1), recognized as belonging to a single endemic species, C.

In this study, we reconstruct the colonization and evolutionary history of Galapagos giant tortoises ( Chelonoidis spp.) from San Cristóbal Island (formerly Chatham Island, Fig. These activities have reduced the number of tortoises on the archipelago to 10% of their historical population levels before humans arrived (Tapia et al. Three of the recognized species have gone extinct in the last century, and several others are in danger of extinction because of human impacts, including historical overharvesting and habitat degradation (IUCN 2020). These species are genetically distinct with generally one species per island, except for the tortoises on Isabela and Santa Cruz Islands, where multiple species occur in allopatry (Caccone et al. 2020).įourteen species of giant tortoise have been described from the Galapagos Archipelago, with one additional known but undescribed extinct species (Rhodin et al. Tortoises arrived on the oldest island and from there colonized the rest of the archipelago by a combination of active dispersal mediated by ocean currents, and vicariance closely matching the merging and splitting of islands (Poulakakis et al. 2019), including the Galapagos giant tortoises. This geological history impacted phylogeographic patterns of diverse native flora and fauna in some predictable ways (Parent et al. The complex history of the archipelago includes the islands drifting, merging and splitting, with some subsiding into the ocean (Ali and Aitchison 2014). It is volcanic in origin, with islands formed by orogenetic activity along the Nazca plate, such that islands to the west are younger than islands to the east (Geist 1996 Geist et al. The Galapagos Archipelago includes 13 major islands larger than 10 km 2, six smaller islands, and over 200 islets and rocks, located in the Pacific Ocean ~900 km west of the South American continent and straddling the equator (Dirección del Parque Nacional Galápagos 2014). Moreover, island systems with well-known geological histories and ages of emergence (e.g., Hawaiian and Galapagos archipelagos) can also add a temporal axis to the study of the emergence of biological diversity (Cowie and Holland 2008 Parent et al. Remote oceanic islands and archipelagos have piqued the interest of evolutionary biologists for decades as these landscapes offer ideal settings to study colonization and subsequent establishment and diversification of species, largely owing to their isolation and discrete boundaries (Gillespie 2007). Without the museum samples, this important discovery of an additional lineage of Galapagos giant tortoise would not have been possible, underscoring the value of such collections and providing insights into the early evolution of this iconic radiation. Given the geographic and temporal proximity of the two deeply divergent mitochondrial lineages in the historical samples, they were likely sympatric, raising the possibility that the lineages coexisted.

Only a single mitochondrial haplotype was found, with no evidence to suggest substructure based on the nuclear markers.

To search for traces of a second lineage in the contemporary population on San Cristóbal, we closely examined the population by sequencing the mitochondrial control region for 129 individuals and genotyping 70 of these for both 21 microsatellite loci and >12,000 genome-wide single nucleotide polymorphisms. The haplotype of the individual collected alive in 1906 is in the same clade as the haplotype in the contemporary population. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased individuals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave are from a clade that is distinct among known Galapagos giant tortoises but closely related to the species from Española and Pinta Islands. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes.

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