description, BioEssays, vol.3, issue.2
DOI : 10.1002/bies.201000036

O. Meara and B. , New Heuristic Methods for Joint Species Delimitation and Species Tree Inference, Systematic Biology, vol.59, issue.1, pp.59-73, 2010.
DOI : 10.1093/sysbio/syp077

N. Puillandre, A. Lambert, S. Brouillet, and G. Achaz, ABGD, Automatic Barcode Gap Discovery for primary species delimitation, Molecular Ecology, vol.75, issue.8, 2011.
DOI : 10.1111/j.1365-294X.2011.05239.x

URL : https://hal.archives-ouvertes.fr/hal-00704914

C. Meyer and G. Paulay, DNA Barcoding: Error Rates Based on Comprehensive Sampling, PLoS Biology, vol.85, issue.12, p.422, 2005.
DOI : 10.1371/journal.pbio.0030422.st003

J. Padial and I. De-la-riva, A response to recent proposals for integrative taxonomy, Biological Journal of the Linnean Society, vol.101, issue.3, pp.747-756, 2011.
DOI : 10.1111/j.1095-8312.2010.01528.x

G. Musser and M. Carleton, Superfamily Muroidea Mammal species of the world: a taxonomic and geographic reference, pp.894-1531, 2005.

J. Kennis, V. Nicolas, J. Hulselmans, P. Katuala, and W. Wendelen, The impact of the Congo River and its tributaries on the rodent genus Praomys: speciation origin or range expansion limit?, Zoological Journal of the Linnean Society, vol.163, issue.3
DOI : 10.1111/j.1096-3642.2011.00733.x

B. Winnepenninckx, T. Backeljau, D. Wachter, and R. , Extraction of high molecular weight DNA from molluscs, Trends Genet, vol.9, p.407, 1993.

J. Ducroz, V. Volobouev, and L. Granjon, An assessment of the 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

S. Palumbi, A. Martin, S. Romano, W. Mcmillan, and L. Stice, The Simple Fool's Guide to PCR, 1991.

S. Quérouil, R. Hutterer, P. Barrière, M. Colyn, and J. Peterhans, Phylogeny and Evolution of African Shrews (Mammalia: Soricidae) Inferred from 16s rRNA Sequences, Molecular Phylogenetics and Evolution, vol.20, issue.2, pp.185-195, 2001.
DOI : 10.1006/mpev.2001.0974

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980.
DOI : 10.1007/BF01731581

D. Swofford, PAUP: phylogenetic analysis using parsimony. Version 4b10 ed, 2000.

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, pp.406-425, 1987.

L. Knowles and B. Carstens, Delimiting Species without Monophyletic Gene Trees, Systematic Biology, vol.56, issue.6, pp.887-895, 2007.
DOI : 10.1080/10635150701701091

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

B. Clarke, E. Fokoué, and H. Zhang, Principles and Theory for Data Mining and Machine Learning, 2009.
DOI : 10.1007/978-0-387-98135-2

E. Fix and J. Hodges, Discriminatory Analysis. Nonparametric Discrimination: Consistency Properties, International Statistical Review / Revue Internationale de Statistique, vol.57, issue.3, 1951.
DOI : 10.2307/1403797

T. Cover and P. Hart, Nearest neighbor pattern classification, IEEE Transactions on Information Theory, vol.13, issue.1, pp.21-27, 1967.
DOI : 10.1109/TIT.1967.1053964

L. Breiman, Random forests, Machine Learning, vol.45, issue.1, pp.5-32, 2001.
DOI : 10.1023/A:1010933404324

L. Breiman, J. Freidman, R. Olshen, and C. Stone, Classification and regression trees, 1984.

K. De-queiroz, The general lineage concept of species, species criteria and the process of speciation. A conceptual unification and terminological recommendations Endless forms: species and speciation, pp.57-75, 1998.

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

C. Group, A DNA barcode for land plants, Proceedings of the National Academy of Sciences, vol.106, issue.31, pp.12794-12797, 2009.
DOI : 10.1073/pnas.0905845106

M. Hollingsworth, A. Clarck, L. Forrest, J. Richardson, and R. Pennington, Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants, Molecular Ecology Resources, vol.274, issue.2, pp.439-457, 2009.
DOI : 10.1111/j.1755-0998.2008.02439.x

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, pp.29-46, 2009.
DOI : 10.1111/j.1095-8312.2009.01273.x

V. Nicolas, J. Mboumba, E. Verheyen, C. Denys, and E. Lecompte, Phylogeographical structure and regional history of Lemniscomys striatus (Rodentia: Muridae) in tropical Africa, J Biogeogr, vol.35, pp.2072-2089, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00336791

M. Matocq, Q. Shurtliff, and C. Feldman, Phylogenetics of the woodrat genus Neotoma (Rodentia: Muridae): Implications for the evolution of phenotypic variation in male external genitalia, Molecular Phylogenetics and Evolution, vol.42, issue.3, pp.637-652, 2007.
DOI : 10.1016/j.ympev.2006.08.011

P. Colangelo, L. Granjon, P. Taylor, and M. Corti, Evolutionary systematics in African gerbilline rodents of the genus Gerbilliscus: Inference from mitochondrial genes, Molecular Phylogenetics and Evolution, vol.42, issue.3, pp.797-806, 2007.
DOI : 10.1016/j.ympev.2006.10.001

S. Derycke, J. Vanaverbeke, A. Rigaux, T. Backeljau, and T. Moens, Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes, PLoS ONE, vol.38, issue.10, p.13716, 2010.
DOI : 10.1371/journal.pone.0013716.s001

C. Moritz and C. Cicero, DNA Barcoding: Promise and Pitfalls, PLoS Biology, vol.103, issue.10, p.354, 2004.
DOI : 10.1371/journal.pbio.0020354

URL : http://doi.org/10.1371/journal.pbio.0020354

C. Pwg, A DNA barcode for land plants, Proc Natl Acad Sci U S A, vol.106, pp.12794-12797, 2009.

N. Nesi, E. Nakouné, C. Cruaud, and A. Hassanin, DNA barcoding of African fruit bats (Mammalia, Pteropodidae). The mitochondrial genome does not provide a reliable discrimination between Epomophorus??gambianus and Micropteropus??pusillus, Comptes Rendus Biologies, vol.334, issue.7, pp.544-554, 2011.
DOI : 10.1016/j.crvi.2011.05.003