Using a new combination of computational tools to analyze ancient DNA, Yale researchers have discovered two ancient, extinct giant tortoise lineages that once lived on the Galapagos Islands.

The researchers’ pioneering approach, which employs computational genome analysis tools, showed that museum specimens previously considered too genetically degraded to be useful in this type of research can help reveal evolutionary history. The findings could also aid ongoing efforts to expand giant tortoise populations in the Galapagos archipelago.

Results of the study are published in the journal Proceedings of the Royal Society B.

For researchers exploring evolutionary lineages, unlocking the DNA of extinct species in ancient samples has always been a challenge, because DNA degrades over time, leaving behind just scattered fragments of genetic information, and researchers struggle to fill in the missing pieces.

But in their new study, the Yale-led researchers developed a computational approach that can maximize the insights gained from the genomes of degraded specimens and then fill in the missing links, bypassing the need for a more complete DNA sample.

“The challenge of this study was to reconstruct the genetic relationships of extinct Galapagos giant tortoises, knowing that the DNA we were able to obtain from museum specimens was going to be highly degraded and fragmented and have a high proportion of contamination,” said study lead author Alexander Ochoa, former associate research scientist in Yale’s Department of Ecology and Evolutionary Biology who is beginning a new position as an assistant professor at the State University of New York at Old Westbury this fall.
Ochoa was part of the research team in the lab of Adalgisa Caccone, a senior research scientist and lecturer in Yale’s Department of Ecology and Evolutionary Biology, a member of Yale’s Faculty of Arts and Sciences, and co-author of the new study. The research is part of the lab’s ongoing initiative to understand the genetic diversity of Galapagos giant tortoises.

In their work, the researchers extracted DNA from dried bones of historical museum specimens, including five specimens of two extinct tortoise lineages. They then combined the scraps of recovered genetic information and superimposed, or placed, this information onto a reference phylogenetic tree built with high-quality genomes from living and other historical tortoises.

In some of the degraded tortoise specimens studied, less than 1% of the genome could be read. Conventional genomic analyses often discard such samples because the missing information can distort evolutionary relationships. But the researchers’ new computational approach, which combined several powerful computing tools, successfully identified specimens from the extinct San Cristóbal and Santa Fe island lineages.

“These are two distinct lineages,” Ochoa said, adding that linking the past with the present underscores current conservation efforts across the Galapagos archipelago. Historically, sailors visiting the Galapagos carried tortoises, which they used as a food source, from one island to another as cargo, Ochoa said. Some of these displaced turtles survived and were able to breed with tortoises from a different island. Due to these human-driven migration events, the genomes of extinct lineages may still be “living” in extant, hybrid tortoises.
“In this regard, captive breeding programs that mate these hybrids may be able to recover the genomes of the extinct lineages in future generations,” Ochoa said. “The tools developed in our study are not only useful for the discovery of extinct lineages but could also be applied to broader wildlife conservation efforts.”

Collaborators in the study include researchers from Newcastle University, the University of California, Berkeley, the University of Connecticut, Woods Hole Oceanographic Institution, Pacific Northwest Oceanographic Laboratory, the University of New Mexico, the University of Crete, the Foundation for Research and Technology – Hellas (FORTH), and MacEwan University.