Genetic Study Confirms Two Additional Extinct Lineages of Galápagos Giant Tortoises

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How many species of Galápagos giant tortoises are there, exactly? There is probably no simple answer to this question. On the archipelago’s different islands and volcanoes, separate populations evolved, some of which differ markedly in body shape, behavior, and genetic makeup.

One classification system commonly used today groups them as subspecies of a single species, the Galápagos giant tortoise (Chelonoidis niger). Other scientists, however, regard the individual lineages as distinct species. A genomic study published last year challenges this classification. The researchers conclude that the living forms constitute a species complex of at least nine species; most of their analyses even support recognizing all 13 lineages examined as distinct species.

A new genetic study now shows that even this already complex picture does not fully reflect the giant tortoises’ former diversity. The research team confirmed two additional evolutionarily distinct lineages: one from San Cristóbal Island and one from Santa Fe. Both are now extinct—and only a few old bones remain.

At least four lineages disappeared in historical times

In their study, Alexander Ochoa and his team deliberately refer to lineages rather than species or subspecies. In total, the researchers distinguish 13 extant lineages of Galápagos giant tortoises and at least four extinct ones: the Floreana giant tortoise and the Pinta giant tortoise, the previously known but scientifically undescribed lineage from Santa Fe, and an extinct historical lineage from San Cristóbal.

The new study focuses on the latter two. Using genomic data, the researchers have now confirmed that the historical tortoises from San Cristóbal and Santa Fe represented distinct evolutionary lineages and determined more precisely how they were related to the other Galápagos giant tortoises.

Two distinct tortoise lineages on San Cristóbal

The situation on San Cristóbal is particularly fascinating. Giant tortoises still live on the island today. Their population numbers several thousand and is concentrated primarily in the island’s drier northeast. But it appears that these were not the island’s only giant tortoises in the past.

During a California Academy of Sciences expedition in 1906, the bones of several tortoises were discovered in a cave in the central part of the island. The tortoises had presumably fallen into the cave and died there. Radiocarbon dating showed that one of the tortoises found in the cave had most likely died between 1450 and 1630.

As early as 2022, genetic analyses of these bones produced a surprise: Their mitochondrial DNA differed markedly from that of the tortoises living on San Cristóbal today. This means that at least two distinct genetic lineages existed on the same island. At the time, however, the available data could not establish with certainty whether the differences involved only mitochondrial ancestry or whether there had indeed been two permanently separate evolutionary entities.

The current study fills this gap. Ochoa and his colleagues were able to analyze highly fragmented DNA from the nuclear genome as well. The nuclear genomic data confirm that two distinct lineages of giant tortoises existed on San Cristóbal—only one of which has survived to the present day.

Possibly separated for hundreds of thousands of years

It is not yet possible to determine exactly how long the two lineages existed separately. Earlier studies, however, dated the split between related mitochondrial lineages to approximately 720,000 years ago. The authors therefore consider it possible that the two San Cristóbal lineages also diverged around this time. One possible explanation is changes in sea level and the landscape. Populations may have become temporarily isolated from one another within the island and subsequently continued to evolve independently.

They may not have remained entirely separate, however. A tortoise captured alive on San Cristóbal in 1906 has a divergent genetic pattern: Its nuclear genome is, overall, more closely related to the extinct historical lineage, whereas its mitochondrial DNA resembles that of the living population. This could indicate that the two lineages eventually came back into contact and interbred.

A nomenclatural problem on San Cristóbal

The discovery could even have consequences for the scientific name of the San Cristóbal giant tortoise. One of the bones found in 1906, specimen CAS 8127, was used as the type specimen for the San Cristóbal giant tortoise later named Chelonoidis chathamensis. Genetic analyses show, however, that this particular tortoise belongs to the now-extinct historical lineage—not to the population living on San Cristóbal today.

If the two lineages are eventually recognized taxonomically as separate species or subspecies, this could therefore lead to a nomenclatural problem: The name chathamensis would properly be tied to the extinct lineage, while the tortoises living today would require a different name. The researchers do not yet resolve this question in the current study, however.

Santa Fe: did the bones even come from native tortoises?

