Whole genome assessment of the possibility of a third lineage of Galapagos Giant Tortoises on Santa Cruz Island

Abstract Taxonomic assignment of population fragments is important for conservation planning yet can be particularly complex in species radiations across island archipelagos due to a combination of dynamic geography and recent divergence. The Galapagos Archipelago hosts endemic giant tortoise (Chelonoidis spp.) lineages across seven islands, with a unique feature of different carapace morphologies. The taxonomic status of a small group of saddleback tortoises on Cerro Montura in Northwestern Santa Cruz Island has remained uncertain since their initial discovery. Previous studies suggested that they are not closely related to the other two Santa Cruz lineages, but rather the lineage on nearby Pinzón Island, although it remains unclear whether this is the result of natural processes or recent human translocation. Here, we use new and existing whole genome sequencing data to answer this question at a deeper resolution. Using population genetic and phylogenetic analyses interpreted within the historical and biogeographic context of the Galapagos, we conclude that the giant tortoises on Cerro Montura are not a unique lineage and are likely the result of recent, human-mediated transport from Pinzón Island. Confirming this has important conservation implications, since while it seems that the Cerro Montura population has recently died out, this does not represent the extinction of a unique, overlooked lineage within the Galapagos giant tortoise radiation.