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It’s the first time that a new lineage of elephant bird has been identified from ancient eggshells alone, a pioneering achievement that will allow scientists to learn more about the diversity of birds that once roamed the world and why so many have since gone extinct in the past 10,000 years.

“This is the first time a taxonomic identification has been derived from an elephant bird eggshell and it opens up a field that nobody would have thought about before,” said paper co-author Gifford Miller, distinguished professor of geological sciences and faculty fellow at the Institute of Arctic and Alpine Research (INSTAAR) at CU Boulder. “Here may be another way of looking into the past and asking, ‘Was there more diversity in birds than we’re aware of?’”

Surface scatter of Aepyornis eggshell exposed by active wind erosion of sand dunes in which the birds nested. Credit: Gifford Miller

Akin to a small continent, Madagascar has been separated from Africa and neighboring continents by deep ocean water for at least 60 million years. This geology has allowed evolution to run wild, producing lemurs, elephant birds and all kinds of animals that exist nowhere else on the planet. For the Polynesian peoples who arrived here around 2,000 years ago, the largest of the elephant birds, Aepyornis, was a feathery terror to behold: at more than 9 feet tall, weighing more than 1,500 pounds each, and outfitted with a pointy beak and deadly foot talons, it was Madagascar’s largest land animal.

Due to limited skeletal remains—and the fact that bone DNA degrades quickly in warm, humid areas—it was not known until recently where the birds fit into the evolutionary tree. The most scientists knew was that they were part of the flightless ratite family, a genetic sister to the New Zealand kiwi, the world’s smallest living ratite.

Ancient eggshell DNA, however, has confirmed not only where the elephant birds sit in this tree, but revealed more about the diversity within the lineage.

“While we found that there were fewer species living in southern Madagascar at the time of their extinction, we also uncovered novel diversity from Madagascar’s far north,” said lead author Alicia Grealy, who conducted this research for her doctoral thesis at Curtin University in Australia. “These findings are an important step forward in understanding the complex history of these enigmatic birds. There’s surprisingly a lot to discover from eggshell.”

An eggshell-ent idea

Miller has analyzed eggshell remains in Australia and around the world for more than 20 years—one of few scientists who study these fragments. So, in 2005, when he was awarded $25,000 as part of the Geological Society of America’s Easterbrook Distinguished Scientist Award, Miller gathered a small team to study the evolutionarily elusive elephant bird.

The team initially set out in 2006 to collect elephant bird eggshells from the dry, southern half of the island. When an unaffiliated researcher used bone fragments to solve this evolutionary mystery before they could, Miller and Grealy’s team turned their attention to the wet, forested north half of the island, hoping to better understand the bird in a different biome.

The field team in May 2007, while in northeastern Madagascar where the samples in the paper were collected. From left to right: Ramil, lead guide from the National Museum in Antananarivo, the Capital City; Gifford Miller; Steve DeVogel; and a local guide. Credit: Gifford Miller

Using high-resolution satellite imagery, the team scouted locations where winds had blown the sands away and exposed ancient eggshells. No birds of any similar size currently live on the island, so the cracked pieces are easily recognizable to the naked eye. After the team traversed the island and gathered more than 960 ancient eggshell fragments from 291 locations, the challenging work began: analyzing the ancient DNA.

Due to their chemical makeup, skeletons can be “leaky” with their DNA, making them less ideal for this kind of work. In comparison, the physical chemistry of these thick eggshells locks in its organic matter for up to 10,000 years and protects its DNA like it did the baby bird that once grew inside of it. This means it can be rather difficult to extract for analysis.

Another problem is finding long enough strands of DNA to analyze, as ancient DNA is often degraded. As a result, the scientists pieced together the shorter fragments in a kind of “genetic jigsaw puzzle”—with no idea it would lead them to discover a new type of elephant bird.

“Science often advances in obscure pathways. You don’t always find what you were looking for,” said Miller, director for the Center for Geochemical Analysis of the Global Environment (GAGE) at CU Boulder. “And it’s much more interesting to find what you didn’t know you were looking for.”

The human or the egg?

Miller studies the “Quaternary,” the most recent geological period in Earth’s history and when humans first appeared on the landscape. When humans appeared, he said, often large animals went extinct—but scientists still don’t know why the elephant bird was one of them.

“What is it that early humans are doing that’s resulting in extinction of big animals, especially? This is a debate that’s been going on for my whole life,” said Miller, whose career now spans five decades.

If geologists, archaeologists, and biologists are able to gather and date more eggshell fragments from around the world, however, Miller and Grealy’s pioneering work in the field of eggshell DNA science could lead to a better understanding of why large animals like the elephant bird went extinct after the arrival of humans.

“With lots of little contributions from a whole bunch of people, you actually can solve some interesting questions,” said Miller. “This might open up a new way of looking at things.”

Reference: “Molecular exploration of fossil eggshell uncovers hidden lineage of giant extinct bird” by Alicia Grealy, Gifford H. Miller, Matthew J. Phillips, Simon J. Clarke, Marilyn Fogel, Diana Patalwala, Paul Rigby, Alysia Hubbard, Beatrice Demarchi, Matthew Collins, Meaghan Mackie, Jorune Sakalauskaite, Josefin Stiller, Julia A. Clarke, Lucas J. Legendre, Kristina Douglass, James Hansford, James Haile and Michael Bunce, 28 February 2023, Nature Communications.
DOI: 10.1038/s41467-023-36405-3

Additional authors on this paper include: Matthew J. Phillips, Queensland University of Technology; Simon J. Clarke, Integrity Ag & Environment; Marilyn Fogel, University of California Riverside; Diana Patalwala, Paul Rigby and Alysia Hubbard, The University of Western Australia; Beatrice Demarchi, University of Turin; Matthew Collins, Meaghan Mackie, Jorune Sakalauskaite, and Josefin Stiller, University of Copenhagen; Julia A. Clarke and Lucas J. Legendre, The University of Texas at Austin; Kristina Douglass, Columbia University; James Hansford, Zoological Society of London, Northern Illinois University, University College London; James Haile, Oxford University; and Michael Bunce, Curtin University.

Funding for this work was supported by the Easterbrook Distinguished Scientist Award from the Quaternary Geology and Geomorphology Division of the Geological Society of America (GSA), the National Science Foundation, the Australian Research Council (ARC), an ARC future fellowship, and the National Geography Society.