Peabody digitization project facilitates ‘time travel’ to Cretaceous period

The Yale Peabody Museum of Natural History houses tens of thousands of fossil specimens collected from the chalk deposits left behind by the Western Interior Seaway. Now it's digitizing its fossil collections to enable researchers and students to better understand this once-vibrant and long-disappeared ecosystem.
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Hesperornis, discovered by Othniel Charles Marsh, is a near relative of modern birds that still retain teeth. It once dove for prey in the Western Interior Seaway.

During the Cretaceous period — when the polar icecaps did not exist — an ocean stretched from the arctic to the Gulf of Mexico, dividing North America and covering the Midwest.

That shallow inland sea, known as the Western Interior Seaway, teemed with life. Fearsome predators — such as mosasaurus, aquatic lizards that grew as long as 50 feet, and plesiosaurs, marine reptiles with a distinctly long neck — prowled its warm waters along with sharks and giant squid. It was home to gigantic sea turtles and massive boney fish. Marine birds armed with teeth soared over the water and dove into it for prey. Ammonoids, mollusks with chambered shells and tentacles, flourished along with clams and other shellfish.     

The Yale Peabody Museum of Natural History houses tens of thousands of fossil specimens collected from the chalk deposits the seaway left behind — from one-celled foraminifera to alpha predators. Several particularly noteworthy specimens are displayed in the museum’s Great Hall of Dinosaurs, including skeletons of Platycarpus, a mosasaur,and Archelon, the largest sea turtle ever discovered, as well as skeletons of Hesperornis and Ichytornis, two species of toothed birds that Charles Darwin cited as among the best evidence for his theory of natural selection.  

The museum has partnered with eight natural history institutions nationwide to digitize their fossil collections related to the seaway in order to enable researchers and students to better understand this once-vibrant and long-disappeared ecosystem. The project, funded by a grant from the National Science Foundation, involves compiling high-res digital images and associated data of nearly a hundred thousand seaway specimens into an online database hosted by Integrated Digitized Biocollections (iDigBio), a collaborative effort to digitize collections at natural history institutions throughout the United States.

Lilly Scheibe ‘19 had the painstaking work of making digital images of thousands of invertebrate fossils from the Western Interior Seaway.

“The idea is to make all these collections accessible to researchers easily and with robust data and images,” said Susan Butts, senior collections manager for Peabody’s Division of Invertebrate Paleontology. “The Western Interior Seaway has fossils of well-known creatures that people understand. That makes it a fun project for the public and one that we’ll use to create educational opportunities for young people.”

During the project’s first year, the Peabody digitized about 41,000 specimens, mostly from its invertebrate collection. Over the course of the three-year project, the museum will digitize all invertebrates, vertebrates, and microfossils from the seaway, and produce 3D scans of about 50 fossils for educational use.

When the project is completed, the combined collections will provide a trove of information about the seaway’s ecosystem, said Chris Norris, senior collection manger for the Peabody’s Division of Vertebrate Paleontology.

“Our collections effectively allow us to time travel and create a picture of what the world was like, however long ago,” Norris said. “The problem is that to build a complete picture, you have to draw evidence from multiple institutions because all of our collections have different strengths — some are stronger in vertebrates, others in invertebrates or microfossils — and we all have fossils from different locations.” 

Next best thing to a time machine

Digitizing thousands of fossil specimens is painstaking work.

Four undergraduate workers, three from Yale and one from Southern Connecticut State University, spent the academic year photographing invertebrate fossils and recording the accompanying data, which is often more valuable than the image, said Butts.

“At first, you might think that digitization only concerns taking pictures of everything in the museum, but there is a lot of associated data that is very important for paleo-environmental analyses, and the images and data allow for verifying identification of the animals and where specimens were found both geographically and in the rock record,” she said.    

One of the Yale students is continuing the digitization work this summer along with undergraduates from Worcester Polytechnic Institute, Oberlin College, and Southern Connecticut State University. Two interns from local high schools will help as well.

The work can be very complicated. For example, a large chunk of rock might have dozens of clam specimens embedded in it.

“Our goal is to digitize every seaway specimen in the collection,” Butts said.

Butts developed a protocol for digitally capturing each tiny clam cemented in a concretion, or chunk of rock. First, Peabody staff use automated imaging equipment and software to merge hundreds of photos of the concretion into one extremely high-resolution image that captures every centimeter of the entire concretion. Student workers draw boxes around the individual fossils using another computer program, which also assigns individual specimen numbers and annotates images. A series of scripts created by Larry Gall, the Peabody’s head of computer systems, imports the images and ties the specimen data and images together in the Peabody database.

Hundreds of fossils can be embedded in a single piece of rock. A digital image was made of every fossil in this drawer. (Photo by Christina Lutz)

“We’ve really streamlined the process,” Butts said, adding that one particular tray of concretions contained more than 4,000 individual fossils. 

Digitization of the vertebrate fossils just recently began. While the most imposing vertebrate specimens are displayed in the Great Hall, most of the specimens in the collection are individual bones or fragments. (For any one seaway specimen on display in the museum, there are thousands more “behind the scenes” in the Peabody collections.)

“We have trays full of fish vertebrae, but each of those pieces is important in doing an analysis of biodiversity and identifying food chains,” Butts said.

The digital data will provide researchers the building blocks for reconstructing the seaway’s environment. They can analyze its biodiversity and how the organisms interacted with one another, Norris said. 

“Absent having a time machine, the only way you can do these analyses is to pull all of these data together from the different collections and organize them into a form that you can access, query, and sort,” Norris said. “That’s what this project is about.”

Some of the most important specimens are the tiniest ones, he noted. The microfossils look like grains of sand to the naked eye, but they provide essential data, he said.

“They are spectacularly beautiful when magnified and incredibly informative about climate and seawater chemistry,” Norris said. “They provide information about the seawater temperature, water depths, and biostratigraphy — the rock layer and exactly how old it is relative to other fossil beds.”

The Western Interior Seaway expanded and receded drastically over the course of the Cretaceous period, which spanned 80 million years and ended with the mass extinction of the dinosaurs and ammonoids. Studying its fossil record allows researchers to better understand what happens to an ecosystem during sea level changes, Butts said.

The seaway also provides evidence of the effects of invasive species, as at various points it opened into other oceans before becoming closed off again, she said.

“The whole nature of the fossil record and biodiversity today depended on invasive species changing the dynamics of an environment and evolving new ecosystems,’ she said.

An educational tool

Digitization also creates opportunities to help young people learn about paleontology and other sciences, Butts said.

“Obviously, we’re driven by research and by making resources available for people to answer research questions, but this project is also creating a fantastic resource for education,” she said.  “We want to allow students to use digitized collections in the same way that researchers use the physical collections.”

A website is being developed to provide grade school and high school teachers with data and images as well as lesson plans and tools that let them work with the specimens online in the same way a researcher would: mapping, measuring, and comparing specimens. The site will feature curated galleries of specimens that teachers can use to ask students to find clues about what a particular animal ate or how it lived, Butts said.

“We’re focusing on building a curriculum based on food webs,” she said. “We have a really interesting and dangerous predator-filled sea — plus the prey, and even the microfossils, the base of the food web . We want to help students figure out how those food webs worked.”

The Peabody collaborated with other institutions on a similar project called “iDigPaleo,” which is based on digitized insect fossils.

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