Molecular systematics of the freshwater stingrays (myliobatiformes: potamotrygonidae) of the Amazon, Orinoco, Magdalena, Esequibo, Caribbean, and Maracaibo basins (Colombia – Venezuela): evidence from three mitochondrial genes

References

• Araújo ML, Charvet-Almeida P, Almeida MP, Pererira H. (2004). Freshwater Stingrays (Potamotrygonidae): Status, conservation and management challenges. Twentieth Meeting of the Animals Committee
   Google Scholar
• Baker CS. (2008). A truer measure of the market: The molecular ecology of fisheries and wildlife trade. Mol Ecol 17:3985–98
   PubMed Web of Science ®Google Scholar
• Bernardi G, Sordino P, Powers DA. (1993). Concordant mitochondrial and nuclear DNA phylogenies for populations of the teleost fish Fundulus heteroclitus. Proc Natl Acad Sci USA 90:9271–4
   PubMed Web of Science ®Google Scholar
• Bos DH, Posada D. (2005). Using models of nucleotide evolution to build phylogenetic trees. Dev Comp Immunol 29:211
   PubMed Web of Science ®Google Scholar
• Buhay JE. (2009). “COI-Like” sequences are becoming problematic in molecular systematic and DNA barcoding studies. J Crustacean Biol 29:96–110
   Web of Science ®Google Scholar
• Burleigh JG, Matthews L. (2004). Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life. Am J Bot 91:1599–613
   PubMed Web of Science ®Google Scholar
• Caballero S, Jackson J, Mignucci-Giannoni AA, Barrios-Garrido H, Beltrán Pedreros S, Montiel-Villalobos MG, Robertson KM, Baker CS. (2008). Molecular systematics of South American dolphins Sotalia: Sister taxa determination and phylogenetic relationships, with insights into a multilocus phylogeny of the Delphinidae. Mol Phylogenet E 46:252–68
   PubMed Web of Science ®Google Scholar
• Caballero S, Cardeñosa D, Soler G, Hyde J. (2012). Application of multiplex PCR approaches for shark molecular identification: Feasibility and applications for fisheries management and conservation in the Eastern Tropical Pacific. Mol Ecol Resour 12:233–7
   PubMed Web of Science ®Google Scholar
• Caldas JP, Castro-González E, Puentes V, Rueda M, Lasso C, Duarte LO, Grijalba-Bendeck M, et al. (2010). Plan de Acción Nacional para la Conservación y Manejo de Tiburones, Rayas y Quimeras de Colombia (PAN-Tiburones Colombia). Bogotá, Colombia: Editorial Produmedios
   Google Scholar
• Carvalho MR. (2001). Freshwater Stingrays from South America. Copeia 4:1167–9
   Google Scholar
• Charvet-Almeida P, Araújo ML, Rosa RS, Rincon G. (2002). Neotropical freshwater stingrays: Diversity and conservation status. IUCN Shark News 14:1–2
   Google Scholar
• Charvet-Almeida P, Goes M, Pinto M. (2005). Reproductive aspects of freshwater stingrays (Chondrichthyes: Potamotrygonidae) in the Brazilian Amazon Basin. J Northwest Atl Fish Sci 35:165–71
   Google Scholar
• Charvet-Almeida P, Pinto de Almeida M. (2009). Potamotrygon magdalenae. Available at: IUCN Red List of Threatened Species. Version 2012.2. <www.iucnredlist.org> (Accessed 4 November 2012)
   Google Scholar
• Crandall KA, Olaf RP, Bininda-Emond MM, Wayne RK. (2000). Considering evolutionary processes in conservation biology. Trends Ecol Evol (Amst.) 15:290–5
   PubMed Web of Science ®Google Scholar
• Carvalho D, Lovejoy NR. (2011). Morphology and phylogenetic relationships of a remarkable new genus and two new species of Neotropical freshwater stingrays from the Amazon basin (Chondrichthyes: Potamotrygonidae). Zootaxa 2776:13–48
   Google Scholar
