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Background  Although not unusual to find captive relicts of species lost in the wild, rarely are presumed extinct species rediscovered outside of their native range. A recent study detected living descendents of an extinct Galápagos tortoise species ( Chelonoidis elephantopus ) once endemic to Floreana Island on the neighboring island of Isabela. This finding adds to the growing cryptic diversity detected among these species in the wild. There also exists a large number of Galápagos tortoises in captivity of ambiguous origin. The recently accumulated population-level haplotypic and genotypic data now available for  C. elephantopus  add a critical reference population to the existing database of 11 extant species for investigating the origin of captive individuals of unknown ancestry.    Methodology/Findings  We reanalyzed mitochondrial DNA control region haplotypes and microsatellite genotypes of 156 captive individuals using an expanded reference database that included all extant Galápagos tortoise species as well as the extinct species from Floreana. Nine individuals (six females and three males) exhibited strong signatures of Floreana ancestry and a high probability of assignment to  C. elephantopus  as detected by Bayesian assignment and clustering analyses of empirical and simulated data. One male with high assignment probability to  C. elephantopus  based on microsatellite genotypic data also possessed a “Floreana-like” mitochondrial DNA haplotype.    Significance  Historical DNA analysis of museum specimens has provided critical spatial and temporal components to ecological, evolutionary, taxonomic and conservation-related research, but rarely has it informed  ex situ  species recovery efforts. Here, the availability of population-level genotypic data from the extinct  C. elephantopus  enabled the identification of nine Galápagos tortoise individuals of substantial conservation value that were previously misassigned to extant species of varying conservation status. As all captive individuals of  C. elephantopus  ancestry currently reside at a centralized breeding facility on Santa Cruz, these findings permit breeding efforts to commence in support of the reestablishment of this extinct species to its native range.

DNA from the Past Informs Ex Situ Conservation for the Future: An “Extinct” Species of Galápagos Tortoise Identified in Captivity