W. T. White and P. R. Last, A review of the taxonomy of chondrichthyan fishes: a modern perspective, Journal of Fish Biology, vol.59, issue.5, pp.901-917, 2012.
DOI : 10.1111/j.1095-8649.2011.03192.x

S. Weigmann, Annotated checklist of the living sharks, batoids and chimaeras (Chondrichthyes) of the world, with a focus on biogeographical diversity, Journal of Fish Biology, vol.51, issue.3, pp.837-1037, 2016.
DOI : 10.1111/jfb.12874

S. J. Blaber, C. M. Dichmont, W. White, R. Buckworth, L. Sadiyah et al., Elasmobranchs in southern Indonesian fisheries: the fisheries, the status of the stocks and management options, Elasmobranchs in southern Indonesian fisheries: the fisheries, the status of the stocks and management options, pp.367-391, 2009.
DOI : 10.1007/s11160-009-9110-9

W. T. White and P. M. Kyne, The status of chondrichthyan conservation in the Indo-Australasian region, Journal of Fish Biology, vol.91, issue.9, pp.2090-2117, 2010.
DOI : 10.1111/j.1095-8649.2010.02654.x

N. K. Dulvy, S. L. Fowler, J. A. Musick, R. D. Cavanagh, P. M. Kyne et al., Author response, eLife, vol.325, issue.10, p.590, 2014.
DOI : 10.7554/eLife.00590.027

C. L. Dudgeon, D. C. Blower, D. Broderick, J. L. Giles, B. J. Holmes et al., A review of the application of molecular genetics for fisheries management and conservation of sharks and rays, Journal of Fish Biology, vol.97, issue.Suppl. 1, pp.1789-1843, 2012.
DOI : 10.1111/j.1095-8649.2012.03265.x

J. Müller and F. G. Henle, Systematische Beschreibung der Plagiostomen, mit sechzig Steindrucktafeln

W. T. White and . Dharmadi, Species and size compositions and reproductive biology of rays (Chondrichthyes, Batoidea) caught in target and non-target fisheries in eastern Indonesia, Journal of Fish Biology, vol.1970, issue.6, pp.1809-1837, 2007.
DOI : 10.2307/1445395

W. T. Fahmi, I. P. White, N. Jacobsen, and . Kuhlii, The IUCN red list of threatened species, pp.2015-2015

N. Knowlton, Molecular genetic analyses of species boundaries in the sea, Hydrobiologia, vol.420, pp.73-90, 2000.
DOI : 10.1007/978-94-017-2184-4_8

J. Mallet, Why was Darwin???s view of species rejected by twentieth century biologists?, Biology & Philosophy, vol.1, issue.345???347, pp.497-527, 2010.
DOI : 10.1007/s10539-010-9213-7

R. D. Ward, B. H. Holmes, W. T. White, and P. R. Last, DNA barcoding Australasian chondrichthyans: results and potential uses in conservation, Marine and Freshwater Research, vol.59, issue.1, pp.59-57, 2008.
DOI : 10.1071/MF07148

G. J. Naylor, J. N. Caira, K. Jensen, K. A. Rosana, W. T. White et al., A DNA Sequence???Based Approach To the Identification of Shark and Ray Species and Its Implications for Global Elasmobranch Diversity and Parasitology, Bulletin of the American Museum of Natural History, vol.367, pp.367-368, 2012.
DOI : 10.1206/754.1

P. Borsa, I. S. Arlyza, W. J. Chen, J. Durand, M. G. Meekan et al., Resurrection of New Caledonian maskray Neotrygon trigonoides (Myliobatoidei: Dasyatidae) from synonymy with N.??kuhlii, based on cytochrome-oxidase I gene sequences and spotting patterns, Comptes Rendus Biologies, vol.336, issue.4, pp.221-232, 2013.
DOI : 10.1016/j.crvi.2013.05.005

URL : https://hal.archives-ouvertes.fr/ird-00847459

M. Puckridge, P. R. Last, W. T. White, and N. , ): a complex example of chondrichthyan radiation in the Cenozoic, Ecology and Evolution, vol.92, issue.2, pp.217-232, 2013.
DOI : 10.1002/ece3.448