• De Carvalho M, Perez MHS, Lovejoy NR. (2011). Potamotrygon tigrina, a new species of freshwater stingray from the upper Amazon basin, closely related to Potamotrygon schroederi Fernandez-Yepez, 1958 (Chondrichthyes: Potamotrygonidae). Zootaxa 2827:1–30
   Google Scholar
• De Carvalho M, Ragno MP. (2011). A unusual, dwarf new species of Neotropical freshwater stingray Plesiotrygon nana sp. nov., from the upper and mid Amazon Basin: The second species of Plesiotrygon (Chondrichthyes: Potamotrygonidae). Pap Avulsos De Zool 51:101–38
   Google Scholar
• Degnan J, Rosenberg N. (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol (Amst.) 24:332–40
   PubMed Web of Science ®Google Scholar
• Duchêne S, Archer FI, Vilstrup J, Caballero S, Morin A. (2011). Mitogenome phylogenetics: The impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS One 6:e27138
   PubMed Web of Science ®Google Scholar
• Dunn KA, McEachran JD, Honeycutt RL. (2003). Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood. Mol Phylogenet Evol 27:259–70
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Rambaut A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
   PubMed Web of Science ®Google Scholar
• Edwards SV. (2009). Is a new and general theory of molecular systematics emerging? Evolution 63:1–19
   PubMed Web of Science ®Google Scholar
• Falla P, Poveda J. (2008). Contribución a la gestión sostenible y al conocimiento biológico y socio económico de la cadena de valor de peces ornamentales de Puerto Carreño, Reserva de Biósfera El Tuparro (Vichada-Colombia). Bogotá, Colombia: Fundación Omacha-Fundación Horizonte Verde
   Google Scholar
• Fontenelle JP, Da Silva JPC, Carvalho DMR. (2014). Potamotrygon limai, sp. nov., a new species of freshwater stingray from the upper Madeira River system, Amazon basin (Chondrichthyes: Potamotrygonidae). Zootaxa 3765:249–68
   PubMed Web of Science ®Google Scholar
• Galvis G, Mojica JI, Provenzano F, Lasso C, Royero R, Castellanos C, Gutierrez CA, et al. (2007). Peces de la Orinoquia colombiana con enfasis en especies de interes ornamental. Bogota, Colombia: Instituto Colombiano de Desarrollo Rural-Incoder y Universidad Nacional de Colombia
   Google Scholar
• Garcia G, Wlasiuk G, Lessa E. (2000). High levels of mitochondrial Cytochrome b divergence in annual killifishes of the genus Cynolebias (Cyprininodontformes, Rivulidae). Zool J Linn Soc 129:93–110
   Web of Science ®Google Scholar
• Hebert PD, Ratnasingham S, de Waard JR. (2003a). Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci 270:S96–9
   PubMed Web of Science ®Google Scholar
• Hebert PD, Cywinska A, Ball SL, de Waard JR. (2003b). Biological identifications through DNA barcodes. Proc Biol Sci 270:313–21
   PubMed Web of Science ®Google Scholar
• Hubert N, Renno JF. (2006). Historical Biogeography of South American freshwater fishes. Journal of Biogeography 33:1414–36
   Web of Science ®Google Scholar
• Huelsenbeck JP, Ronquist F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–5
   PubMed Web of Science ®Google Scholar
• Ishijara H, Taniuchi T. (1995). A strange Potamotrygonid ray (Chondrichthyes: Potamotrygonidae) from the Orinoco river system. J Aquaric Aquat Sci 7:91–7
   Google Scholar
• Kearse M, Moir R, Wilson A., Stones-Havas S, Cheung M, Sturrock S, Buxton S, et al. (2012). Geneious Basic: an integrated and Extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–9
   PubMed Web of Science ®Google Scholar
• Kocher TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villablanca FX, Wilson AC. (1989). Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc Natl Acad Sci USA 86:6196–200
