Nearly Destroyed DNA Reveals Two Extinct Giant Tortoise Lineages

Yale researchers have used a new method to study highly damaged DNA. They identified two extinct types of giant tortoises from the Galapagos Islands. This discovery came from museum specimens where less than one percent of the DNA could be read.

The findings could also help efforts to grow giant tortoise populations. Traces of these extinct types might still exist in living hybrid tortoises today.

Unlocking Clues from Damaged DNA

Studying ancient DNA is often hard because genetic material breaks down over time. This leaves many gaps, making it tough to figure out how different animals were related.

The Yale team developed a computer-based approach to get evolutionary information from these incomplete genomes. This method works even when DNA samples are very degraded.

Alexander Ochoa, the lead author, explained the challenge. He said they needed to reconstruct relationships of extinct Galapagos giant tortoises. They knew the DNA from museum samples would be very fragmented and contaminated.

Ochoa worked with Adalgisa Caccone, a senior research scientist at Yale. Her lab studies the genetic diversity of Galapagos giant tortoises.

Identifying Extinct Tortoise Types

The researchers took DNA from dried bones in old museum collections. These included five specimens from two extinct tortoise types. They combined the surviving DNA fragments and placed this information onto a reference "phylogenetic tree." This tree shows evolutionary relationships.

The reference tree was built using high-quality DNA from living tortoises and other historical samples. It helped the researchers figure out where the degraded samples fit into the tortoises' evolutionary history.

Some of the degraded samples had less than one percent of their genome readable. Normally, such samples are discarded because the missing data can mess up estimates of evolutionary relationships. But by using several computer tools, the team successfully identified specimens from the extinct San Cristóbal and Santa Fe island lineages.

Hope for Conservation

Ochoa noted that these are two distinct lineages. Connecting these extinct populations to tortoises alive today could help conservation efforts in the Galapagos.

Historically, sailors moved Galapagos tortoises between islands. They used them as food. Some tortoises survived and bred with animals from other islands. This means genetic material from extinct lineages might still exist in living hybrid tortoises.

Ochoa believes that captive breeding programs could help recover the genomes of these extinct lineages in future generations. The tools developed in this study could also be useful for broader wildlife conservation.

Deep Dive & References

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, 2026