DOI: 10.6078/d16428
title: Galapagos giant tortoise trafficking case demonstrates the utility and applications of long-term comprehensive genetic monitoring

description: 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.
description: 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.
description: The .txt file contains the microsatellite genotypes at 12 loci
 for 302 Galapagos tortoise samples (277 reference and 25 smuggled
 individuals) in GenePop format (https://genepop.curtin.edu.au/) from
 Quinzin et al. (2023) <em>If using STRUCTURE
 (https://web.stanford.edu/group/pritchardlab/structure.html), 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.</em>