   PubMed Web of Science ®Google Scholar
• Lasso CA, Rosa RS, Sánchez-Duarte P, Morales-Betancourt MA, Agudelo-Córdoba E. (2013). IX. Rayas de agua dulce (Potamotrygonidae) de Suramérica. Parte I. Colombia, Venezuela, Ecuador, Perú, Brasil, Guyana, Surinam y Guayana Francesa: Diversidad, bioecología, uso y conservación. Bogotá, Colombia: Serie Editorial Recursos Hidrobiológicos y Pesqueros Continentales de Colombia. Instituto De Investigación De Los Recursos Biológicos Alexander Von Humboldt (IAvH)
   Google Scholar
• Loboda TS, Carvalho MR. (2013). Systematic revision of the Potamotrygon motoro (Müller & Henle, 1841) species complex in the Paraná-Paraguay basin, with description of two new ocellated species (Chondrichthyes: Myliobatiformes: Potamotrygonidae). Neotrop Ichthyol 11:693–737
   Web of Science ®Google Scholar
• Longhorn SJ, Pohl HW, Vogler AP. (2010). Ribosomal protein genes of holometabolan insects reject the Halteria, instead revealing a close affinity of Strepsiptera with Coleoptera. Mol Phylogenet Evol 55:846–59
   PubMed Web of Science ®Google Scholar
• Lovejoy N. (1996). Systematics of myliobatoid elasmobranchs: With emphasis on the phylogeny and historical biogeography of neotropical freshwater stingrays (Potamotrygonidae: Rajiformes). Zool J Linn Soc 117:207–57
   Web of Science ®Google Scholar
• Lovejoy NR, Bermingham E, Martin AP. (1998). Marine incursion into South America. Nature 396:421–2
   Web of Science ®Google Scholar
• Lundberg J, Linares OJ, Antonio ME, Nass P. (1988). Phractocephalus hemiliopterus (Pimelodidae: Siluriformes) from the upper Miocene Urumaco formation, Venezuela: A further case of evolutionary stasis and local extinction among South American fishes. J Vertebr Paleontol 8:131–8
   Google Scholar
• Lundberg JG, Marshall LG, Guerrero J. (1998). The stage for Neotropical fish diversification: A history of tropical South American rivers. In: Malabarba LR, Vari RP, Lucena ZMS, Lucena CAS, editors. Phylogeny and classification of neotropical fishes. Porto Alegre, Brazil: Edipucrs
   Google Scholar
• Machado-Allison A. (2008). On the origin of the Orinoco, its relationship with neighbor basins, the biological paleontological evidences, and the conservation of aquatic habitat: A revision based on ichthyological data. Bol Acad C Fís, Mat Y Nat 68:1–2
   Google Scholar
• Mancera-Rodríguez NJ, Álvarez-León R. (2008). Comercio de peces ornamentales en Colombia. Acta Biol Colomb 13:23–52
   Google Scholar
• Marques F. (2000). Evolution of Neotropical freshwater stingrays and their parasites: Taking into account space and time. Toronto: Department of Zoology. University of Toronto
   Google Scholar
• Marshall HD, Baker AJ. (1998). Rates and patterns of mitochondrial DNA sequence evolution in fringilline finches (Fringilla spp.) and the greenfinch (Carduelis chloris). Mol Biol Evol 15:638–46
   PubMed Web of Science ®Google Scholar
• Martin AP, Naylor GJP, Palumbi SR. (1992). Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357:153–5
   PubMed Web of Science ®Google Scholar
• Mejía-Falla PA, Ramírez-Luna V, Usma JS, Muñoz-Osorio LA, Maldonado JA, Sanabria AI, Alonso JC. (2009). Estado del conocimiento de las rayas dulceacuícolas de Colombia. In: Puentes V, Navia AF, Mejía-Falla PA, Caldas JP, Diazgranados MC, Zapata LA, editors. Avances en el conocimiento de tiburones, rayas y quimeras de Colombia. Bogotá, Colombia: Fundación SQUALUS, Ministerio de Ambiente Vivienda y Desarrollo Territorial, Instituto Colombiano Agropecuario, COLCIENCIAS Conservación Internacional, WWF
