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Galapagos giant tortoise trafficking case demonstrates the utility and applications of long-term comprehensive genetic monitoring


Quinzin, Maud et al. (2023), Galapagos giant tortoise trafficking case demonstrates the utility and applications of long-term comprehensive genetic monitoring, Dryad, Dataset,


Illegal Wildlife Trade (IWT) is a cause for global concern as pressure stemming from IWT threatens wild species and can even lead to extinction. Galapagos giant tortoises are a group of threatened species protected under CITES, which forbids their import-export for international trade; however, IWT of this group persists. In this study, we describe the use of two extensive genetic repositories of mitochondrial and nuclear microsatellite markers for Galapagos giant tortoises to identify an unsuspected source of trafficked juvenile tortoises. Our genetic analyses, together with morphological and captive-born registry data, provide evidence that the smuggled juveniles were from two breeding centers dedicated to conservation located on the Galapagos islands of San Cristobal and Isabela. This is the first documentation of smuggled tortoises being taken from breeding centers rather than the wild. The findings from our genetic analysis provided key evidence that enabled legal investigation. This case demonstrates the importance of the comprehensive genetic characterization of Galapagos giant tortoises and the suitability of standard genetic markers for identifying the species and islands of origin of trafficked animals. We also discuss the efficacy, adequacy, and reach of existing measures against IWT. Overall, this case illustrates an important application of long-term and comprehensive genetic repositories of endangered species and the crucial role of collaborations among academic laboratories maintaining those repositories, local practitioners responsible for the specie's protection, and the bodies that implement and enforce anti-trafficking regulations.


This dataset contains microsatellite data for 277 reference and 25 smuggled Galapagos tortoise individuals from Quinzin et al. (2023). The 277 microsatellite reference samples come from 12 genetically distinct populations of 10 extant and 2 extinct species from the Galapagos (Miller et al 2017). We first called alleles for the 25 smuggled tortoise samples in GeneMapper 5 (Applied BioSystems) and raw allele sizes were then binned using Tandem 2 (Matschiner & Salzburger 2009) for consistency across datasets. We then jointly analyzed the 25 smuggled tortoise samples and the 277 sample reference with the Bayesian clustering method implemented in STRUCTURE v2.3 to determine population assignments (Pritchard et al 2000). Run settings were as follows: correlated allele frequency and admixture models, 2x105 burn-in and 8x105 MCMC iterations with K = 12 as a fixed parameter, with 25 replicate runs combined using CLUMPAK (Kopelman et al. 2015). Membership coefficients (Q-values) to each species were also estimated. For more information, please see the original Quinzin et al. (2023) study.

Usage notes

The .txt file contains the microsatellite genotypes at 12 loci for 302 Galapagos tortoise samples (277 reference and 25 smuggled individuals) in GenePop format ( from Quinzin et al. (2023)

If using STRUCTURE (, make sure to set MARKERNAMES=1, LABEL=1, POPDATA=1, NUMINDS=302, NUMLOCI=12, MISSING=-9, POPFLAG=0, LOCDATA=0, PHENOTYPE=0, and EXTRACOLS=0 when using this file.


Yale Institute for Biospheric Studies

Galapagos Conservancy Inc.