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

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. © 2016, Springer Science+Business Media Dordrecht