The giant tortoises of the small island of Santa Fe have long been a mystery. In fact, there are no historical records of living tortoises there. Only a few old bones were found in 1906, with more remains discovered later. They included damaged and partially charred bones.

This led to speculation that Santa Fe might never have had its own giant tortoise population. At the time, sailors commonly transported Galápagos giant tortoises between the islands and carried them aboard as a live food supply. The bones on Santa Fe could therefore have come from tortoises that people had brought from another island before slaughtering and eating them there.

The new genomic data contradict this explanation: The Santa Fe tortoises examined form a genetically distinct group that differs from the populations on other islands. Their nuclear genomes place them particularly close to the giant tortoises of Española, but they are not identical. This makes it much more likely that Santa Fe once had a naturally established, distinct tortoise lineage that is now extinct.

Their precise evolutionary history remains complex, however. While the nuclear genome primarily indicates a relationship with the Española giant tortoise (Chelonoidis hoodensis), the mitochondrial DNA paints a somewhat different picture. The authors therefore even consider it possible that Santa Fe was colonized from multiple source populations, perhaps from Española and San Cristóbal. Better-preserved samples would be needed for a definitive reconstruction, however. Such specimens probably no longer exist.

Less than one percent of the genome was enough

It is remarkable that these questions can still be investigated at all, because no well-preserved tissue samples remain from either extinct lineage. The researchers therefore had to extract DNA from old, dried bones.

This DNA was extremely degraded and also contaminated with foreign DNA. Only a small fraction of the genome could be recovered from the historical tortoises from Santa Fe and San Cristóbal. In some cases, less than one percent of the DNA obtained came from the tortoise being studied.

Normally, such samples are unusable for most genomic studies. The research team therefore combined several computational methods and compared the few surviving DNA segments with more completely sequenced genomes from other Galápagos giant tortoises. This allowed the researchers to determine the most likely position of the historical tortoises in the evolutionary tree.

The method could also be important far beyond Galápagos giant tortoises. Museum collections contain numerous remains of extinct animals whose DNA had previously been considered too poorly preserved for extensive genomic analyses.

Have two new extinct Galápagos giant tortoises now been discovered?

Not yet. For now, the genetic results show only that the historical tortoises from San Cristóbal and Santa Fe were evolutionarily distinct lineages. But this does not mean that they must automatically be described as separate species. The question is particularly difficult to answer for Galápagos giant tortoises because there is disagreement even over whether the extant forms represent species, subspecies, or separate populations.

The study’s authors therefore refrain from assigning a particular taxonomic rank to the two extinct lineages. Doing so would require specific species-delimitation analyses and a more comprehensive taxonomic investigation.

Part of their diversity is only now coming to light

The history of Galápagos giant tortoises is therefore even more complex than previously thought. Populations arose on different islands, became separated from one another, in some cases came back into contact, and finally disappeared when humans reached the Galápagos Islands.

We know about some of these lost forms only because individual bones were collected more than a century ago and preserved in museums. The new study managed to make another part of this history visible through these unassuming remains: In addition to the known extinct giant tortoises from Floreana and Pinta, there were at least two additional distinct lineages on San Cristóbal and Santa Fe.

Whether they will eventually be recognized as separate species or subspecies remains an open question. The new genomic data leave no doubt, however, that they represented a distinct part of the evolutionary diversity of Galápagos giant tortoises.

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Sources

• Gaughran, S. J., Gray, R., Ochoa, A., et al. (2025). Whole-genome sequencing confirms multiple species of Galapagos giant tortoises. Evolution, 79(2), 296–308. https://doi.org/10.1093/evolut/qpaf003
• Jensen, E. L., Quinzin, M. C., Miller, et al. (2022). A new lineage of Galapagos giant tortoises identified from museum samples. Heredity, 128(4), 261–270. https://doi.org/10.1038/s41437-022-00510-8
• Ochoa, A., Gaughran, S. J., Gray, R., et al. (2026). Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises. Proceedings of the Royal Society B: Biological Sciences, 293(2075), 20260103. https://doi.org/10.1098/rspb.2026.0103