Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops g
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METHODS AND RESOUrCES ArTICLE
Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines) Vinícius Tadeus de Carvalho1,2,6 · José Gregorio Martínez1,3,4 · Sandra M. Hernández-Rangel1 · Spartaco Astolfi-Filho5 · Richard C. Vogt6 · Izeni Pires Farias1 · Tomas Hrbek1
Received: 12 September 2016 / Accepted: 4 October 2016 © Springer Science+Business Media Dordrecht 2016
Abstract We developed forensic nuclear SNPs for the sidenecked turtle, Phrynops geoffroanus, using next-generation sequencing-based genotyping. We created a reduced-representation library for 23 individuals representing four previously identified lineages of P. geoffroanus using the ddRAD methodology for sequencing on the IonTorrent PGM. We analyzed the sequence data using the Stacks pipeline. We found 811 loci containing 1380 private SNPs. Of these, 473 were fixed in lineages 1, 2 and 3, or with frequency >0.91 in lineage 4. Seventy-three SNPs could be useful for forensics purpose (assignment of individuals to lineage of origin) using traditional PCR-based genotyping methods. Keywords Geoffroy’s side-necked turtle · Wildlife molecular forensics · Illegal trade/smuggling · Molecular markers for individual traceability · Conservation genomics · IonTorrent PGM Electronic supplementary material The online version of this article (doi:10.1007/s12686-016-0626-8) contains supplementary material, which is available to authorized users.
Tomas Hrbek [email protected] 1
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Laboratório de Evolução e Genética Animal, Departamento de Genética, Universidade Federal do Amazonas, Av. Rodrigo Octávio Jordão Ramos, 3000, Manaus, Amazonas 69077-000, Brazil Programa de Pós-graduação em Biodiversidade e Biotecnologia da Amazônia Legal—Rede Bionorte, Universidade Federal do Amazonas, Av. Rodrigo Octávio Jordão Ramos, 3000, Manaus, Amazonas 69077-000, Brazil 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
The Geoffroy’s side-necked turtle, Phrynops geoffroanus (Schweigger, 1812), is a Neotropical freshwater turtle with the broadest geographical distribution of all species of the Chelidae family, occurring from southern Venezuela to northern Argentina (van Dijk et al. 2014). In Brazil, this species occurs in the Amazon, Caatinga, Cerrado and Atlantic Forest biomes (van Dijk et al. 2014) where it inhabits a diversity of aquatic habitat ranging from streams to large rivers and lakes (Rueda-Almonacid et al. 2007; Vogt 2008; Páez et al. 2012). The species is morphologically variable, which combined with its extensive geographical distribution, raises the possibility of the existence of cryptic taxa (Rueda-Almonacid et al. 2007; Vogt 2008; Schneider et al. 2011). The turtles are the world’s most threatened vertebrates with approximately 60 % of the species listed in one of the endangered categories of the IUCN (van D
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