The online version of this article (doi: 10.1007/s12686-016-0610-3 ) contains supplementary material, which is available to authorized users.  José Gregorio Martínez grema48@hotmail.com 1 Laboratório de Evolução e Genética Animal, Instituto de Ciências Biológicas, Departamento de Genética, Programa de Pós-graduação em Biodiversidade e Biotecnologia da Amazônia Legal/Bionorte, Universidade Federal do Amazonas, Av. Rodrigo Octávio Jordão Ramos, 3000, 69077-000 Manaus, Amazonas, Brazil 2 Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Cra 1 Nº 18A- 12, Código Postal 4-72, Bogotá, Colombia 3 Laboratório de Proteômica e Genômica, Programa de Pós- graduação Mestrado em Biotecnologia e Recursos Naturais (MBT), Grupo de Pesquisa em Genética Molecular e Citogenética, Universidade do Estado do Amazonas, Manaus, Amazonas 69065-001, Brazil 4 Programa de Pós-graduação em Recursos Pesqueiros, Universidade Federal do Amazonas, Manaus, Amazonas 69065-001, Brazil Received: 23 August 2016 / Accepted: 30 August 2016 © Springer Science +Business Media Dordrecht 2016 SNPs markers for the heavily overfshed tambaqui , a Neotropical fsh, using next-generation sequencing-based de novo genotyping José Gregorio Martínez · Valéria Nogueira Machado · Susana J. Caballero-Gaitán Maria da C. Freitas Santos · Rodrigo Maciel Alencar · Maria Doris Escobar L. Tomas Hrbek · Izeni Pires Farias Conservation Genet Resour DOI 10.1007/s12686-016-0610-3 could be useful for conservation/population genetics using traditional PCR-based genotyping methods. Keywords De novo SNPs development · Conservation/population genomics · IonTorrent PGM · Orinoco/Amazon basins The tambaqui/cachama negra, , is the largest characin in South-America and the second largest Neotropical fsh, reaching at least one meter in total length and 30 kg in weight (Goulding and Carvalho 1982). This species is widely distributed throughout the western and - tral Amazon and Orinoco Basins (Isaac and Ruffno 1996; Araujo-Lima and Goulding 1997). The tambaqui is commer - cially overexploited, being one of the ten most captured spe - cies in the Amazon (Ruffno and Isaac 1994). In the last third of the twentieth century, the average length of adult individu - als decreased from 60 to 45 cm, and its contribution measured in tons of fsh commercially, especially in the central Ama- zon, fell from 40 % at the end of the 70 s to 2.8 % in the past decade (Ruffno et al. 2005; Sánchez-Botero et al. 2006). The International Union for the Conservation of Nature (IUCN) has not assessed the tambaqui, however, the Red List of Freshwater Fishes of Colombia (also valid for Ven - ezuela) (Mojica 2012), and the last evaluation of fshes of Brazil lists it as near threatened (NT) ( http://www.icmbio. gov.br/portal/faunabrasileira/lista-de-especies-dados-insu - fcientes) (ICMBio 2014), due to overfshing and lowland rainforest destruction in the Amazon and Orinoco basins. There are only a few population genetic studies of tambaqui (Santos et al. 2007, 2009; Hamoy et al. 2010; Farias et al. 2010), and no study of the Orinoco basin populations. SNPs or others genomics markers have not been reported for this species either. Abstract We developed nuclear SNPs for the heavily over - fshed tambaqui/cachama negra using next-generation sequencing-based genotyping. We cre - ated a reduced-representation library for 30 individuals from Orinoco and Amazon basins following the ddRAD method - ology for sequencing on the IonTorrent PGM. We analyzed the sequence data using the software Stacks. We detected 22,476 tags characterized by 7,181 polymorphic sites, recov - ering 177 (268 SNPs) shared between both basins. A signifcant difference in the allelic frequencies was observed between basins for a subset of these SNPs. Thirty-nine SNPs 1 3