Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines)
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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.
KeywordsGeoffroy’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.
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Conflict of interest
The authors declare that they have no conflict of interest.
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