P. Borsa, I. S. Arlyza, M. Laporte, and P. Berrebi, Population genetic structure of blue-spotted maskray Neotrygon kuhlii and two other Indo-West Pacific stingray species (Myliobatiformes: Dasyatidae), inferred from size-polymorphic intron markers, Journal of Experimental Marine Biology and Ecology, vol.438, pp.32-40, 2012.
DOI : 10.1016/j.jembe.2012.09.010

URL : https://hal.archives-ouvertes.fr/ird-00747306

I. S. Arlyza, K. Shen, J. Durand, and P. Borsa, Mitochondrial Haplotypes Indicate Parapatric-like Phylogeographic Structure in Blue-Spotted Maskray (Neotrygon kuhlii) from the Coral Triangle Region, Journal of Heredity, vol.104, issue.5, pp.725-733, 2013.
DOI : 10.1093/jhered/est044

URL : https://hal.archives-ouvertes.fr/ird-00853606

F. De-castelnau, Contribution to the ichthyology of Australia, Proc. Zool. Acclim. Soc. Victoria, pp.37-158, 1873.

P. Borsa, Molecular genetics as a valid contribution to the taxonomy of species complexes in stingrays: comment on Weigmann's global checklist of chondrichthyan fishes, J. Fish Biol, vol.88, pp.837-1037, 2016.

P. Borsa, J. Durand, W. Chen, N. Hubert, D. Muths et al., Comparative phylogeography of the western Indian Ocean reef fauna, Acta Oecologica, vol.72, pp.72-86, 2016.
DOI : 10.1016/j.actao.2015.10.009

URL : https://hal.archives-ouvertes.fr/ird-01278855

P. R. Last, W. T. White, and B. Séret, Taxonomic status of maskrays of the Neotrygon kuhlii species complex (Myliobatoidei: Dasyatidae) with the description of three new species from the Indo- West Pacific, Zootaxa, pp.4083-2016

S. Garman, Notes and descriptions taken from selachians in the U. S. National Museum, Proc. U.S. Natl. Mus, pp.39-44, 1885.
DOI : 10.5479/si.00963801.482.39

M. E. Watanabe, The Nagoya Protocol on Access and Benefit Sharing: International treaty poses challenges for biological collections, BioScience, vol.65, issue.6, pp.543-550, 2015.
DOI : 10.1093/biosci/biv056

J. Saltford, The United Nations and the Indonesian takeover of West Papua, 1962.

G. Harvey, The price of protest in West Papua, Griffiths J. Law Hum. Dignity, vol.3, pp.170-203, 2015.

C. Budiardjo, Resource-rich West Papua, but who benefits? Jakarta Post, 2010.

Y. Baskin, GenBank ? Storehouse for life's secret code, Sci. Digest, vol.91, pp.94-95, 1983.

N. Yagishita, K. Furumitsu, and A. Yamaguchi, Molecular evidence for the taxonomic status of an undescribed species of Dasyatis (Chondrichthyes: Dasyatidae) from Japan, pp.14-157, 2009.

N. C. Aschliman, M. Nishida, M. Miya, J. G. Inoue, K. M. Rosana et al., Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea), Molecular Phylogenetics and Evolution, vol.63, issue.1, pp.63-91, 2012.
DOI : 10.1016/j.ympev.2011.12.012

F. Cerutti-pereyra, M. G. Meekan, N. W. Wei, O. O. Shea, C. J. Bradshaw et al., Identification of Rays through DNA Barcoding: An Application for Ecologists, PLoS ONE, vol.23, issue.6, p.36479, 2012.
DOI : 10.1371/journal.pone.0036479.s003

I. S. Arlyza, K. Shen, D. D. Solihin, D. Soedharma, P. Berrebi et al., Species boundaries in the Himantura uarnak species complex (Myliobatiformes: Dasyatidae), Species boundaries in the Himantura uarnak species complex (Myliobatiformes: Dasyatidae), pp.429-435, 2013.
DOI : 10.1016/j.ympev.2012.09.023

URL : https://hal.archives-ouvertes.fr/ird-00758049

X. Chen, D. Xiang, J. Q. Yu, W. Y. Ding, and S. L. Zhang, Complete mitochondrial genome of the bluespotted stingray Neotrygon kuhlii (Myliobatiformes: Dasyatidae), Mitochondr, DNA, vol.25, pp.429-430, 2014.