   Google Scholar
• Miller MA, Pfeiffer W, Schwartz T. (2010). Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE) New Orleans, LA, p 1–8
   Google Scholar
• Mojica JI, Usma JS, Álvarez-León R, Lasso CA. (2012). Libro rojo de peces dulceacuícolas de Colombia 2012. Bogotá, Colombia: Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Instituto de Ciencias Naturales de la Universidad Nacional de Colombia, WWF Colombia y Universidad de Manizales
   Google Scholar
• Posada D, Crandall KA. (1998). MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817–18
   PubMed Web of Science ®Google Scholar
• Posada D, Crandall KA. (2001). Intraspecific gene genealogies: Trees grafting into networks. Trends Ecol Evol (Amst.) 16:37–45
   PubMed Web of Science ®Google Scholar
• Rosa RS. (1985). A systematic revision of the South American freshwater stingrays (Chondrichthyes: Potamotrygonidae). Williamsburg: College of William and Mary
   Google Scholar
• Rosa R, Charvet-Almeida P, Diban C. (2010). Biology of the South American Potamotrygonid stingrays. In: Jeffrey C, Carrier J, Musick A, Heithaus MR, editors. Sharks and their relatives II. London, England: CRC Press
   Google Scholar
• Shimodaira H, Hasegawa M. (1999). Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol Biol E 16:1114–16
   Web of Science ®Google Scholar
• Song HM, Mu XD, Wei MX, Wang XJ, Luo JR, Hu YC. (2014). Complete mitochondrial genome of the ocellate river stingray (Potamotrygon motoro). Mitochondr DNA Early Online 26:2015
   Web of Science ®Google Scholar
• Stamatakis A. (2006). RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–90
   PubMed Web of Science ®Google Scholar
• Swofford DL. (2003). PAUP: Phylogenetic analysis using parsimony, version 4.0 b10. Champaign IL: Illinois Natural History Survey
   Google Scholar
• Toffoli D, Hrbek T, de Araujo MLG, de Almeida MP, Charvet-Almeida P, Farias IP. (2008). A test of the utility of DNA barcoding in the radiation of the freshwater stingray genus Potamotrygon (Potamotrygonidae, Myliobatiformes). Genet Mol Biol 31:324–36
   Web of Science ®Google Scholar
• Walsh PS, Metzger DA, Higuchi R. (1991). Chelex® 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10:506–13
   PubMed Web of Science ®Google Scholar
• Ward RD, Holmes BH, White WT, Last PRPR. (2008). DNA barcoding Australasian chondrichthyans: Results and potential uses in conservation. Mar Freshwater Res 59:57–71
   Web of Science ®Google Scholar
• Ward RD, Hanner R, Hebert PDN. (2009). The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74:329–56
   PubMed Web of Science ®Google Scholar
• Winemiller KO, López-Fernández H, Taphorn DC, Nico LG, Duque AB. (2008). Fish assemblages of the Casiquiare River, a corridor and zoogeographical filter for dispersal between the Orinoco and Amazon basins. J Biogeogr 35:1551–63
   Web of Science ®Google Scholar
• Yan Z, Rannala B. (2012). Molecular phylogenetics: Principles and practice. Nat Rev Genet 13:303–14
   PubMed Web of Science ®Google Scholar
• Zhang AB, He LJ, Crozier RH, Muster C, Zhu C-D. (2010). Estimating sample sizes for DNA barcoding. Mol Phylogenet Evol 54:1035–9
   PubMed Web of Science ®Google Scholar
• Zhu D, Jamieson BGM, Hugall A, Moritz C. (1994). Sequence evolution and phylogenetic signal in control-region and Cytochrome b sequences of rainbow fishes (Melanotaeniidae). Mol Biol Evol 11:672–83
   PubMed Web of Science ®Google Scholar