A tortoise from a Galápagos species that was thought to be extinct has been discovered living. The tortoise, called Fernanda after her habitat on Fernandina Island, is the first of its kind to be discovered in over a century.
The only known specimen of the Fernandina Island Galápagos giant tortoise (Chelonoidis phantasticus, or “fantastic giant tortoise”) was recovered in 1906. The finding of a female tortoise on Fernandina Island in 2019 provides an opportunity to see if the species still exists. Princeton’s Stephen Gaughran demonstrated that the two known Fernandina tortoises are members of the same species, genetically distinct from the other 13 species of Galápagos giant tortoises, by sequencing the genomes of both the living individual and the museum specimen and comparing them to the other 13 species of Galápagos giant tortoises. He’s a co-first author on research published in the current edition of Communications Biology that confirms her species’ survival.
“For many years, it was assumed that the original specimen collected in 1906 had been transplanted to the island because it was the only one of its kind,” said Peter Grant, Princeton’s Class of 1877 Professor of Zoology, Emeritus, and an emeritus professor of ecology and evolutionary biology who has spent over 40 years studying evolution in the Galápagos Islands. “It now appears to be one of only a few people who lived a century ago.”
Many ecologists questioned if Fernanda was a native phantasticus turtle when she was discovered. She lacks the male historical specimen’s distinctive saddleback flare, though scientists suggest that her clearly restricted growth may have affected her looks. Tortoises cannot swim from one island to another, although they can float and can be dragged from one island to another in the Galápagos during hurricanes or other big storms. Seafarers have also been known to transport tortoises across islands in the past.
“Like many others, my first instinct was that this was not a Fernandina Island native tortoise,” said Gaughran, a Princeton postdoctoral research fellow in ecology and evolutionary biology.
Gaughran sequenced Fernanda’s entire genome and matched it to the genome he was able to retrieve from the specimen taken in 1906 to firmly confirm her species. He also compared those two genomes to samples from the other 13 species of Galápagos tortoises—three individuals from each of the 12 living species and one from the extinct C. abingdonii—in order to see how similar, they were.
“We observed that Fernanda was extremely similar to the one that they found on that island more than 100 years ago, and both of those were highly distinct from all of the other islands’ tortoises,” said Gaughran, who conducted the analyses after arriving at the university in February 2021.
“As part of my postdoc, I’m working on a technique to examine DNA from ancient museum specimens so we can compare them to present samples,” Gaughran explained.
His tool is adaptable enough to work on nearly any antique artefact. “It doesn’t matter if it’s a seal, a tortoise, a human, or a Neanderthal,” he explained. “For the most part, genetics is genetics. It’s how the DNA is interpreted that determines what kind of creature it came from.”
Gaughran is studying the evolution of pinnipeds (seals and walruses) at Princeton with Andrea Graham and Bridgett vonHoldt.
“Stephen uses the sophisticated and thorough application of genetic and bioinformatic technologies to solve conservation problems in species ranging from tortoises to pinnipeds,” said Graham, an ecology and evolutionary biology professor.
VonHoldt, an associate professor of ecology and evolutionary biology, stated, “He has such a curiosity for unearthing the secrets and codes nestled away in ancient remnants.” “Stephen has been collecting specimens ranging in age from hundreds to thousands of years, and these are the key to understanding when and how genomes altered across time. He also led the attempt to solve the mystery of Fernanda, the wonderful ghost tortoise uncovered through molecular study, which comes as no surprise to me. What a fantastic find!”
A long-standing puzzle
Since 1906, there has been scarce but persuasive evidence that giant tortoises may still exist on Fernandina Island, an active volcano on the western border of the Galápagos Archipelago that is said to be the world’s biggest unspoiled island.
During a 1906 voyage, explorer Rollo Beck acquired a solitary specimen of C. phantasticus, also known as “the fantastic big tortoise.” The “fantastic” character alludes to the males’ shells’ remarkable shape, which has considerable flaring along the outer border and prominent saddlebacking in the front. Saddlebacking is a feature only found in Galápagos tortoises, and the phantasticus tortoise displays it more dramatically than the other species.
The Fernandina tortoise’s survival has been a mystery to biologists since its discovery in 1906. On the western slopes of the island, 18 scats attributed to tortoises were reported in 1964. During the early 2000s, scats and a probable visual observation from an aircraft were reported, and another possible tortoise scat was detected in 2014.
Due to massive lava fields restricting access to the island’s interior, the island has remained largely undiscovered.
“Fernandina is the highest of the Galápagos islands, geologically young, and primarily a vast pile of jagged stones of brown lava; Rosemary and I once ascended to the summit,” stated Grant, referring to his wife and Princeton research colleague Rosemary Grant. “The plant grows in island-like clumps in a sea of newly congealed lava at lower levels. Fernanda was discovered in one of them, and evidence suggests that a few relatives may also be present in others.”
Fernanda is believed to be well over 50 years old, yet she is little due to the lack of greenery, which may have slowed her growth. Recent tracks and scat of at least 2 or 3 more tortoises were discovered during other recent visits on the island, which is encouraging.
The Galápagos Tortoises
A hurricane moved one or more gigantic tortoises from the South American mainland westwards two or three million years ago. Because they can’t swim, the tortoises primarily bred with other tortoises on their own islands, resulting in rapid evolution—similar to the Galápagos finches. There are 14 species of gigantic Galápagos tortoises today, all descended from a common ancestor.
(Some scientists disagree over whether these are species or subspecies, but the Princeton-Yale researchers determined that they are divergent enough to be classified separate species based on thousands of genetic markers.)
Diversification of Galápagos tortoises exhibits a continuum of shell morphologies, with rounder, domed shells on the easternmost islands and the most extreme saddlebacking on the westernmost island, Ferdinanda. Domed tortoises prefer humid, higher-elevation surroundings, whereas saddlebacked tortoises prefer drier, lower-elevation habitats. The IUCN Red List classifies all 14 as vulnerable, endangered, highly endangered, or extinct.
European seamen devastated tortoise populations for food after discovering that they could keep tortoises alive on their ships with little effort because the reptiles could survive with little food or water. “They were a tremendous source of fresh meat for the sailors,” Gaughran explained, “but it meant that many of the species were severely overhunted.” “And the populations have a hard time rebounding quickly since they have such a long generation span.”
“The genomic research offers fascinating signs of gene mixing with members of another population,” Grant added. “It would be amazing if future genomic research validated this. Another intriguing discovery is that the nearest relatives are not on the nearest large island (Isabela), but on a separate island (Espaola) far away on the other side of Isabela. The mystery of how the ancestors arrived in Fernandina remains unsolved.”
Fernanda has been relocated to the Galápagos National Park Tortoise Center, a rescue and breeding facility where scientists are assessing what may be done to save her species.
“The discovery educates us about rare species that may persist for a long time in isolated settings,” Grant added. “This information is crucial for environmental protection. It motivates biologists to look for the last few members of a population in order to save them from extinction.”