K. C. Lim, P. E. Lim, V. C. Chong, and K. H. Loh, Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes), PLoS One, vol.10, 2015.

K. Shen, C. Chang, S. Tsai, S. Wu, Z. Lin et al., Next generation sequencing yields the complete mitogenomes of leopard whipray (Himantura leoparda) and blue-spotted maskray (Neotrygon kuhlii) (Chondrichthyes: Dasyatidae), Mitochondr, DNA Pt A, vol.27, pp.2613-2614, 2015.

S. R. Palumbi, A. P. Martin, S. Romano, W. O. Mcmillan, L. Stice et al., The Simple Fool's Guide to PCR, Version 2.0, p.46, 1991.

T. Kitamura, A. Takemura, S. Watabe, T. Taniuchi, and M. Shimizu, Molecular phylogeny of the sharks and rays of Superorder Squalea based on mitochondrial cytochrome b gene, Fisheries Sci, pp.62-340, 1996.

M. Hassan, C. Lemaire, C. Fauvelot, and F. Bonhomme, Seventeen new exon-primed intron-crossing polymerase chain reaction amplifiable introns in fish, Molecular Ecology Notes, vol.11, issue.3, pp.334-340, 2002.
DOI : 10.1046/j.1365-294x.1998.00351.x

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

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-2729, 2013.
DOI : 10.1093/molbev/mst197

K. Tamura and M. Nei, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol. Biol. Evol, vol.10, pp.512-526, 1993.

N. Puillandre, A. Lambert, S. Brouillet, and G. Achaz, ABGD, Automatic Barcode Gap Discovery for primary species delimitation, Molecular Ecology, vol.75, issue.8, pp.1864-1877, 2012.
DOI : 10.1111/j.1365-294X.2011.05239.x

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

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

J. Pons, T. G. Barraclough, J. Gomez-zurita, A. Cardoso, D. P. Duran et al., Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects, Systematic Biology, vol.55, issue.4, pp.55-595, 2006.
DOI : 10.1080/10635150600852011

R. Development and C. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing

T. Fujisawa and T. G. Barraclough, Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets, Systematic Biology, vol.62, issue.5, pp.62-707, 2013.
DOI : 10.1093/sysbio/syt033

A. J. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, 2007.
DOI : 10.1186/1471-2148-7-214

T. H. Jukes and C. R. Cantor, Evolution of Protein Molecules, Mammalian protein metabolism, pp.21-132, 1969.
DOI : 10.1016/B978-1-4832-3211-9.50009-7

I. Gordon, Pre-copulatory behaviour of captive sandtiger sharks,Carcharias taurus, Environmental Biology of Fishes, vol.17, issue.1-3, pp.159-164, 1993.
DOI : 10.1007/BF00842912

S. J. Pierce, S. A. Pardo, and M. B. Bennett, Reproduction of the blue-spotted maskray Neotrygon kuhlii (Myliobatoidei: Dasyatidae) in south-east Queensland, Australia, J. Fish Biol, pp.74-1291, 2009.

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

C. M. Bull, Ecology of Parapatric Distributions, Annual Review of Ecology and Systematics, vol.22, issue.1, pp.19-36, 1991.
DOI : 10.1146/annurev.es.22.110191.000315

I. S. References, K. Arlyza, J. Shen, P. Durand, and . Borsa, Mitochondrial haplotypes indicate parapatric-like phylogeographic structure in blue-spotted maskray (Neotrygon kuhlii) from the Coral Triangle region, J. Hered, vol.104, pp.725-733, 2013.

