Conservation Genetics Resources

, Volume 9, Issue 1, pp 157–163 | Cite as

Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines)

  • Vinícius Tadeus de Carvalho
  • José Gregorio Martínez
  • Sandra M. Hernández-Rangel
  • Spartaco Astolfi-Filho
  • Richard C. Vogt
  • Izeni Pires Farias
  • Tomas Hrbek
Methods and Resources Article


We developed forensic nuclear SNPs for the side-necked 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.


Geoffroy’s side-necked turtle Wildlife molecular forensics Illegal trade/smuggling Molecular markers for individual traceability Conservation genomics IonTorrent PGM 



This work was supported by the SISBIOTA/Conselho Nacional de Desenvolvimento Científico e Tecnológico/Fundação de Amparo à Pesquisa do Amazonas (CNPq/FAPEAM/SISBIOTA-BioPHAM) Grant No. 563348/2010 to IPF; CNPq Ciencia sem Fronteiras Project No. 400771/2013-6 to RCV; and Mohamed bin Zayed Species Conservation Fund Project No. 1025921 to RCV and VTC. We thank the Instituto Chico Mendes de Conservação da Biodiversidade for collection permits (ICMBio, processes 22885-1 and 43175-2). All specimens used were deposited in the Collection of Amphibians and Reptiles of the Instituto Nacional de Pesquisas da Amazonia. We are grateful to Enedina Nogueira of the Laboratório de Tecnologias de DNA for technical support during sequencing. VC was supported by Bolsa de Pesquisa scholarship from FAPEAM during his Doctoral studies in the Biodiversidade e Biotecnologia/Rede BIONORTE Program in the UFAM. IPF and TH were supported by a Bolsa de Pesquisa scholarship from CNPq during this study. JGM was supported by postdoctoral scholarship from CAPES in the MBT program of UEA.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12686_2016_626_MOESM1_ESM.txt (2 kb)
Supplementary material 1. Online Resource 1 Command line script file used for running Stacks pipeline programs components (, and for de novo SNPs genotyping across all individuals (Lineages 1, 2, 3 and 4) of the side-necked turtle Phrynops geoffroanus (TXT 2 KB)
12686_2016_626_MOESM2_ESM.txt (6 kb)
Supplementary material 2. Online Resource 2 SUMSTATS (summary statistics) file from Stacks pipeline ( showing the loci, SNP position in the tag loci, population source, most frequent allele, alternative allele, frequency of the most frequent allele, number of individuals from which the SNP was recovered, heterozygosis for each one of the final 73 recovered SNPs from the Lineages 1, 2, 3 and 4 of the side-necked turtle, Phrynops geoffroanus (TXT 6 KB)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Vinícius Tadeus de Carvalho
    • 1
    • 2
    • 6
  • José Gregorio Martínez
    • 1
    • 3
    • 4
  • Sandra M. Hernández-Rangel
    • 1
  • Spartaco Astolfi-Filho
    • 5
  • Richard C. Vogt
    • 6
  • Izeni Pires Farias
    • 1
  • Tomas Hrbek
    • 1
  1. 1.Laboratório de Evolução e Genética Animal, Departamento de GenéticaUniversidade Federal do AmazonasManausBrazil
  2. 2.Programa de Pós-graduação em Biodiversidade e Biotecnologia da Amazônia Legal—Rede BionorteUniversidade Federal do AmazonasManausBrazil
  3. 3.Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Facultad de Ciencias, Departamento de Ciencias BiológicasUniversidad de los AndesBogotáColombia
  4. 4.Laboratório de Proteômica e Genômica, Programa de Pós-graduação Mestrado em Biotecnologia e Recursos Naturais (MBT), Grupo de Pesquisa em Genética Molecular e CitogenéticaUniversidade do Estado do AmazonasManausBrazil
  5. 5.Centro de Apoio Muldisciplinar, Laboratório de Tecnologias de DNAUniversidade Federal do AmazonasManausBrazil
  6. 6.Coleção de Anfíbios e Répteis, Instituto Nacional de Pesquisas da AmazôniaCoordenação em BiodiversidadeManausBrazil

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