Nearly Destroyed DNA Reveals Two Extinct Giant Tortoise Lineages

Yale researchers have used a new computational approach to extract evolutionary information from severely degraded DNA, identifying two extinct lineages of Galapagos giant tortoises from museum specimens that conventional methods would likely have discarded. The findings, published in Proceedings of the Royal Society B, come from bone fragments in which less than 1% of the genome could be read.

The team, led by Alexander Ochoa of Yale's Department of Ecology and Evolutionary Biology, combined several genome analysis tools built to work with highly fragmented and contaminated genetic material. Ancient DNA breaks into scattered pieces as it deteriorates, leaving gaps that normally make it hard to determine how individuals and populations are related.

The researchers extracted DNA from dried bones held in historical museum collections, including five specimens representing two extinct tortoise lineages. They placed the surviving fragments onto a reference phylogenetic tree — a diagram mapping evolutionary relationships — built from high-quality genomes of living tortoises and other historical specimens. That framework let them determine where the degraded samples fit within the tortoises' evolutionary history.

By combining these tools, the researchers identified specimens belonging to the extinct San Cristóbal and Santa Fe island giant tortoise lineages. Adalgisa Caccone, a senior research scientist in Yale's Department of Ecology and Evolutionary Biology, co-authored the study.

Ochoa said genetic material from these extinct lineages may still survive in living hybrid tortoises, because sailors historically carried Galapagos tortoises between islands as food and some displaced animals bred with tortoises from other islands. He said captive breeding programs that mate these hybrids could potentially recover genomes of the extinct lineages in future generations, and that the tools developed in the study could also apply to broader wildlife conservation efforts.