I. S. Arlyza, K. Shen, D. D. Solihin, D. Soedharma, P. Berrebi et al., Species boundaries in the Himantura uarnak species complex (Myliobatiformes: Dasyatidae), Species boundaries in the Himantura uarnak species complex (Myliobatiformes: Dasyatidae), pp.429-435, 2013.
DOI : 10.1016/j.ympev.2012.09.023

URL : https://hal.archives-ouvertes.fr/ird-00758049

N. C. Aschliman, M. Nishida, M. Miya, J. G. Inoue, K. M. Rosana et al., Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea), Molecular Phylogenetics and Evolution, vol.63, issue.1, pp.63-91, 2012.
DOI : 10.1016/j.ympev.2011.12.012

P. Borsa, I. S. Arlyza, W. J. Chen, J. Durand, M. G. Meekan et al., Resurrection of New Caledonian maskray Neotrygon trigonoides (Myliobatoidei: Dasyatidae) from synonymy with N.??kuhlii, based on cytochrome-oxidase I gene sequences and spotting patterns, Comptes Rendus Biologies, vol.336, issue.4, pp.221-232, 2013.
DOI : 10.1016/j.crvi.2013.05.005

URL : https://hal.archives-ouvertes.fr/ird-00847459

F. De-castelnau, Contribution to the ichthyology of Australia, Proc. Zool. Acclim. Soc. Victoria, pp.37-158, 1873.

F. Cerutti-pereyra, M. G. Meekan, N. W. Wei, O. O. Shea, C. J. Bradshaw et al., Identification of Rays through DNA Barcoding: An Application for Ecologists, PLoS ONE, vol.23, issue.6, p.36479, 2012.
DOI : 10.1371/journal.pone.0036479.s003

X. Chen, D. Xiang, J. Q. Yu, W. Y. Ding, and S. L. Zhang, Complete mitochondrial genome of the blue-spotted stingray Neotrygon kuhlii (Myliobatiformes: Dasyatidae), Mitochondr, DNA, vol.25, pp.429-430, 2014.

S. Garman, Notes and descriptions taken from selachians in the U. S. National Museum, Proc. U.S. Natl. Mus, pp.39-44, 1885.
DOI : 10.5479/si.00963801.482.39

P. R. Last, W. T. White, and B. Séret, Taxonomic status of maskrays of the Neotrygon kuhlii species complex (Myliobatoidei: Dasyatidae) with the description of three new species from the Indo-West Pacific, Zootaxa, pp.4083-2016

K. C. Lim, P. E. Lim, V. C. Chong, and K. H. Loh, Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes), PLoS One, vol.10, 2015.

M. Puckridge, P. R. Last, W. T. White, and N. , ): a complex example of chondrichthyan radiation in the Cenozoic, Ecology and Evolution, vol.92, issue.2, pp.217-232, 2013.
DOI : 10.1002/ece3.448

K. Shen, C. Chang, S. Tsai, S. Wu, Z. Lin et al., Next generation sequencing yields the complete mitogenomes of leopard whipray (Himantura leoparda) and blue-spotted maskray (Neotrygon kuhlii) (Chondrichthyes: Dasyatidae), Mitochondr, DNA, pp.10-3109, 2015.

M. Su, H. Chen, and D. Hwang, Mitochondrial cytochrome b gene sequences of five common stingrays in Taiwan, J. Fish. Soc. Taiwan, vol.38, pp.41-54, 2011.

K. Tamura, Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + Ccontent biases, Mol. Biol. Evol, vol.9, pp.678-687, 1992.

K. Tamura and M. Nei, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol. Biol. Evol, vol.10, pp.512-526, 1993.

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-2729, 2013.
DOI : 10.1093/molbev/mst197

R. D. Ward, B. H. Holmes, W. T. White, and P. R. Last, DNA barcoding Australasian chondrichthyans: results and potential uses in conservation, Marine and Freshwater Research, vol.59, issue.1, pp.59-57, 2008.
DOI : 10.1071/MF07148

N. Yagishita, K. Furumitsu, and A. Yamaguchi, Molecular evidence for the taxonomic status of an undescribed species of Dasyatis (Chondrichthyes: Dasyatidae) from Japan, pp.14-157, 2009.

W. T. White and P. R. Last, A review of the taxonomy of chondrichthyan fishes: a modern perspective, Journal of Fish Biology, vol.59, issue.5, pp.901-917, 2012.
DOI : 10.1111/j.1095-8649.2011.03192.x

J. Bali1 and K. , PEL3-44 KNS-PEL4-45 KNS-PEL1-43 KNS-PEL2-65 KNS-PEL5-46 KNS-PEL6-78 KNS-PEL9-16